Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_069663669.1 BCR25_RS11100 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_001730305.1:WP_069663669.1 Length = 489 Score = 631 bits (1628), Expect = 0.0 Identities = 310/481 (64%), Positives = 386/481 (80%), Gaps = 2/481 (0%) Query: 3 LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62 L+D +TEL L+ KEI +DL + + RI+ + V +F+ + EE+A AK +D + Sbjct: 4 LYDKSLTELHDLLVSKEITATDLTNATLDRIKETEKDVDSFITISEEKALELAKAID--L 61 Query: 63 DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122 G +E L G+PIG+KDNIVTK + TT +SK+L NF+PIYDATV+ +L ++ + +GKL Sbjct: 62 KGITESNPLAGIPIGIKDNIVTKDILTTAASKMLHNFNPIYDATVMDKLYQSDMIPVGKL 121 Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 NMDEFAMG+STE S +K TKN W+ VPGGSSGGSAAAVAAG+VP SLGSDTGGSIRQP Sbjct: 122 NMDEFAMGASTETSYFKKTKNAWDHTKVPGGSSGGSAAAVAAGQVPVSLGSDTGGSIRQP 181 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 ASF G+VG+KPTYGRVSR+GL+AF+SSLDQIGP+TR V+DNA L AISG D+ D TSA Sbjct: 182 ASFNGIVGMKPTYGRVSRFGLIAFSSSLDQIGPMTRNVQDNALALNAISGFDEKDGTSAG 241 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302 V VPDF + LTGDIKG+K+A+PKEYLGEGV RE+VL A + + LGAT EEVSLPHS Sbjct: 242 VSVPDFTAGLTGDIKGMKVALPKEYLGEGVDAGVREAVLKAAETFKALGATVEEVSLPHS 301 Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362 KY +A YY+++SSEAS+NL RFDGIRYGYR++N NL D+Y +R+EGFG EVKRRIMLG Sbjct: 302 KYGVAVYYIIASSEASSNLQRFDGIRYGYRSENVKNLEDVYVNSRSEGFGLEVKRRIMLG 361 Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422 TF+LS+GYYDAY+KKA +VRTLIK+DF+ VFE YD+I+GP +PT AF +GEN DP+TMY Sbjct: 362 TFSLSAGYYDAYFKKAGQVRTLIKQDFDKVFETYDIIIGPASPTVAFGLGENINDPITMY 421 Query: 423 ANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482 ND+LTIPVNLAG+PG+SVP G ++GLP+GLQIIGK FDEST+Y+ A+AFEQATD H K Sbjct: 422 MNDLLTIPVNLAGLPGMSVPAGFSEGLPVGLQIIGKAFDESTMYKAAYAFEQATDFHTKK 481 Query: 483 P 483 P Sbjct: 482 P 482 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: 725 Number of extensions: 24 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: 489 Length adjustment: 34 Effective length of query: 451 Effective length of database: 455 Effective search space: 205205 Effective search space used: 205205 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_069663669.1 BCR25_RS11100 (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.242610.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-198 644.1 0.9 7.4e-198 643.9 0.9 1.0 1 NCBI__GCF_001730305.1:WP_069663669.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069663669.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 643.9 0.9 7.4e-198 7.4e-198 2 465 .. 13 476 .. 12 477 .. 0.99 Alignments for each domain: == domain 1 score: 643.9 bits; conditional E-value: 7.4e-198 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvake.kklagipiavKdniavkd 73 ++ll++ke++++++++++l+ri+++++++++f+++++ekal+ ak++d k +e ++lagipi++Kdni++kd NCBI__GCF_001730305.1:WP_069663669.1 13 HDLLVSKEITATDLTNATLDRIKETEKDVDSFITISEEKALELAKAIDLKGITEsNPLAGIPIGIKDNIVTKD 85 678999******************************************88765647***************** PP TIGR00132 74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsa 146 i tt+aSk+L+n++++ydatV+ +l +++++ +Gk N+DEFamG+stetS+f+ tkn +++++vpGGSsgGsa NCBI__GCF_001730305.1:WP_069663669.1 86 ILTTAASKMLHNFNPIYDATVMDKLYQSDMIPVGKLNMDEFAMGASTETSYFKKTKNAWDHTKVPGGSSGGSA 158 ************************************************************************* PP TIGR00132 147 aavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219 aavaa++vp++lgsDTGgSiRqPAsf g+vG+KPtYG+vSR+Gl+a++sSldqiG+++++v+d al l++isg NCBI__GCF_001730305.1:WP_069663669.1 159 AAVAAGQVPVSLGSDTGGSIRQPASFNGIVGMKPTYGRVSRFGLIAFSSSLDQIGPMTRNVQDNALALNAISG 231 ************************************************************************* PP TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkla 292 D+kD ts+ v+v++++ l+ d+kg+kv++ ke+ +e++d +v+e++ k+ e++++lga+++evslp++k+ NCBI__GCF_001730305.1:WP_069663669.1 232 FDEKDGTSAGVSVPDFTAGLTGDIKGMKVALPKEYLGEGVDAGVREAVLKAAETFKALGATVEEVSLPHSKYG 304 ************************************************************************* PP TIGR00132 293 laiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkA 365 +a+Yyii++sEassnl+r+dgiryG+r e++k+l+++y+++Rsegfg evkrRimlG++ ls++yyd+y+kkA NCBI__GCF_001730305.1:WP_069663669.1 305 VAVYYIIASSEASSNLQRFDGIRYGYRSENVKNLEDVYVNSRSEGFGLEVKRRIMLGTFSLSAGYYDAYFKKA 377 ************************************************************************* PP TIGR00132 366 qkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglp 438 +vrtli+++f+k+fe +D+i++p++pt+af lge+ +dp++my++D+lt+p+nlaGlp++svP+g + +glp NCBI__GCF_001730305.1:WP_069663669.1 378 GQVRTLIKQDFDKVFETYDIIIGPASPTVAFGLGENINDPITMYMNDLLTIPVNLAGLPGMSVPAGFS-EGLP 449 ********************************************************************.7*** PP TIGR00132 439 iGlqiigkafddkkllsvakaleqald 465 +Glqiigkafd+++++++a+a+eqa+d NCBI__GCF_001730305.1:WP_069663669.1 450 VGLQIIGKAFDESTMYKAAYAFEQATD 476 ************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (489 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 33.59 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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