Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_043743836.1 AMB_RS07995 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000009985.1:WP_043743836.1 Length = 490 Score = 477 bits (1228), Expect = e-139 Identities = 255/489 (52%), Positives = 338/489 (69%), Gaps = 11/489 (2%) Query: 3 LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62 L D + E + + K +L D K +A + AF+ + A AK D Sbjct: 4 LTDLTMAEARDGLAKGAFTAVELTDAHIKATEA-QRHLNAFIVETPDLALEAAKASDARR 62 Query: 63 DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122 + G + G+PIG+KD T+G++TT +S ILE F P Y++TV +L+ A A+++GKL Sbjct: 63 QAGTA-GSMDGLPIGIKDLFCTEGVQTTAASHILEGFKPPYESTVSGKLKAAGAISLGKL 121 Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDT------VPGGSSGGSAAAVAAGEVPFSLGSDTG 176 N+DEFAMGSS + S + +NPW + VPGGSSGGSAAAVAA V + G+DTG Sbjct: 122 NLDEFAMGSSNQTSYFGAVENPWKKTSDPKAKLVPGGSSGGSAAAVAARMVLGATGTDTG 181 Query: 177 GSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKM 236 GSIRQPA+FCG+ G+KPTYGR SR+G+VAFASSLDQ GP+ RTV D A +L A++G D Sbjct: 182 GSIRQPAAFCGITGIKPTYGRCSRFGIVAFASSLDQAGPMARTVRDCAIMLGAMAGHDPK 241 Query: 237 DSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEE 296 DSTS N+ VPDF +LTGDI+GLK+ +PKEY +G+ E + ++ L+ GAT E Sbjct: 242 DSTSVNMAVPDFERALTGDIRGLKVGIPKEYRPDGLSDEVAKVWDRGIEWLKAAGATPVE 301 Query: 297 VSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVK 356 +SLPH+KYALATYY+++ +E S+NLAR+DG+RYG R L D+YK++RA GFG EV+ Sbjct: 302 ISLPHTKYALATYYIIAPAECSSNLARYDGLRYGLRVP-GKTLDDMYKKSRAAGFGAEVR 360 Query: 357 RRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTK 416 RRI++GT+ LS+GYYDAYY KAQKVR LI +DF FE DVI+ PT P+ AF +GE T Sbjct: 361 RRILIGTYVLSAGYYDAYYAKAQKVRRLIAEDFRKAFETVDVILTPTAPSAAFGMGEGTD 420 Query: 417 DPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475 DP+TM+ ND+ TIP ++AG+PG+S+P GL ADGLPLGLQ+IG+ FDE TV+RVA E A Sbjct: 421 DPVTMWLNDVFTIPTSMAGLPGLSLPAGLSADGLPLGLQLIGRPFDEETVFRVAGVMETA 480 Query: 476 TDHHKAKPE 484 + AKPE Sbjct: 481 A-NFTAKPE 488 Lambda K H 0.315 0.134 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 613 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 490 Length adjustment: 34 Effective length of query: 451 Effective length of database: 456 Effective search space: 205656 Effective search space used: 205656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
Align candidate WP_043743836.1 AMB_RS07995 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00132.hmm # target sequence database: /tmp/gapView.9811.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-175 568.4 0.0 6.7e-175 568.2 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043743836.1 AMB_RS07995 Asp-tRNA(Asn)/Glu-tR Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043743836.1 AMB_RS07995 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 568.2 0.0 6.7e-175 6.7e-175 6 463 .. 17 480 .. 12 483 .. 0.96 Alignments for each domain: == domain 1 score: 568.2 bits; conditional E-value: 6.7e-175 TIGR00132 6 kkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 k ++++e++++ +++ ea+++ +naf+ t++ al++ak++d++ + + + g+pi++Kd ++++ lcl|NCBI__GCF_000009985.1:WP_043743836.1 17 AKGAFTAVELTDAHIKATEAQRH-LNAFIVETPDLALEAAKASDARRQaGTaGSMDGLPIGIKDLFCTE 84 56677888888999998888887.********************9988655369*************** PP TIGR00132 73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPene......e 135 +++tt+aS+iLe++++py++tV +lk+aga+ +Gk NlDEFamGss +tS+fg+++nP+++ + lcl|NCBI__GCF_000009985.1:WP_043743836.1 85 GVQTTAASHILEGFKPPYESTVSGKLKAAGAISLGKLNLDEFAMGSSNQTSYFGAVENPWKKtsdpkaK 153 ***********************************************************8762222226 PP TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204 vpGGSsgGsaaavaa +v a g+DTGgSiRqPA+fcg+ G+KPtYG+ SR+G+va+asSldq G++a lcl|NCBI__GCF_000009985.1:WP_043743836.1 154 LVPGGSSGGSAAAVAARMVLGATGTDTGGSIRQPAAFCGITGIKPTYGRCSRFGIVAFASSLDQAGPMA 222 8******************************************************************** PP TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllek 273 ++v d a++l +++g+D kDsts++++v+++ ++l+ d++glkvg+ ke++ ++l++ev++ +++ +e lcl|NCBI__GCF_000009985.1:WP_043743836.1 223 RTVRDCAIMLGAMAGHDPKDSTSVNMAVPDFERALTGDIRGLKVGIPKEYRPDGLSDEVAKVWDRGIEW 291 ********************************************************************* PP TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342 l++ ga+ ve+slp+ k+ala+Yyii+p+E ssnlarydg+ryG rv ++ l+++y+k+R++gfg+ev lcl|NCBI__GCF_000009985.1:WP_043743836.1 292 LKAAGATPVEISLPHTKYALATYYIIAPAECSSNLARYDGLRYGLRVPGKT-LDDMYKKSRAAGFGAEV 359 ***********************************************9999.***************** PP TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyls 411 +rRi++G+y+ls++yyd+yy+kAqkvr+li+++f+k+fe vDvi++ptap af +ge ++dp++m+l+ lcl|NCBI__GCF_000009985.1:WP_043743836.1 360 RRRILIGTYVLSAGYYDAYYAKAQKVRRLIAEDFRKAFETVDVILTPTAPSAAFGMGEGTDDPVTMWLN 428 ********************************************************************* PP TIGR00132 412 DvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463 Dv+t+p ++aGlp++s+P+g + +glp+Glq+ig+ fd++++++va +e a lcl|NCBI__GCF_000009985.1:WP_043743836.1 429 DVFTIPTSMAGLPGLSLPAGLSADGLPLGLQLIGRPFDEETVFRVAGVMETA 480 *********************************************9988865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (490 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.79 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory