Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_022949813.1 H035_RS0115180 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000421465.1:WP_022949813.1 Length = 483 Score = 498 bits (1283), Expect = e-145 Identities = 249/482 (51%), Positives = 333/482 (69%), Gaps = 2/482 (0%) Query: 3 LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62 + + + EL + +E +L+ RI +D + AF+ + E+ A A D + Sbjct: 1 MHNKSLVELAAGLRAREFSSRELIRHFLDRIARHNDTLNAFVTVTEDSAEEAAAAADAVL 60 Query: 63 DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122 + R E G L G+P+ KD T G+RT+C SK+L+NF YDATV R A A +GKL Sbjct: 61 E-RGEGGPLTGIPVAQKDIFCTLGIRTSCGSKMLDNFTAPYDATVATRFNRAGAPLLGKL 119 Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 NMDEFAMGSS E S Y +NPW+ D VPGGSSGGSAAAVAAG P + G+DTGGSIRQP Sbjct: 120 NMDEFAMGSSNETSYYGPVRNPWHTDCVPGGSSGGSAAAVAAGLTPAATGTDTGGSIRQP 179 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+FCG+ GLKPTYGRVSR+G++AFASSLDQ GP+ R+ ED A LLQA++G D DSTS + Sbjct: 180 AAFCGITGLKPTYGRVSRWGMIAFASSLDQGGPLARSAEDCALLLQAMAGFDAKDSTSVD 239 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302 VPD+ ++L D+ GLK+ +PKE+ + + + + + A+ LG ++EVSLP+ Sbjct: 240 RPVPDYAAALDQDLTGLKVGLPKEFFTD-LSADMAQVLEVAMAEYRKLGVEFKEVSLPNL 298 Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362 ++ YY+++ SE S+NLARFDG RYGYR ++ NL DLY ++R EGFG EVKRRI+ G Sbjct: 299 NLSVPAYYVIAPSECSSNLARFDGARYGYRCEDPKNLEDLYTRSRGEGFGAEVKRRILTG 358 Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422 T+ALS+GYYDAYY KAQK+R LI DF+ FE DV++GP TPTPAF IGE T DP++MY Sbjct: 359 TYALSAGYYDAYYLKAQKIRRLIADDFKRAFESVDVLLGPATPTPAFGIGEKTDDPISMY 418 Query: 423 ANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482 +DI TI +NLAG+P +S P G DG P G+Q+IG +FDE+ + VAH ++Q T+ H+ + Sbjct: 419 LSDIYTIAINLAGLPALSAPAGFIDGKPAGMQLIGNYFDEARLLNVAHRYQQVTEWHRRR 478 Query: 483 PE 484 PE Sbjct: 479 PE 480 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: 606 Number of extensions: 19 Number of successful extensions: 2 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: 483 Length adjustment: 34 Effective length of query: 451 Effective length of database: 449 Effective search space: 202499 Effective search space used: 202499 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_022949813.1 H035_RS0115180 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.22877.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-183 597.0 0.0 1.4e-183 596.9 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022949813.1 H035_RS0115180 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022949813.1 H035_RS0115180 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 596.9 0.0 1.4e-183 1.4e-183 5 465 .. 13 473 .. 9 474 .. 0.98 Alignments for each domain: == domain 1 score: 596.9 bits; conditional E-value: 1.4e-183 TIGR00132 5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 l ++e+s++e+++++l+ri +++d++naf++vt+++a ++a++ d+ ++ e +l+gip+a Kd +++ lcl|NCBI__GCF_000421465.1:WP_022949813.1 13 LRAREFSSRELIRHFLDRIARHNDTLNAFVTVTEDSAEEAAAAADAVLErGEgGPLTGIPVAQKDIFCT 81 6788999***************************************99876646*************** PP TIGR00132 72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140 +i+t+c+Sk+L+n+++pydatV +r ++aga ++Gk N+DEFamGss etS++g+++nP+ ++ vpGG lcl|NCBI__GCF_000421465.1:WP_022949813.1 82 LGIRTSCGSKMLDNFTAPYDATVATRFNRAGAPLLGKLNMDEFAMGSSNETSYYGPVRNPWHTDCVPGG 150 ********************************************************************* PP TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209 SsgGsaaavaa+l p a g+DTGgSiRqPA+fcg+ GlKPtYG+vSR+G++a+asSldq G+la++ ed lcl|NCBI__GCF_000421465.1:WP_022949813.1 151 SSGGSAAAVAAGLTPAATGTDTGGSIRQPAAFCGITGLKPTYGRVSRWGMIAFASSLDQGGPLARSAED 219 ********************************************************************* PP TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278 al+l++++g D+kDsts++ +v+++ +l +dl glkvg+ ke++ + l+ ++++ +e ++ + ++lg lcl|NCBI__GCF_000421465.1:WP_022949813.1 220 CALLLQAMAGFDAKDSTSVDRPVPDYAAALDQDLTGLKVGLPKEFFTD-LSADMAQVLEVAMAEYRKLG 287 ************************************************.******************** PP TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347 +e++evslp+++l++++Yy+i+psE ssnlar+dg ryG+r e++k+l++ly+++R egfg+evkrRi+ lcl|NCBI__GCF_000421465.1:WP_022949813.1 288 VEFKEVSLPNLNLSVPAYYVIAPSECSSNLARFDGARYGYRCEDPKNLEDLYTRSRGEGFGAEVKRRIL 356 ********************************************************************* PP TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416 G+yals++yyd+yy+kAqk+r+li+d+f+ +fe+vDv+++p++pt af +gek++dp++mylsD++t+ lcl|NCBI__GCF_000421465.1:WP_022949813.1 357 TGTYALSAGYYDAYYLKAQKIRRLIADDFKRAFESVDVLLGPATPTPAFGIGEKTDDPISMYLSDIYTI 425 ********************************************************************* PP TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 +nlaGlpa+s P+g +g p G+q+ig++fd+ +ll+va+ ++q ++ lcl|NCBI__GCF_000421465.1:WP_022949813.1 426 AINLAGLPALSAPAGFI-DGKPAGMQLIGNYFDEARLLNVAHRYQQVTE 473 *****************.7*************************99765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (483 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.15 // [ok]
This GapMind analysis is from Apr 10 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