RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780151|ref|YP_003064564.1| tRNA-specific 2-thiouridylase
MnmA [Candidatus Liberibacter asiaticus str. psy62]
(408 letters)
>gnl|CDD|178898 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
Length = 346
Score = 494 bits (1274), Expect = e-140
Identities = 173/365 (47%), Positives = 226/365 (61%), Gaps = 20/365 (5%)
Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80
RVVV MSGGVDSSV AALLK GY+VIGV ++L++ KG CCA +D+ DARRV
Sbjct: 1 KRVVVGMSGGVDSSVAAALLKEQGYEVIGVFMKLWDD-DDETGKGGCCAEEDIADARRVA 59
Query: 81 DTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGADV 140
D + + HYV D+E+ F + VI F Y AG TP PCV CN+ +KF L R+LGAD
Sbjct: 60 DKLGIPHYVVDFEKEFWDRVIDYFLDEYKAGRTPNPCVLCNKEIKFKAFLEYARELGADY 119
Query: 141 LATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKESV 200
+ATGHY R R R + R +D +DQSYFL+ TQ+QL L FPLG++ K V
Sbjct: 120 IATGHYARIR--------DGRELLRGVDPNKDQSYFLYQLTQEQLAKLLFPLGELTKPEV 171
Query: 201 RDLAREMGLDIADKSDSQDICFVQQGKYFDVVKRINAGIALEGDIVHLNGQILGRHNGII 260
R++A E GL +A K DSQ ICF+ + Y D +KR A G+IV L+G++LG H G++
Sbjct: 172 REIAEEAGLPVAKKKDSQGICFIGERDYRDFLKRYLP--AQPGEIVDLDGKVLGEHKGLM 229
Query: 261 NYTIGQRRGLGVA-MGEPLFVVYLDKNSSRVIVGPRESLEVHRIYLREINWLGDGLFEDA 319
YTIGQR+GLG+ GEP +VV D ++ V+VG E+L + ++NW+G E
Sbjct: 230 YYTIGQRKGLGIGGDGEPWYVVGKDPETNTVVVGQGEALYSRELIASDLNWVGGEPPE-- 287
Query: 320 VVDGFKCFVKIRSSQDPVPVFVQRNDDGVYVDFEKSEVGVASGQACVFYTSDSNEARVLG 379
+ F+C KIR Q PVP V+ DD V V+F++ + V GQA VFY D RVLG
Sbjct: 288 --EPFECTAKIRYRQKPVPATVELEDDRVEVEFDEPQRAVTPGQAAVFYDGD----RVLG 341
Query: 380 GGIIS 384
GGII
Sbjct: 342 GGIIE 346
>gnl|CDD|161871 TIGR00420, trmU, tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase.
tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase
(trmU, asuE, or mnmA) is involved in the biosynthesis of
the modified nucleoside
5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
the wobble position of some tRNAs. This enzyme appears
not to occur in the Archaea.
Length = 352
Score = 313 bits (804), Expect = 5e-86
Identities = 135/368 (36%), Positives = 206/368 (55%), Gaps = 21/368 (5%)
Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80
+V+V +SGGVDSSV A LLK+ GY+V+GV ++ + + G C + +D+ DA+ +C
Sbjct: 1 KKVIVGLSGGVDSSVSAYLLKQQGYEVVGVFMKNWEEDDKNDGHG-CTSAEDLRDAQAIC 59
Query: 81 DTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQ-LGAD 139
+ + + ++++ + N V PF Y G TP P + CN+ +KF L + LG D
Sbjct: 60 EKLGIPLEKVNFQKEYWNKVFEPFIQEYKEGRTPNPDILCNKFIKFGAFLEYAAELLGND 119
Query: 140 VLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKES 199
+ATGHY R +GK + R +D +DQSYFL+ + +QL L FPLG++ K
Sbjct: 120 KIATGHYARIA---EIEGKSL--LLRALDKNKDQSYFLYHLSHEQLAKLLFPLGELLKPE 174
Query: 200 VRDLAREMGLDIADKSDSQDICFVQQGKYFDVVKRINAGIALEGDIVHLNGQ-ILGRHNG 258
VR +A+ GL A+K DSQ ICF+ + K+ D +K+ G I+ ++GQ ++G H+G
Sbjct: 175 VRQIAKNAGLPTAEKKDSQGICFIGERKFRDFLKKYLP--VKPGVIITVDGQSVIGEHDG 232
Query: 259 IINYTIGQRRGLGVAMG-EPLFVVYLDKNSSRVIVG-PRESLEVHRIYLREINWLGDGLF 316
+ YTIGQR+GLG+ EP FVV D ++ +IV + L + ++ +WL D
Sbjct: 233 LWFYTIGQRKGLGIGGAAEPWFVVEKDLETNELIVSHGKPDLASRGLLAQQFHWLDDEPN 292
Query: 317 EDAVVDGFKCFVKIRSSQDPVPVFVQRNDDGVY-VDFEKSEVGVASGQACVFYTSDSNEA 375
+ +C VKIR Q PV ++ DD + V F++ + GV GQ+ V Y D
Sbjct: 293 PFEM----RCTVKIRYRQVPVQCKLKLLDDNLIEVIFDEPQAGVTPGQSAVLYKGD---- 344
Query: 376 RVLGGGII 383
LGGGII
Sbjct: 345 ICLGGGII 352
>gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA;
Provisional.
Length = 362
Score = 194 bits (493), Expect = 5e-50
Identities = 127/389 (32%), Positives = 193/389 (49%), Gaps = 59/389 (15%)
Query: 17 NPKDMRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDA 76
RV+V MSGG+DS+ +L+ GY+++GVT++++ G + DA
Sbjct: 2 KESKKRVLVGMSGGIDSTATCLMLQEQGYEIVGVTMRVW--------------GDEPQDA 47
Query: 77 RRVCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQL 136
R + + + HYV D F++ ++ F Y G TP PCV CN KF L+ +L
Sbjct: 48 RELAARMGIEHYVADERVPFKDTIVKNFIDEYRQGRTPNPCVMCNPLFKFRMLIEWADKL 107
Query: 137 GADVLATGHYIR-----SRLYV--GDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLR 189
G +ATGHY R +Y+ GDD K +DQSYFL+ Q L
Sbjct: 108 GCAWIATGHYSRLEERNGHIYIVAGDDDK------------KDQSYFLWRLGQDILRRCI 155
Query: 190 FPLGDMKKESVRDLAREMGLDIADKS-DSQDICFVQQGKYFDVVKRINAGIALE---GDI 245
FPLG+ K++VR+ RE G + K +S ++CF+ +G Y D ++ + E G
Sbjct: 156 FPLGNYTKQTVREYLREKGYEAKSKEGESMEVCFI-KGDYRDFLREQCPELDTEVGPGWF 214
Query: 246 VHLNGQILGRHNGIINYTIGQRRGLGVAMGEPLFVVYLDKNSSRVIVGPRESLEVHRIYL 305
V+ G LG+H G YTIGQR+GL +A+G+P +V+ ++ + V++G E L+ +
Sbjct: 215 VNSEGVKLGQHKGFPYYTIGQRKGLEIALGKPAYVLKINPQKNTVMLGDAEQLKAEYMLA 274
Query: 306 REINWLGDGLFEDAVVDG---FKC---FVKIRSSQDPVPVFVQRNDDG-VYVDFEKSEVG 358
+D +VD F C V+IR P+P V+R +DG + V F
Sbjct: 275 E----------QDNIVDEQELFACPDLAVRIRYRSRPIPCRVKRLEDGRLLVRFLAEASA 324
Query: 359 VASGQACVFYTSDSNEARVLGGGIISGSK 387
+A GQ+ VFY RVLGG I+ +
Sbjct: 325 IAPGQSAVFYEG----RRVLGGAFIASQR 349
>gnl|CDD|173128 PRK14665, mnmA, tRNA-specific 2-thiouridylase MnmA; Provisional.
Length = 360
Score = 181 bits (460), Expect = 4e-46
Identities = 113/380 (29%), Positives = 183/380 (48%), Gaps = 40/380 (10%)
Query: 19 KDMRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARR 78
K+ RV++ MSGG DSSV A LL GY+V GVT + Y +++ + DAR
Sbjct: 4 KNKRVLLGMSGGTDSSVAAMLLLEAGYEVTGVTFRFYEFNGSTEY---------LEDARA 54
Query: 79 VCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGA 138
+ + + + H +D + FR +I F Y +G TP+PC CN +K+ L + ++G
Sbjct: 55 LAERLGIGHITYDARKVFRKQIIDYFIDEYMSGHTPVPCTLCNNYLKWPLLAKIADEMGI 114
Query: 139 DVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKE 198
LATGHY+R + G+ + D+++DQS+FL+ Q+ L + P+G M K
Sbjct: 115 FYLATGHYVRKQWIDGN-----YYITPAEDVDKDQSFFLWGLRQEILQRMLLPMGGMTKS 169
Query: 199 SVRDLAREMG-LDIADKSDSQDICFVQQGKYFDVVK-----------RINAGIALEGDIV 246
R A E G +A K DS +CF Y +K R G +
Sbjct: 170 EARAYAAERGFEKVAKKRDSLGVCFCPM-DYRSFLKKCLCDESGDKNRNIYRKVERGRFL 228
Query: 247 HLNGQILGRHNGIINYTIGQRRGLGVAMGEPLFVVYLDKNSSRVIVGPRESLEVHRIYLR 306
+G + H G YTIGQRRGLG+ + +FV + ++ V++ ++LE ++L+
Sbjct: 229 DESGNFIAWHEGYPFYTIGQRRGLGIQLNRAVFVKEIHPETNEVVLASLKALEKTEMWLK 288
Query: 307 EINWLGDGLF---EDAVVDGFKCFVKIRSSQDPVPVFVQRNDDGVYVDFEKSEVGVASGQ 363
+ N + + +D +V ++ R ++ V + D+ ++V + +A GQ
Sbjct: 289 DWNIVNESRLLGCDDIIVK-----IRYRKQENHCTVTITP-DNLLHVQLHEPLTAIAEGQ 342
Query: 364 ACVFYTSDSNEARVLGGGII 383
A FY +LGGGII
Sbjct: 343 AAAFYKDGL----LLGGGII 358
>gnl|CDD|184435 PRK13980, PRK13980, NAD synthetase; Provisional.
Length = 265
Score = 47.1 bits (113), Expect = 7e-06
Identities = 53/219 (24%), Positives = 84/219 (38%), Gaps = 80/219 (36%)
Query: 22 RVVVAMSGGVDSSVVAALLKRD-GYD-VIGVTLQLYNSRKASKRKGSCCAGQDVYDARRV 79
VV+ +SGG+DS+VVA L + G + V+ + + S D+ DA V
Sbjct: 32 GVVLGLSGGIDSAVVAYLAVKALGKENVLALLMPSSVSPPE-----------DLEDAELV 80
Query: 80 CDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSV------T 133
+ + + + V + I P ++ + + +D L V T
Sbjct: 81 AEDLGIEYKVIE---------ITPIVDAFFS------------AIPDADRLRVGNIMART 119
Query: 134 R---------QLGADVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQ-- 182
R + VL TG+ +S L +G YF T+
Sbjct: 120 RMVLLYDYANRENRLVLGTGN--KSELLLG--------------------YF----TKYG 153
Query: 183 QQLCDLRFPLGDMKKESVRDLAREMGL--DIADKSDSQD 219
DL P+GD+ K VR+LAR +G+ DI +K S D
Sbjct: 154 DGAVDLN-PIGDLYKTQVRELARHLGVPEDIIEKPPSAD 191
>gnl|CDD|129369 TIGR00268, TIGR00268, conserved hypothetical protein TIGR00268.
The N-terminal region of the model shows similarity to
Argininosuccinate synthase proteins using PSI-blast and
using the recognize protein identification server.
Length = 252
Score = 47.1 bits (112), Expect = 8e-06
Identities = 46/195 (23%), Positives = 79/195 (40%), Gaps = 47/195 (24%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81
+V++A SGGVDSS++AA+ G +V+ +T+ S S R ++ DA +
Sbjct: 14 KVLIAYSGGVDSSLLAAVCSDAGTEVLAITVV---SPSISPR--------ELEDAIIIAK 62
Query: 82 TINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGADVL 141
I V+H ++ +I PF ++ C C + V S L+ + G DV+
Sbjct: 63 EIGVNHEFVKIDK-----MINPFRAN-----VEERCYFCKKMV-LSILVKEAEKRGYDVV 111
Query: 142 ATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMK--KES 199
G DD R R + E + P + K+
Sbjct: 112 VDGTN-------ADDLFDHRPGYRAVK-EF---------------NGVSPWAEFGITKKE 148
Query: 200 VRDLAREMGLDIADK 214
+R++A+ +G+ DK
Sbjct: 149 IREIAKSLGISFPDK 163
>gnl|CDD|148238 pfam06508, ExsB, ExsB. This family includes putative
transcriptional regulators from Bacteria and Archaea.
Length = 137
Score = 45.3 bits (108), Expect = 3e-05
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81
+ VV +SGG+DS+ A K++GY+V +T Y R + + + A+++
Sbjct: 1 KAVVLLSGGLDSTTCLAWAKKEGYEVYALTFD-YGQRHSKELEC----------AKKIAK 49
Query: 82 TINVSHYVFD 91
+ V H + D
Sbjct: 50 ALGVEHKIVD 59
>gnl|CDD|178842 PRK00074, guaA, GMP synthase; Reviewed.
Length = 511
Score = 45.0 bits (108), Expect = 4e-05
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 19 KDMRVVVAMSGGVDSSVVAALLKR 42
D +V++ +SGGVDSSV A LL +
Sbjct: 214 GDKKVILGLSGGVDSSVAAVLLHK 237
>gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional.
Length = 394
Score = 43.4 bits (103), Expect = 1e-04
Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 20/88 (22%)
Query: 21 MRVVVAMSGGVDSSVVAALLK-RDGYD-VIGVTLQLYNSRKASKRKGSCCAGQ---DVYD 75
+VV+A SGG+D+SV LLK + GYD VI VT+ + GQ ++ +
Sbjct: 3 KKVVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDV---------------GQPEEEIKE 47
Query: 76 ARRVCDTINVSHYVFDYEERFRNAVIVP 103
A + HY D +E F I P
Sbjct: 48 AEEKAKKLGDKHYTIDAKEEFAKDYIFP 75
>gnl|CDD|129461 TIGR00364, TIGR00364, exsB protein. This protein family is
represented by a single member in nearly every completed
large (> 1000 genes) prokaryotic genome. In Rhizobium
meliloti, a species in which the exo genes make
succinoglycan, a symbiotically important
exopolysaccharide, exsB is located nearby and affects
succinoglycan levels, probably through polar effects on
exsA expression or the same polycistronic mRNA. In
Arthrobacter viscosus, the homologous gene is designated
ALU1 and is associated with an aluminum tolerance
phenotype. The function is unknown.
Length = 201
Score = 42.8 bits (101), Expect = 2e-04
Identities = 32/128 (25%), Positives = 55/128 (42%), Gaps = 18/128 (14%)
Query: 24 VVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCDTI 83
VV +SGG DS+ A+ K +GY+V +T Y R +++ AR++ + +
Sbjct: 2 VVVLSGGQDSTTCLAIAKDEGYEVHAITFD-YGQR----------HSRELESARKIAEAL 50
Query: 84 NVSHYVFDY---EERFRNAV----IVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQL 136
+ H+V D ++ +A+ +P S P V + S S L
Sbjct: 51 GIEHHVIDLSLLKQLGGSALTDESEIPPQKSNEEDTLPNTFVPGRNAIFLSIAASYAEAL 110
Query: 137 GADVLATG 144
GA+ + TG
Sbjct: 111 GAEAVITG 118
>gnl|CDD|161924 TIGR00552, nadE, NAD+ synthetase. NAD+ synthetase is a nearly
ubiquitous enzyme for the final step in the biosynthesis
of the essensial cofactor NAD. The member of this family
from Bacillus subtilis is a strictly NH(3)-dependent
NAD(+) synthetase of 272 amino acids. Proteins
consisting only of the domain modeled here may be named
as NH3-dependent NAD+ synthetase. Amidotransferase
activity may reside in a separate protein, or not be
present. Some other members of the family, such as from
Mycobacterium tuberculosis, are considerably longer,
contain an apparent amidotransferase domain, and show
glutamine-dependent as well as NH(3)-dependent activity.
Length = 250
Score = 39.7 bits (93), Expect = 0.001
Identities = 47/195 (24%), Positives = 73/195 (37%), Gaps = 54/195 (27%)
Query: 23 VVVAMSGGVDSSVVAALLKRD-GYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81
VV+ +SGG+DS+VVAAL G + L + QDV DA + +
Sbjct: 25 VVLGLSGGIDSAVVAALCVEALGEQNHALLLPHSVQ--TPE--------QDVQDALALAE 74
Query: 82 TINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVD-------CNRTVKFSDLLSVTR 134
+ +++ D AS A ET D R + + L ++
Sbjct: 75 PLGINYKNIDIA--------PIAASFQAQTETGDELSDFLAKGNLKARL-RMAALYAIAN 125
Query: 135 QLGADVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQL-CDLRFPLG 193
+ VL TG+ +S L +G YF T CD+ P+G
Sbjct: 126 KHNLLVLGTGN--KSELMLG--------------------YF---TKYGDGGCDIA-PIG 159
Query: 194 DMKKESVRDLAREMG 208
D+ K V +LA+ +
Sbjct: 160 DLFKTQVYELAKRLN 174
>gnl|CDD|129143 TIGR00032, argG, argininosuccinate synthase. argG in bacteria,
ARG1 in Saccharomyces cerevisiae. There is a very
unusual clustering in the alignment, with a deep split
between one cohort of E. coli, H. influenzae, and
Streptomyces, and the other cohort of eukaryotes,
archaea, and the rest of the eubacteria.
Length = 394
Score = 39.7 bits (93), Expect = 0.002
Identities = 33/128 (25%), Positives = 51/128 (39%), Gaps = 20/128 (15%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQ--DVYDA--R 77
+VV+A SGG+D+SV L+ GY+VI T + GQ + DA
Sbjct: 1 KVVLAYSGGLDTSVCLKWLREKGYEVIAYTADV---------------GQPEEDIDAIPE 45
Query: 78 RVCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDC-NRTVKFSDLLSVTRQL 136
+ + +HY D E F + A E P R + L+ ++
Sbjct: 46 KALEYGAENHYTIDAREEFVKDYGFAAIQANAFYEGTYPLSTALARPLIAKKLVEAAKKE 105
Query: 137 GADVLATG 144
GA+ +A G
Sbjct: 106 GANAVAHG 113
>gnl|CDD|179859 PRK04527, PRK04527, argininosuccinate synthase; Provisional.
Length = 400
Score = 39.0 bits (91), Expect = 0.002
Identities = 30/125 (24%), Positives = 45/125 (36%), Gaps = 14/125 (11%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81
+V+A SGG+D+S L+ GY V V G A + + +R +
Sbjct: 4 DIVLAFSGGLDTSFCIPYLQERGYAVHTVFAD----------TGGVDAEERDFIEKRAAE 53
Query: 82 TINVSHYVFDYEERFRNAVIVPF--ASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGAD 139
SH D + P A G+ PL D R + L +LG
Sbjct: 54 LGAASHVTVDGGPAIWEGFVKPLVWAGEGYQGQYPLLVSD--RYLIVDAALKRAEELGTR 111
Query: 140 VLATG 144
++A G
Sbjct: 112 IIAHG 116
>gnl|CDD|162088 TIGR00884, guaA_Cterm, GMP synthase (glutamine-hydrolyzing),
C-terminal domain or B subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains
in most of the Archaea. This C-terminal region would be
the larger subunit.
Length = 311
Score = 38.1 bits (89), Expect = 0.004
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 19 KDMRVVVAMSGGVDSSVVAALLKR 42
D +V++A+SGGVDSSV A L R
Sbjct: 15 GDAKVIIALSGGVDSSVAAVLAHR 38
>gnl|CDD|162854 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
vs. UGG (Trp). In all bacteria, the wobble position of
the tRNA(Ile) recognizing AUA is lysidine, a lysine
derivative of cytidine. This family describes a protein
domain found, apparently, in all bacteria in a single
copy. Eukaryotic sequences appear to be organellar. The
domain archictecture of this protein family is variable;
some, including characterized proteins of E. coli and B.
subtilis known to be tRNA(Ile)-lysidine synthetase,
include a conserved 50-residue domain that many other
members lack. This protein belongs to the ATP-binding
PP-loop family ( pfam01171). It appears in the
literature and protein databases as TilS, YacA, and
putative cell cycle protein MesJ (a misnomer).
Length = 189
Score = 37.6 bits (88), Expect = 0.006
Identities = 25/131 (19%), Positives = 46/131 (35%), Gaps = 31/131 (23%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQL----YNSRKASKRKGSCCAGQDVYDAR 77
R++VA+SGGVDS + LL + + + L + R S +A
Sbjct: 1 RILVAVSGGVDSMALLHLLLKL-QPKLKIRLIAAHVDHGLRPESDE-----------EAE 48
Query: 78 RV---CDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTR 134
V C +N+ + + + + A R ++ + +
Sbjct: 49 FVQQFCKKLNIPLEIKKVDVKALA--KGKKKNLEEAA----------REARYDFFEEIAK 96
Query: 135 QLGADVLATGH 145
+ GAD + T H
Sbjct: 97 KHGADYILTAH 107
>gnl|CDD|179150 PRK00876, nadE, NAD synthetase; Reviewed.
Length = 326
Score = 37.6 bits (88), Expect = 0.006
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 13/71 (18%)
Query: 23 VVVAMSGGVDSSVVAALLKRD-GYD-VIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80
VV+ +SGG+DSSV AAL R G + V G+ + +S S R G R V
Sbjct: 36 VVLGLSGGIDSSVTAALCVRALGKERVYGLLMPERDSSPESLRLG-----------REVA 84
Query: 81 DTINVSHYVFD 91
+ + V + V D
Sbjct: 85 EHLGVEYVVED 95
>gnl|CDD|179167 PRK00919, PRK00919, GMP synthase subunit B; Validated.
Length = 307
Score = 36.4 bits (85), Expect = 0.013
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 13 DLDKNPKDMRVVVAMSGGVDSSVVAALLKRDGYDVIG 49
++ + D + ++A+SGGVDSSV A L + IG
Sbjct: 14 EIREEIGDGKAIIALSGGVDSSVAAVL----AHRAIG 46
Score = 27.6 bits (62), Expect = 6.3
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 191 PLGDMKKESVRDLAREMGLD 210
PL D+ K+ VR++AR +GL
Sbjct: 159 PLRDLYKDEVREVARALGLP 178
>gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional.
Length = 399
Score = 35.8 bits (84), Expect = 0.022
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 21 MRVVVAMSGGVDSSVVAALLKRD-GYDVIGVTLQL 54
+VV+A SGG+D+SV+ LK G +VI T +
Sbjct: 3 KKVVLAYSGGLDTSVIIKWLKETYGCEVIAFTADV 37
>gnl|CDD|185431 PTZ00077, PTZ00077, asparagine synthetase-like protein;
Provisional.
Length = 586
Score = 34.7 bits (80), Expect = 0.040
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 25 VAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAG----QDVYDARRVC 80
+ +SGG+DSS+VAA++ + + ++ S++ + S C G D+ AR+V
Sbjct: 242 LFLSGGLDSSIVAAIVAK-----LIKNGEIDLSKRGMPKLHSFCIGLEGSPDLKAARKVA 296
Query: 81 DTINVSHYVFDYE 93
+ + H+ F +
Sbjct: 297 EYLGTEHHEFTFT 309
>gnl|CDD|179454 PRK02628, nadE, NAD synthetase; Reviewed.
Length = 679
Score = 34.1 bits (79), Expect = 0.062
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 13/54 (24%)
Query: 6 ATRLNSLDLDKNPKDMRVVVAMSGGVDSS---VVAA----LLKRDGYDVIGVTL 52
A RL + L K VV+ +SGG+DS+ +VAA L +++ T+
Sbjct: 353 AQRLRATGLKK------VVIGISGGLDSTHALLVAAKAMDRLGLPRKNILAYTM 400
>gnl|CDD|178164 PLN02549, PLN02549, asparagine synthase (glutamine-hydrolyzing).
Length = 578
Score = 32.8 bits (75), Expect = 0.17
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 19/76 (25%)
Query: 25 VAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKG----SCCAGQ----DVYDA 76
V +SGG+DSS+VA++ R KA+++ G S C G D+ A
Sbjct: 230 VLLSGGLDSSLVASIAARH-----------LAETKAARQWGQQLHSFCVGLEGSPDLKAA 278
Query: 77 RRVCDTINVSHYVFDY 92
R V D + H+ F +
Sbjct: 279 REVADYLGTVHHEFHF 294
>gnl|CDD|184745 PRK14561, PRK14561, hypothetical protein; Provisional.
Length = 194
Score = 32.5 bits (75), Expect = 0.23
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVT 51
M+ V SGG DSS+ A LL+R YDV VT
Sbjct: 1 MKAGVLFSGGKDSSLAAILLERF-YDVELVT 30
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 31.7 bits (72), Expect = 0.33
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 12/88 (13%)
Query: 3 VSEATRLNSLDLDKNPKDMRVVVAMSGG-VDSSVVAALLKRDGYDVIGVTLQLYNSRKAS 61
+ A K PKD+ V+V + G + VV L++R GY+V+ V R+ S
Sbjct: 43 RATAAAAAQSFRSKEPKDVTVLVVGATGYIGKFVVRELVRR-GYNVVAVA------REKS 95
Query: 62 K---RKGSCCAGQDVYDARRV-CDTINV 85
+ G +++ A V D +
Sbjct: 96 GIRGKNGKEDTKKELPGAEVVFGDVTDA 123
>gnl|CDD|162406 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff.
Length = 467
Score = 31.5 bits (72), Expect = 0.35
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42
D+ V V +SGG+DSS+VAA+ +R
Sbjct: 253 DVPVGVLLSGGLDSSLVAAIARR 275
>gnl|CDD|163334 TIGR03573, WbuX, N-acetyl sugar amidotransferase. This enzyme
has been implicated in the formation of the acetamido
moiety (sugar-NC(=NH)CH3) which is found on some
exopolysaccharides and is positively charged at neutral
pH. The reaction involves ligation of ammonia with a
sugar N-acetyl group, displacing water. In E. coli
(O145 strain) and Pseudomonas aeruginosa (O12 strain)
this gene is known as wbuX and ifnA respectively and
likely acts on sialic acid. In Campylobacter jejuni,
the gene is known as pseA and acts on pseudaminic acid
in the process of flagellin glycosylation. In other
Pseudomonas strains and various organisms it is unclear
what the identity of the sugar substrate is, and in
fact, the phylogenetic tree of this family sports a
considerably deep branching suggestive of possible
major differences in substrate structure. Nevertheless,
the family is characterized by a conserved
tetracysteine motif (CxxC.....[GN]xCxxC) possibly
indicative of a metal binding site, as well as an
invariable contextual association with homologs of the
HisH and HisF proteins known as WbuY and WbuZ,
respectively. These two proteins are believed to supply
the enzyme with ammonium by hydrolysis of glutamine and
delivery through an ammonium conduit.
Length = 343
Score = 31.5 bits (72), Expect = 0.37
Identities = 11/31 (35%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 23 VVVAMSGGVDSSVVAALLKRD-GYDVIGVTL 52
++ +SGG DS+ A +LK+ G + + VT+
Sbjct: 62 CIIGVSGGKDSTYQAHVLKKKLGLNPLLVTV 92
>gnl|CDD|169417 PRK08384, PRK08384, thiamine biosynthesis protein ThiI;
Provisional.
Length = 381
Score = 31.5 bits (71), Expect = 0.40
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGV 50
+VV +SGG+DS V A L+ + G +VI V
Sbjct: 182 KVVALLSGGIDSPVAAFLMMKRGVEVIPV 210
>gnl|CDD|185554 PTZ00323, PTZ00323, NAD+ synthase; Provisional.
Length = 294
Score = 31.7 bits (72), Expect = 0.41
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 24 VVAMSGGVDSSVVAALLKR 42
V ++SGG+DS+VV AL R
Sbjct: 50 VTSVSGGIDSAVVLALCAR 68
>gnl|CDD|184436 PRK13981, PRK13981, NAD synthetase; Provisional.
Length = 540
Score = 30.5 bits (70), Expect = 0.79
Identities = 10/17 (58%), Positives = 16/17 (94%)
Query: 23 VVVAMSGGVDSSVVAAL 39
VV+ +SGG+DS++VAA+
Sbjct: 283 VVLGLSGGIDSALVAAI 299
>gnl|CDD|163136 TIGR03104, trio_amidotrans, asparagine synthase family
amidotransferase. Members of this protein family are
closely related to several isoforms of asparagine
synthetase (glutamine amidotransferase) and typically
have been given this name in genome annotation to date.
Each is part of a conserved three-gene cassette sparsely
distributed across at least twenty different species
known so far, including alpha, beta, and gamma
Proteobacteria, Mycobacterium, and Prosthecochloris,
which is a member of the Chlorobi. The other two members
of the cassette are a probable protease and a member of
the GNAT family of acetyltransferases.
Length = 589
Score = 30.4 bits (69), Expect = 0.93
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 20 DMRVVVAMSGGVDSSVVAALLKRDGYD 46
D+ V V +SGG+DSS++ LL G D
Sbjct: 260 DVPVGVLLSGGLDSSLIVGLLAEAGVD 286
>gnl|CDD|177981 PLN02347, PLN02347, GMP synthetase.
Length = 536
Score = 30.4 bits (69), Expect = 0.94
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42
D V+ A+SGGVDS+V A L+ +
Sbjct: 229 DEHVICALSGGVDSTVAATLVHK 251
>gnl|CDD|169396 PRK08349, PRK08349, hypothetical protein; Validated.
Length = 198
Score = 29.7 bits (67), Expect = 1.3
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGV 50
M+ V +S G+DS V L+ R G +V V
Sbjct: 1 MKAVALLSSGIDSPVAIYLMLRRGVEVYPV 30
>gnl|CDD|161829 TIGR00342, TIGR00342, thiazole biosynthesis/tRNA modification
protein ThiI. The protein product of the thiI gene is
required for the synthesis of the thiazole moiety in
thiamine biosynthesis. It also acts in the generation of
4-thiouridine in tRNA, and may occur in species (such as
Mycoplasma genitalium) that lack de novo thiamine
biosynthesis.
Length = 371
Score = 28.9 bits (65), Expect = 2.2
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTL 52
+V+ +SGG+DS V A ++ + G V+ V
Sbjct: 174 KVLALLSGGIDSPVAAFMMMKRGCRVVAVHF 204
>gnl|CDD|181851 PRK09431, asnB, asparagine synthetase B; Provisional.
Length = 554
Score = 28.7 bits (65), Expect = 3.1
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42
D+ V +SGG+DSS+++A+ K+
Sbjct: 227 DVPYGVLLSGGLDSSLISAIAKK 249
>gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional.
Length = 237
Score = 28.6 bits (64), Expect = 3.4
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 197 KESVRDLAREMGLDIADKSDSQD----ICFVQQGKYFDVVKRINAGIALEGDIVHLN 249
K++ LA+E G A ++DS D I V++ D++ +NAGIA+ GD + L+
Sbjct: 41 KDAAERLAQETGAT-AVQTDSADRDAVIDVVRKSGALDILV-VNAGIAVFGDALELD 95
>gnl|CDD|177973 PLN02339, PLN02339, NAD+ synthase (glutamine-hydrolysing).
Length = 700
Score = 28.5 bits (64), Expect = 3.7
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 14/54 (25%)
Query: 27 MSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80
+SGG DSS VAA+ +G QL + R+G Q DARR+
Sbjct: 355 LSGGADSSSVAAI--------VGSMCQLVV---KAIREGD---EQVKADARRIG 394
>gnl|CDD|163033 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP
family. This model represents a subfamily of pfam00107
as defined by Pfam, a superfamily in which some members
are zinc-binding medium-chain alcohol dehydrogenases
while others are quinone oxidoreductases with no bound
zinc. This subfamily includes proteins studied
crystallographically for insight into function: YhdH
from Escherichia coli and YhfP from Bacillus subtilis.
Members bind NADPH or NAD, but not zinc.
Length = 323
Score = 28.3 bits (64), Expect = 3.8
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 17 NPKDMRVVV-AMSGGVDSSVVAALLKRDGYDVIGVT 51
P+D V+V +GGV S+ A+L + GY+V+ T
Sbjct: 143 TPEDGPVLVTGATGGV-GSLAVAILSKLGYEVVAST 177
>gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional.
Length = 404
Score = 28.2 bits (63), Expect = 4.6
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 18 PKDMRVVVAMSGGVDSSVVAALLKRD-GYDVIGVT 51
K +VV+A SGG+D+SV+ L+ + G +V+ T
Sbjct: 3 GKLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFT 37
>gnl|CDD|182548 PRK10559, PRK10559, p-hydroxybenzoic acid efflux subunit AaeA;
Provisional.
Length = 310
Score = 27.8 bits (62), Expect = 5.5
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 157 GKRRRIMCRPMDLER-DQSYFLFATTQQQLCDLRFPLGDMKKESVRDLAR 205
G+R R+ + M E DQ+ + T QL K ++ RDLA+
Sbjct: 109 GRRNRLGVQAMSREEIDQANNVLQTVLHQLA---------KAQATRDLAK 149
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 27.7 bits (62), Expect = 6.3
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 22 RVVVAMSGGVDSSVVAALL 40
+++VA SGG+DS+V+ LL
Sbjct: 17 QILVAFSGGLDSTVLLHLL 35
>gnl|CDD|184135 PRK13551, PRK13551, agmatine deiminase; Provisional.
Length = 362
Score = 27.6 bits (62), Expect = 6.3
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 295 RESLEVHRIYLREINWLGDGLFEDAV---VDGFKCFVK 329
R+ L V ++ WL DG++ D VD CFV+
Sbjct: 190 RDYLGVEKVI-----WLPDGIYNDETDGHVDNVCCFVR 222
>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 27.4 bits (62), Expect = 6.8
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 376 RVLGGGIISGS 386
RVLGGG++ GS
Sbjct: 71 RVLGGGLVPGS 81
>gnl|CDD|179487 PRK02866, PRK02866, cyanate hydratase; Validated.
Length = 147
Score = 27.5 bits (62), Expect = 6.8
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 11 SLDLDK--NPKDMRVVVAMSG 29
LD+DK +PK RVV+ + G
Sbjct: 119 KLDVDKVEDPKGDRVVITLDG 139
>gnl|CDD|162036 TIGR00784, citMHS, citrate transporter, CitMHS family. This family
includes two characterized citrate/proton symporters
from Bacillus subtilis. CitM transports citrate
complexed to Mg2+, while the CitH apparently transports
citrate without Mg2+. The family also includes
uncharacterized transporters, including a third paralog
in Bacillus subtilis.
Length = 431
Score = 27.5 bits (61), Expect = 6.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 381 GIISGSKRSDAVEESLLSVIGDE 403
GI+SG+K DA+ SL+S+I
Sbjct: 300 GILSGTKMVDAMAGSLVSIIPSS 322
>gnl|CDD|180043 PRK05370, PRK05370, argininosuccinate synthase; Validated.
Length = 447
Score = 27.2 bits (61), Expect = 7.0
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 6 ATRLNSLDLDKNPKDMRVVVAMSGGVDSSVVAALLKRDG 44
+T L L P RV +A SGG+D+S +++ G
Sbjct: 2 STILKHL-----PVGQRVGIAFSGGLDTSAALLWMRQKG 35
>gnl|CDD|132036 TIGR02991, ectoine_eutB, ectoine utilization protein EutB. Members
of this protein family are EutB, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti, Silicibacter pomeroyi,
Agrobacterium tumefaciens, and Pseudomonas putida.
Members of this family resemble threonine dehydratases.
Length = 317
Score = 27.5 bits (61), Expect = 7.2
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 14 LDKNPKDMRVVVAMSGGVDSSVVAALLK--RDGYDVIGVTLQLYNSRKASKRKG 65
+++ P V+V +SGG +S VA +K R VIGV+++ + KAS + G
Sbjct: 162 VEQMPDLATVLVPLSGGGLASGVAMAVKAARPDTRVIGVSMERGAAMKASLQAG 215
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 27.3 bits (61), Expect = 7.6
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 201 RDLAREMGLDIADKSDSQDICFVQQGK-YFDVV 232
LAREMG D + D+ + K YFDV
Sbjct: 207 LSLAREMGADKLVNPQNDDLDHYKAEKGYFDVS 239
>gnl|CDD|178010 PLN02384, PLN02384, ribose-5-phosphate isomerase.
Length = 264
Score = 27.1 bits (60), Expect = 8.1
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 180 TTQQQLCDLRFPLGDMKKESVRDLAREMGLDIADKSDS 217
T +Q L PL D+ V DLA +D AD+ D
Sbjct: 88 KTHEQAVSLGIPLSDLDSHPVVDLA----IDGADEVDP 121
>gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed.
Length = 272
Score = 26.8 bits (60), Expect = 9.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 18 PKDMRVVVAMSGGVDSSVVAAL 39
P D+ V + SGG+ +V AAL
Sbjct: 120 PPDLVVALRGSGGMAKAVAAAL 141
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 0.139 0.407
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,671,369
Number of extensions: 442345
Number of successful extensions: 1037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1008
Number of HSP's successfully gapped: 72
Length of query: 408
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 312
Effective length of database: 3,920,105
Effective search space: 1223072760
Effective search space used: 1223072760
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: 58 (26.1 bits)