Alignments for a candidate for gatA in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Chlorobaculum parvum NCIB 8327

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012502991.1 CPAR_RS08940 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000020505.1:WP_012502991.1
          Length = 481

 Score =  444 bits (1141), Expect = e-129
 Identities = 225/462 (48%), Positives = 311/462 (67%), Gaps = 3/462 (0%)

Query: 10  ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHG 69
           +L+  +  +E+    ++ E  +RI +  D    F A+  E A   A+ELD  ++   E G
Sbjct: 8   DLRSKLLSRELTCEQVISEYLQRIDSKKDD-NIFTAVFHEAALERARELDAKLERGEEPG 66

Query: 70  LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAM 129
           +LFGMPI +KDNI  KG   +C+SKIL+ ++ +YDAT ++R+   +A+ +G+ NMDEFAM
Sbjct: 67  VLFGMPIAIKDNISMKGAPLSCASKILDGYESVYDATAIERMVAEDAIFVGRTNMDEFAM 126

Query: 130 GSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVV 189
           GSS ENSA     NP++   VPGGSSGGSAAAVA      +LGSDTGGS+RQP  FC VV
Sbjct: 127 GSSNENSAIGPVPNPFDKTRVPGGSSGGSAAAVANDLCMVALGSDTGGSVRQPGGFCNVV 186

Query: 190 GLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFL 249
           GLKPTYGR+SRYGLVAFASS DQIG +    +D A +L  I+G D  D+TS++ +VPD+ 
Sbjct: 187 GLKPTYGRISRYGLVAFASSFDQIGVLAANCDDAALVLGVIAGQDDRDATSSHHEVPDYE 246

Query: 250 SSLTG-DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALAT 308
           S++    ++GL++ VP  +  E +  +    V A LK LE  GA   E+ LP S YA+A 
Sbjct: 247 STMDHVSLEGLRVGVPSAFFPENLNADVAGVVKAGLKKLEDAGAELVEIELPESDYAIAA 306

Query: 309 YYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSS 368
           YY+L ++EAS+NLARFDG RYGYR+ ++ +L  +Y  +R EGFG EVKRRIMLGT+ LS+
Sbjct: 307 YYILVTAEASSNLARFDGARYGYRSPDSPDLSSMYVNSRTEGFGAEVKRRIMLGTYVLSA 366

Query: 369 GYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILT 428
           GYYD YYKKAQ+VR + ++ + + FEK DVI GPT+P P F IG+   +PL MY  D+ T
Sbjct: 367 GYYDTYYKKAQQVRRVFQEKYREAFEKVDVIAGPTSPFPPFGIGDKMDNPLEMYLADVFT 426

Query: 429 IPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVA 469
           +P ++ G+P +SVP G    GLP+G+ +I   F+E  +  +A
Sbjct: 427 VPASIVGMPAVSVPVGFDSLGLPVGVHLICNFFEEGKMLGIA 468


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: 617
Number of extensions: 24
Number of successful extensions: 3
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: 481
Length adjustment: 34
Effective length of query: 451
Effective length of database: 447
Effective search space:   201597
Effective search space used:   201597
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_012502991.1 CPAR_RS08940 (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.2408.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-181  588.9   0.0   4.1e-181  588.7   0.0    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012502991.1  CPAR_RS08940 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012502991.1  CPAR_RS08940 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 !  588.7   0.0  4.1e-181  4.1e-181       2     463 ..      10     474 ..       9     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 588.7 bits;  conditional E-value: 4.1e-181
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               +++l ++e++ ++v++e+l+ri+++kd  n+f++v +e al++a++ld+k++  +e   l+g+pia+Kd
  lcl|NCBI__GCF_000020505.1:WP_012502991.1  10 RSKLLSRELTCEQVISEYLQRIDSKKD-DNIFTAVFHEAALERARELDAKLErgEEpGVLFGMPIAIKD 77 
                                               6778899*****************999.8**********************9865545*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               ni++k+ +++caSkiL++y s+ydat +er+ +++a+ +G+tN+DEFamGss e+Sa g++ nP +++r
  lcl|NCBI__GCF_000020505.1:WP_012502991.1  78 NISMKGAPLSCASKILDGYESVYDATAIERMVAEDAIFVGRTNMDEFAMGSSNENSAIGPVPNPFDKTR 146
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaava dl+ +algsDTGgS+RqP  fc+vvGlKPtYG++SRyGlva+asS+dqiG+la+
  lcl|NCBI__GCF_000020505.1:WP_012502991.1 147 VPGGSSGGSAAAVANDLCMVALGSDTGGSVRQPGGFCNVVGLKPTYGRISRYGLVAFASSFDQIGVLAA 215
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkk.dlkglkvgvvkelseesldkevkekfekllek 273
                                               + +d+alvl vi+g+D +D ts + +v+++ +++ +  l gl+vgv   ++ e+l+ +v+  +++ l+k
  lcl|NCBI__GCF_000020505.1:WP_012502991.1 216 NCDDAALVLGVIAGQDDRDATSSHHEVPDYESTMDHvSLEGLRVGVPSAFFPENLNADVAGVVKAGLKK 284
                                               ******************************999999789****************************** PP

                                 TIGR00132 274 leelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeev 342
                                               le+ gae+ve++lp++++a+a+Yyi+ ++Eassnlar+dg ryG+r  +  +l+ +y+++R egfg+ev
  lcl|NCBI__GCF_000020505.1:WP_012502991.1 285 LEDAGAELVEIELPESDYAIAAYYILVTAEASSNLARFDGARYGYRSPDSPDLSSMYVNSRTEGFGAEV 353
                                               ********************************************************************* PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyls 411
                                               krRimlG+y+ls++yyd yykkAq+vr++ +++++++fe+vDvi++pt+p  +f +g+k+++plemyl+
  lcl|NCBI__GCF_000020505.1:WP_012502991.1 354 KRRIMLGTYVLSAGYYDTYYKKAQQVRRVFQEKYREAFEKVDVIAGPTSPFPPFGIGDKMDNPLEMYLA 422
                                               ********************************************************************* PP

                                 TIGR00132 412 DvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               Dv+tvpa+++G+pa+svP+g ++ glp+G+ +i + f++ k+l +a++l+++
  lcl|NCBI__GCF_000020505.1:WP_012502991.1 423 DVFTVPASIVGMPAVSVPVGFDSLGLPVGVHLICNFFEEGKMLGIARNLQAL 474
                                               **********************************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (481 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: 00:00:00.03
# Mc/sec: 7.29
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis