RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
(322 letters)
>gnl|CDD|183323 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 470 bits (1212), Expect = e-133
Identities = 162/321 (50%), Positives = 215/321 (66%), Gaps = 11/321 (3%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
M+DWTDRH R+F RLL+ +ALLYTEM+ AI+ GD++ +L F +E P+ALQ+GG+D +
Sbjct: 18 MMDWTDRHCRYFHRLLSRHALLYTEMVTTGAIIHGDRERLLAFDPEEHPVALQLGGSDPA 77
Query: 61 KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
L EAAK+ ED+GY+EINLNVGCPS RV G FGACLM P++V DC+ AM A+SIPVT
Sbjct: 78 DLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVT 137
Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
VK RIG+DDQ L + V ++ ++G + +HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 138 VKHRIGIDDQDSYEFLCDFVDTVAEAGCDTFIVHARKAWLKGLSPKENREIPPLDYDRVY 197
Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
+K++ P L I +NGG++ + +A + L VDGVMIGRAAY N +L VD E F P
Sbjct: 198 RLKRDFPHLTIEINGGIKTLEEAKEHLQHVDGVMIGRAAYHNPYLLAEVDRELFGEP--- 254
Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
+P +R + + +M Y RHL GG+L ITRHM+GLF G P +R R L+
Sbjct: 255 -APPLSRSE------VLEAMLPYIERHLAQGGRLNHITRHMLGLFQGLPGARAWRRYLSE 307
Query: 300 EAGASTATHHIIETAFNLMIE 320
A A ++E A L+ E
Sbjct: 308 NAHKPGAGIEVLEEALALVEE 328
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. Members of this
family show a distant relationship to alpha/beta (TIM)
barrel enzymes such as dihydroorotate dehydrogenase and
glycolate oxidase.
Length = 318
Score = 349 bits (896), Expect = 7e-97
Identities = 154/320 (48%), Positives = 206/320 (64%), Gaps = 9/320 (2%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
M+DWTDRH+R+F RLL+ + LLYTEMI A AI+ GDKK+IL FS +E P+ALQ+GG+D +
Sbjct: 8 MLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKDILKFSPEESPVALQLGGSDPN 67
Query: 61 KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
L + AKI E GY+EINLNVGCPS RV G+FGACLM N D+V DC+ AM +A++IPVT
Sbjct: 68 DLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQEAVNIPVT 127
Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
VK RIG+D L + V+ + G +HARKA L GLSPK+NR+IP L Y+ VY
Sbjct: 128 VKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKAWLSGLSPKENREIPPLRYERVY 187
Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
++KK+ P L I +NGG+++ Q + L VDGVM+GR AY+N +L VD N +
Sbjct: 188 QLKKDFPHLTIEINGGIKNSEQIKQHLSHVDGVMVGREAYENPYLLANVDREIFNE---T 244
Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
I TR + I M Y +L G L ITRH++GLF G P +++ R L+
Sbjct: 245 DEILTRKE------IVEQMLPYIEEYLSQGLSLNHITRHLLGLFQGKPGAKQWRRYLSEN 298
Query: 301 AGASTATHHIIETAFNLMIE 320
A + A ++ETA + E
Sbjct: 299 APKAGAGIEVLETALETVPE 318
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
Members of this family show a distant relationship to
alpha/beta (TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase.
Length = 319
Score = 122 bits (307), Expect = 2e-28
Identities = 81/302 (26%), Positives = 138/302 (45%), Gaps = 29/302 (9%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
M TD +R L EM+ ++AI+ ++ +L + E P+++Q+ G+D
Sbjct: 15 MAGVTDSPFRRLVAEY-GAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSD 73
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
+ EAAKI E+ G + I++N+GCP ++ + G+ L+ +PD++G + A+ A+ IP
Sbjct: 74 PDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIP 133
Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
VTVK RIG DD A N + + +G + +H R +G S + N
Sbjct: 134 VTVKIRIGWDD-----AHINAVEAARIAEDAGAQAVTLHGRTRA-QGYSGEAN------- 180
Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
+DI+ +K+ IG NG + A +L + DGVMIGR A N + +++Y
Sbjct: 181 WDIIARVKQAVRIPVIG-NGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYL 239
Query: 234 -SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
+ ++D R + Y L+ +H+ GFP +
Sbjct: 240 TTGKYKPPPTFAEKLDA-ILRHLQLLADYYGESKG-----LRIARKHIAWYLKGFPGNAA 293
Query: 293 CR 294
R
Sbjct: 294 LR 295
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 75.8 bits (186), Expect = 1e-14
Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 26/228 (11%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
M TDR +R + L +EM+ ++ + DK + E + +QI G+D
Sbjct: 17 MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
++ +AA+I + G I++N+GCP+ +V+ G+ L+ PD+V + + A+ +P
Sbjct: 76 PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135
Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
VT+K R G + RN V+ + G+ + IH R + G
Sbjct: 136 VTLKIRTGWAPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180
Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
+YD + +K++ I NG + D +A +L D +MIGRAA
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAA 227
>gnl|CDD|182540 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 52.9 bits (127), Expect = 1e-07
Identities = 47/163 (28%), Positives = 84/163 (51%), Gaps = 24/163 (14%)
Query: 65 AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122
AA+ VE G ++LN GCPS V+ GA L+ +P+++ AM +A+ +PVTVK
Sbjct: 81 AARAVE-LGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVTVK 139
Query: 123 CRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
R+G D ++ +A +++++G + +H R + +D + ++++ +
Sbjct: 140 VRLGWDSGERKFEIA-----DAVQQAGATELVVHGR-------TKEDGYRAEHINWQAIG 187
Query: 181 EIKKENPDLFIGL--NGGLEDM--SQALKILPSVDGVMIGRAA 219
EI++ L I + NG + D +Q + D VMIGR A
Sbjct: 188 EIRQR---LTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGA 227
>gnl|CDD|180909 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 45.1 bits (108), Expect = 2e-05
Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 30/129 (23%)
Query: 54 IGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDIVGDCIAA 110
+ G+ + E A+ + + I LN+ CP+ V G +FG +P++ + + A
Sbjct: 98 VAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN--VKHGGMAFGT----DPELAYEVVKA 151
Query: 111 MCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVNGIWIHARKAI 159
+ + + +PV VK V D + ++L N +K + I I RK I
Sbjct: 152 VKEVVKVPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKGMA------IDIKTRKPI 205
Query: 160 LK----GLS 164
L GLS
Sbjct: 206 LANVTGGLS 214
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 44.7 bits (106), Expect = 3e-05
Identities = 44/190 (23%), Positives = 76/190 (40%), Gaps = 32/190 (16%)
Query: 49 PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
PL + G+ + + E A+ +E + LN+ CP + + G +P++ D
Sbjct: 92 PLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKGGGIAIG----QDPELSAD 147
Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
+ A+ +PV K V D + K+ +++G +G I I
Sbjct: 148 VVKAVKDKTDVPVFAKLSPNVTDIT------EIAKAAEEAGADGLTLINTLRGMKIDIKT 201
Query: 156 RKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
K IL GLS I + +VY++ K IG+ GG+ AL+ ++
Sbjct: 202 GKPILANKTGGLSGP---AIKPIALRMVYDVYKMVDIPIIGV-GGITSFEDALEFLMAGA 257
Query: 211 DGVMIGRAAY 220
V +G A Y
Sbjct: 258 SAVQVGTAVY 267
>gnl|CDD|181383 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 34.5 bits (80), Expect = 0.041
Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 26/98 (26%)
Query: 64 EAAKIVEDFGYNEINLNVGCPSARVH---EGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
E A +VE+ G + I LN GCP H E G+ + P++V + + +PV
Sbjct: 117 EIAPLVEETGADGIELNFGCP----HGMSERGMGSAVGQVPELVEMYTRWVKRGSRLPVI 172
Query: 121 VKC---------------RIGVDDQIPAVALRNLVKSI 143
VK R G D AV+L N + SI
Sbjct: 173 VKLTPNITDIREPARAAKRGGAD----AVSLINTINSI 206
>gnl|CDD|129443 TIGR00343, TIGR00343, pyridoxal 5'-phosphate synthase, synthase
subunit Pdx1. This protein had been believed to be a
singlet oxygen resistance protein. Subsequent work
showed that it is a protein of pyridoxine (vitamin B6)
biosynthesis, and that pyridoxine quenches the highly
toxic singlet form of oxygen produced by light in the
presence of certain chemicals.
