DIGAP

Table I. General information for the 28 plant pathogens.

Table II. Re-annotation information for the 28 plant pathogens.

Table III. The sensitivity, specificity and accuracy over ten-fold cross-validation tests for the 28 plant pathogens.

Table IV. The PID numbers of the ecognized non-coding ORFs for the 28 plant pathogens.

Table V. The average length for function-known protein-coding genes and the recognized non-coding ORFs in 28 plant pathogens.

Table VI.The identity,similarity and alignment coverage between 'hypothetical genes' in plant pathogens and experimental characterized genes.

Table I. General information for the 28 plant pathogens.

Species	Length (bp)	GC content (%)	Annotated ORFs in RefSeq	Number of Function-known Genes	Number of Hypothetical ORFs
Aac	5,352,772	68.02	4709	3393	1153
At58	2,841,580	59.38	2765	1718	1012
Cmm	3,297,891	72.66	2984	532	1039
Eca	5,064,019	50.97	4472	2246	1254
Psp	5,928,787	58.02	4985	3477	1105
Pss	6,093,698	59.23	5089	3792	1150
Pst	6,397,126	58.40	5476	3352	1646
Rs1000	3,716,416	67.04	3438	711	982
Xac	5,175,554	64.77	4312	2689	1604
Xcc8004	5,148,708	64.96	4273	2643	1592
Xcc33913	5,076,188	65.07	4181	2678	1474
Xcv	5,178,466	64.75	4487	2213	1213
Xoo311018	4,940,217	63.70	4372	2688	1582
Xoo10331	4,941,439	63.69	4144	2538	1279
Xf9a5c	2,679,306	52.67	2766	1253	1507
XfT	2,519,802	51.78	2034	1290	738
Ayw	706,595	26.89	671	346	323
Lxx	2,584,158	67.68	2030	1348	676
MfL	793,224	27.02	682	554	70
Oyp	860,631	27.74	754	398	347
Av4	4,009,526	57.60	4288	2987	1289
Cms	3,258,645	72.60	2941	2113	827
Cpa	879,959	27.40	684	410	266
Cpm	601,943	21.40	479	325	152
Xcc100	5,079,002	65.00	4467	2824	1643
Xoo99A	5,240,075	63.60	4988	3669	1268
XfM12	2,475,130	51.90	2104	1332	772
XfM23	2,535,690	51.80	2161	1486	675

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Table II. Re-annotation information for the 28 plant pathogens.

Species	Number of non-coding ORFs	Number of relocated TISs	Number of HPs assigned with functions	Number of PHX genes	Number of potential targets
Aac	15	699	105	327	35
At58	20	640	233	210	39
Cmm	0	381	197	836	40
Eca	48	436	169	259	46
Psp	20	728	103	166	44
Pss	19	333	133	410	43
Pst	34	766	174	209	44
Rs1000	12	503	200	150	40
Xac	39	1146	167	372	27
Xcc8004	5	1341	134	415	45
Xcc33913	7	1022	131	349	45
Xcv	10	859	124	408	45
Xoo311018	37	1282	131	404	42
Xoo10331	6	1586	152	470	40
Xf9a5c	70	916	194	205	41
XfT	27	459	114	370	41
Ayw	26	91	114	29	6
Lxx	4	612	92	211	47
MfL	0	2	1	49	13
Oyp	9	118	99	25	7
Av4	7	1171	437	76	45
Cms	63	826	181	455	35
Cpa	8	110	2	93	7
Cpm	2	43	7	79	8
Xcc100	0	790	91	432	29
Xoo99A	51	2434	54	673	41
XfM12	0	354	111	224	29
XfM23	0	324	83	734	29

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Table III. The sensitivity, specificity and accuracy over ten-fold cross-validation tests for the 28 plant pathogens.

Species	Sensitivity^a (%)	Specificity^a (%)	Accuracy^b (%)
Aac	99.95±0.0002	99.91±0.0004	99.93
At58	100.0±0.0000	100.0±0.0000	100.0
Cmm	100.0±0.0000	100.0±0.0000	100.0
Eca	99.62±0.0015	99.60±0.0013	99.61
Pss	99.76±0.0014	99.84±0.0005	99.80
Pst	99.83±0.0006	99.71±0.0006	99.77
Rs1000	99.94±0.0011	99.55±0.0036	99.74
Xac	99.86±0.0009	99.84±0.0008	99.85
Xcc8004	99.80±0.0006	99.70±0.0018	99.75
Xcc33913	99.84±0.0008	99.74±0.0011	99.79
Xcv	99.94±0.0004	99.92±0.0009	99.93
Xoo311018	99.90±0.0007	100.0±0.0000	99.95
Xoo10331	99.89±0.0006	99.89±0.0008	99.89
Xf9a5c	99.22±0.0034	99.22±0.0016	99.22
XfT	99.09±0.0035	99.33±0.0015	99.21
Ayw	99.88±0.0024	100±0.0000	100
Lxx	99.94±0.0008	99.70±0.0016	99.85
MfL	99.42±0.0049	99.64±0.0030	99.64
Oyp	100.00±0.0000	100.00±0.0021	100
Av4	99.80±0.0014	99.96±0.0005	99.88
Cms	99.88±0.0016	100.00±0.0000	99.94
Cpa	99.70±0.0031	99.64±0.0050	99.67
Cpm	99.66±0.0036	100.00±0.0000	99.83
Xoo99A	99.71±0.0011	99.52±0.0019	99.61

^a ± means standard deviation.
^b Accuracy is defined as the average of sensitivity and specificity.

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Table IV. The PID numbers of the recognized non-coding ORFs for the 28 plant pathogens.

Species	PID
Aac	120609105 120610021 120610287 120610034 120610287 120609750 120609808 120610963 120612514 120612310 120611994 120611669 120610660 120611075 120611006
At58	159184186 159185336 159185240 17936087 159185096 159185410 159184357 159184891 159184886 159184865 17935555 159184849 159184472 159184826 159184825 159184818 17935366 159184672 159184562 159184611
Eca	50119351 50119496 50119528 50119535 50119540 50119586 50119618 50119623 50119671 50120002 50120006 50120122 50120457 50120518 50120568 50120704 50121049 50121052 50121057 50121161 50121396 50121430 50121437 50121582 50121630 50121783 50121786 50121788 50121798 50121814 50121820 50122248 50122309 50122321 50122328 50122336 50122329 50122338 50122442 50122595 50122597 50122598 50122902 50123207 50123215 50123226 50123360 50123398
Psp	71735750 71733705 71734077 71738167 71734001 71733669 71737725 71735194 71736603 71735483 71735983 71735801 71737719 71733853 71733633 71737251 71737093 71735620 71738044 71734893
Pss	66043328 66043370 66044266 66044923 66044925 66044958 66045582 66045653 66045753 66046027 66046746 66046747 66046960 66047578 66047701 66047950 66047968 66047970 66047971
Pst	28867283 28867567 28867622 28867706 28867836 28868138 28868339 28868615 28868673 28868801 28868874 28868887 28869010 28870035 28870063 28870652 28870781 28871108 28869809 28870931 28871228 28870780 28871229 28869872 28870121 28871238 28871260 28871524 28871575 28871787 28871809 28872712 28872636 28872140
Rs1000	17545542 17545673 17545614 17545675 17547923 17545676 17546424 17546850 17547942 17548140 17548142 17548146
Xac	21240941 21241152 21241165 21241395 21241638 21241817 21242243 21242260 21242269 21242561 21242661 21242666 21242700 21242919 21242938 21243097 21243159 21243175 21243228 21243332 21243337 21243342 21243402 21243718 21243821 21243991 21244020 21244105 21244142 21244222 21244615 21244978 21244983 21245068 21241168 21241829 21242687 21244062 21241907
Xcc8004	66766733 66769302 66768430 66768429 66767857
Xcc33913	21229856 21229873 21231343 21231514 21231515 21232016 21233133
Xcv	78045768 78047411 78047959 78048015 78048126 78048195 78048360 78048949 78049612 78049842
Xoo311018	84621687 84622146 84621827 84621865 84622073 84622158 84622162 84622295 84622409 84622447 84622540 84622752 84622790 84622792 84622794 84623002 84623005 84623654 84623785 84623788 84623795 84623796 84623811 84623816 84623812 84623858 84623867 84623868 84624018 84623920 84624115 84624186 84624524 84624807 84625665 84625950 84625966
Xoo10331	121632057 121632098 58582368 58583125 58583866 121632139
Xf9a5c	15836656 15836657 15836674 15836717 15836731 15836814 15836824 15836871 15836931 15836932 15836938 15836962 15836998 15837091 15837106 15837133 15837176 15837179 15837181 15837241 15837302 15837463 15837551 15837560 15837567 15837573 15837624 15837692 15837721 15837786 15837804 15837810 15837843 15837882 15837908 15837953 15837959 15837995 15837996 15838030 15838067 15838152 15838157 15838357 15838373 15838392 15838465 15838470 15838479 15838661 15838678 15838694 15838714 15838757 15838790 15838847 15838947 15839004 15839016 15839100 15839106 15839122 15839212 15839216 15839239 15839242 15839247 15839267 15839272 15839356
XfT	28198506 28198680 28198671 28198679 28198820 28198823 28198833 28198840 28199010 28199011 28199012 28199015 28199028 28199081 28199131 28199133 28199135 28199198 28199238 28199315 28199628 28199686 28199775 28199888 28199894 28199928 28199973
Ayw	85057325 85057343 85057353 85057404 85057407 85057411 85057445 85057452 85057478 85057481 85057482 85057485 85057511 85057517 85057537 85057541 85057599 85057625 85057626 85057646 85057647 85057652 85057661 85057666 85057669 85057751
Lxx	50955025 50955429 50955848 50955870
Oyp	39938556 39938568 39938736 39938824 39938978 39938983 39939052 39939121 39939124
Av4	222147175 222147206 222147743 222147751 222148632 222149450 222149463
Cms	170780495 170780496 170780593 170780691 170780692 170780831 170780832 170780926 170781233 170781235 170781597 170781826 170782610 170782733 170782784 170782815 170782851 170782852 170783142 170783251 170783283 170783285 170783323 170783324 170780830 170781236 170781288 170781295 170781394 170781485 170781486 170781506 170781510 170781516 170781517 170781518 170781825 170781858 170782075 170782077 170782078 170782132 170782301 170782302 170782645 170782734 170782791 170782794 170782954 170782955 170782956 170782966 170782967 170782973 170783214 170783250 170783252 170783273 170783274 170783279 170783286 170783322 170782138
Cpa	197294183 197294268 197294380 197294477 197294587 197294742 197294826 197294853
Cpm	194246404 194246882
Xoo99A	188574451 188574492 188576412 188574412 188574456 188574458 188574480 188574647 188574729 188574747 188574750 188574782 188575054 188575087 188575236 188575309 188575340 188575611 188575621 188575749 188575848 188575894 188575981 188576038 188576084 188576266 188576269 188576288 188576417 188576472 188576490 188576509 188576530 188576590 188576595 188576804 188576997 188577363 188577763 188578059 188578318 188578667 188578759 188578808 188578923 188578946 188579037 188579038 188579110 188579125 188579228

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Table V. The average length for function-known protein-coding genes and the recognized non-coding ORFs in 28 plant pathogens.

Species	Length of function-known genes (aa)	Length of non-coding ORFs (aa)
Aac	371	231
At58	351.7	100.9
Cmm	397.4	0
Eca	370.7	110
Psp	362.1	131.8
Pss	383.4	140.7
Pst	375.4	103.2
Rs1000	350.3	127.2
Xac	392.6	179.5
Xcc8004	391.1	126.6
Xcc33913	387.7	119.6
Xcv	396.3	150.1
Xoo311018	353	163
Xoo10331	354.8	305.5
Xf9a5c	388.6	90.6
XfT	376.1	114.7
Ayw	343.4	103.9
Lxx	347.7	127.5
MfL	349	0
Oyp	318.9	127.1
Av4	368.1	270.8
Cms	367	232.1
Cpa	335.3	99.2
Cpm	356.2	62
Xoo99A	334.8	56

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Table VI. The identity, similarity and alignment coverage between ‘hypothetical genes’ in plant pathogens and experimental characterized genes in SwissProt

Product	Experimental species	Plantpathogen	DIGAP_ID	Identity	Similarity	Coverage (align/length)
ATP/cobalamin adenosyltransferase	Mycobacterium tuberculosis	Xac	DIGAP34616	43%	53%	188/193
ATP/cobalamin adenosyltransferase	Mycobacterium tuberculosis	Xcc8004	DIGAP41409	43%	53%	188/193
Bleomycin resistance protein	Streptoalloteichus Hindustanus	Pst	DIGAP26205	29%	47%	123/124
Chromosome segregation and condensation protein A	Bacillus subtilis	Xac	DIGAP36014	36%	53%	239/251
		Xcv	DIGAP48982	36%	53%	239/251
		Xoo311018	DIGAP52963	36%	53%	239/251
		Xoo10331	DIGAP57231	36%	53%	239/251
		Xcc33913	DIGAP44465	36%	53%	239/251
		Xcc8004	DIGAP39902	36%	53%	239/251
		Pss	DIGAP23344	34%	55%	239/251
		Pst	DIGAP26648	34%	56%	239/251
		Xf9a5c	DIGAP61801	36%	53%	246/251
		XfT	DIGAP63504	36%	52%	246/251
		Rs1000	DIGAP32707	31%	51%	248/251
Chromosome segregation and condensation protein B	Bacillus subtilis	Xac	DIGAP36015	39%	55%	170/197
		Xcc33913	DIGAP44466	40%	57%	164/197
		Xcc8004	DIGAP39901	40%	57%	164/197
		Xcv	DIGAP48983	39%	56%	164/197
		Xoo10331	DIGAP57230	39%	56%	164/197
		Xoo311018	DIGAP52962	39%	56%	164/197
		Xf9a5c	DIGAP61802	37%	53%	187/197
		Pss	DIGAP23343	36%	55%	180/197
		Pst	DIGAP26649	35%	55%	187/197
		Rs1000	DIGAP31608	34%	55%	180/197
		Cmm	DIGAP09421	35%	56%	173/197
Cyclopropane fatty acyl phospholipid synthase	Escherichia coli K12	Xcc8004	DIGAP40892	28%	46%	276/382
		Xoo10331	DIGAP57008	26%	45%	279/382
		Xoo311018	DIGAP52741	26%	45%	279/382
Di-Haem Cytochrome C Peroxidase	Pseudomonas Aeruginosa	At58	DIGAP07398	32%	45%	287/323
Pentachlorophenol 4-monooxygenase	Sphingobium chlorophenolicum	Pst	DIGAP27463	30%	46%	527/538
Peptidylarginine deiminase	Porphyromonas gingivalis	Xac	DIGAP36000	22%	39%	345/556
Peptidylarginine deiminase	Porphyromonas gingivalis	Xoo311018	DIGAP52977	22%	38%	355/556
Phosphohistidine phosphatase sixA	Escherichia coli K12	Xoo311018	DIGAP55154	29%	47%	127/161
Putative RNA 2'-O-ribose methyltransferase ygdE	Escherichia coli K12	Xoo10331	DIGAP58614	44%	63%	354/366
		Xcc33913	DIGAP43107	43%	62%	354/366
		Xcc8004	DIGAP41388	43%	62%	354/366

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