Length = 287
Score = 30.9 bits (70), Expect = 0.47
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 94 GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
G M +P ++ + + A+SIPV K RIG
Sbjct: 49 GVARMSDPKMIKEIM----DAVSIPVMAKVRIG 77
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
Length = 293
Score = 30.5 bits (70), Expect = 0.53
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 98 MLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
M +P ++ + + A+SIPV K RIG
Sbjct: 60 MADPKMIEEIM----DAVSIPVMAKARIG 84
>gnl|CDD|151243 pfam10788, DUF2603, Protein of unknown function (DUF2603). This
family is conserved in Epsilon-proteobacteria. The
function is not known.
Length = 133
Score = 30.0 bits (68), Expect = 0.81
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 166 KDNRKIPNLDYD-IVYEIKKENPDLFIGLN 194
K K N+D D +V +IKKE+P+LF+ L+
Sbjct: 104 KLAAKDSNIDLDRLVKKIKKEHPNLFVDLD 133
>gnl|CDD|178325 PLN02724, PLN02724, Molybdenum cofactor sulfurase.
Length = 805
Score = 29.1 bits (65), Expect = 1.5
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 10/91 (10%)
Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
+ L Y+ P G PI +F R D+A L+S +L+
Sbjct: 3 SFLKEFGGYYGYP-DGPKPIDELRATEFARLKGVVYLDHAGATLYSESQLEAALADFSSN 61
Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETA 314
+G P+S ++ +S + IE+A
Sbjct: 62 VYGNPHS---------QSDSSMRSSDTIESA 83
>gnl|CDD|184625 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 439
Score = 27.6 bits (62), Expect = 4.0
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 181 EIKKENPDLFIGLNGGL---EDMSQAL-KILPSVDGVMIGRAAYKNSAMLTTVDE 231
++K++NP+L IG+ G + + M++ + K P VD + +K L V E
Sbjct: 66 KLKEKNPNLIIGVCGCMMQQKGMAEKIKKKFPFVDIIFGTHNIHKFPEYLNRVKE 120
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University).
Length = 470
Score = 27.8 bits (62), Expect = 4.2
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL 297
G+ + + + NS CR ++
Sbjct: 348 GQQRTYKLKLYEMMEYCLNSSTCRRLI 374
>gnl|CDD|184898 PRK14905, PRK14905, triosephosphate isomerase/PTS system
glucose/sucrose-specific transporter subunit IIB;
Provisional.
Length = 355
Score = 27.3 bits (60), Expect = 5.2
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
+++ E K+ P L+ GG ++ A +++ P +DG+ IGR+A+ + +
Sbjct: 204 FELFAEESKKIPVLY----GGSVNLENANELIMKPHIDGLFIGRSAWDAQCFHALIADAL 259
Query: 234 SNPLTGSS 241
L GS
Sbjct: 260 -KALAGSK 266
>gnl|CDD|179249 PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase II;
Provisional.
Length = 724
Score = 27.0 bits (61), Expect = 6.2
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 108 IAAMCKALSIPVT 120
+A C+AL PV
Sbjct: 507 LADACRALGTPVV 519
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 27.1 bits (61), Expect = 7.3
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 17/69 (24%)
Query: 57 ADISKLVEAAKIVEDFGYNEINL--NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
D+ L+E AK E+ G + + VG L+P + + + + +A
Sbjct: 142 TDLDFLIEFAKAAEEAGADRVRFCDTVGI---------------LDPFTMYELVKELVEA 186
Query: 115 LSIPVTVKC 123
+ IP+ V C
Sbjct: 187 VDIPIEVHC 195
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 27.0 bits (61), Expect = 7.7
Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 195 GGLEDMS--QALKILPSVDGVMIGRAAY 220
GG+ + +ALK L +V+GV++GRA Y
Sbjct: 197 GGVSSLDDIKALKGLGAVEGVIVGRALY 224
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 26.8 bits (60), Expect = 8.2
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
K +L G+ KD R + N++ + +Y + E + FIG+
Sbjct: 240 KLLLNGVKIKDRRLLDNIEENKLYRVYDEE-NKFIGI 275
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.322 0.137 0.408
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,338,187
Number of extensions: 346282
Number of successful extensions: 703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 28
Length of query: 322
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 228
Effective length of database: 3,963,321
Effective search space: 903637188
Effective search space used: 903637188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)