Alignments for a candidate for gatB in Desulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfovibrio zosterae DSM 11974

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_027720955.1 H589_RS0104660 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000425265.1:WP_027720955.1
          Length = 481

 Score =  458 bits (1179), Expect = e-133
 Identities = 228/480 (47%), Positives = 324/480 (67%), Gaps = 4/480 (0%)

Query: 70  YEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVRL 129
           +E VIG+E H QL T +K FC CS  +G  PN ++C VC G+PG LPV N KV+E+  ++
Sbjct: 4   FETVIGLEVHAQLKTKSKIFCGCSTEFGKEPNENVCEVCSGMPGVLPVFNEKVMEYAAKM 63

Query: 130 GLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGH-RRFG 188
           GLA NC ++ KS F RK YFYPDLPKGYQISQFD+PI   G++D+      G    +R G
Sbjct: 64  GLATNCIINQKSIFARKNYFYPDLPKGYQISQFDLPICEHGHLDIVFENSDGEKQEKRIG 123

Query: 189 ITRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRIAR 248
           ITR+HMEEDAGK +HS   + S VDLNR GVPL+EIVSEPDMRS  EA  Y   ++ I  
Sbjct: 124 ITRIHMEEDAGKNIHSAAENASFVDLNRTGVPLIEIVSEPDMRSADEAVAYLKGLRSILL 183

Query: 249 YLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQALLY 308
           YLG+ +GN++EGS RCD NIS+RP+GQ EFGT+ E+KN+N+F  I +AI +E++RQ  L 
Sbjct: 184 YLGICDGNLEEGSFRCDANISVRPMGQKEFGTRAELKNINSFRNIHKAIRYEVARQIDLI 243

Query: 309 NQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRASLP 368
             G  ++I+ ETRL++     T +MR K    DYRY+P+PDL  V++  + +   +ASLP
Sbjct: 244 EDG--EKIIQETRLYDADKGTTHSMRGKADAHDYRYYPDPDLVPVVIFDDLLGEWQASLP 301

Query: 369 ELP-EAKRRRYEAMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSDIAAYLK 427
           ELP E K R  + M L  +D   ++++  VA+YF+AV+    E K   NWI  D    + 
Sbjct: 302 ELPAERKGRFIDDMELSEEDAELISSEKDVADYFEAVLDYHNEPKKVVNWIKGDFLREVN 361

Query: 428 NEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAKDLVQIT 487
              ++I+D K TP+ +A+L+  ++  TIS KIGK+I  E+ A G   +  +K K LVQI+
Sbjct: 362 QSAMNISDCKFTPEMMAKLVQLVEKDTISIKIGKDIFAEIFADGLDPEKYVKDKGLVQIS 421

Query: 488 DPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKILLEKLN 547
           D + +E +V ++++ENP ++E ++ GK KL  +F GQ+M+ +KGKANPG+++K++ EKL+
Sbjct: 422 DSSSLEAVVDKILAENPDEVEAFKGGKKKLMSFFMGQIMRETKGKANPGMVSKMISEKLS 481


Lambda     K      H
   0.317    0.134    0.379 

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: 727
Number of extensions: 41
Number of successful extensions: 4
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: 550
Length of database: 481
Length adjustment: 35
Effective length of query: 515
Effective length of database: 446
Effective search space:   229690
Effective search space used:   229690
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_027720955.1 H589_RS0104660 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.26384.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-185  602.6   0.1   2.5e-185  602.5   0.1    1.0  1  lcl|NCBI__GCF_000425265.1:WP_027720955.1  H589_RS0104660 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000425265.1:WP_027720955.1  H589_RS0104660 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.5   0.1  2.5e-185  2.5e-185       1     480 [.       1     480 [.       1     481 [] 0.98

  Alignments for each domain:
  == domain 1  score: 602.5 bits;  conditional E-value: 2.5e-185
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               ++++e viGlEvH ql tksK+Fc cs+e+ + +pN+nvc vc g+PG+lPv N+++++ A k++la+n
  lcl|NCBI__GCF_000425265.1:WP_027720955.1   1 MVQFETVIGLEVHAQLKTKSKIFCGCSTEFGK-EPNENVCEVCSGMPGVLPVFNEKVMEYAAKMGLATN 68 
                                               6799***************************9.************************************ PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgks 133
                                               + i+ ++s+F+RK+YfYpDlPkgyqi+q+dlPi+e+G+l+i +e+++     k+igi+r+h+EeD+gk+
  lcl|NCBI__GCF_000425265.1:WP_027720955.1  69 CIIN-QKSIFARKNYFYPDLPKGYQISQFDLPICEHGHLDIVFENSDgekqeKRIGITRIHMEEDAGKN 136
                                               *965.6***********************************99988788888***************** PP

                                 TIGR00133 134 qykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNv 202
                                                +     ++ s+vD+NR+gvPL+EiV++Pd++sa+ea+a+lk lr+il yl+i dg+leeGs+R+D+N+
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 137 IHSAA--ENASFVDLNRTGVPLIEIVSEPDMRSADEAVAYLKGLRSILLYLGICDGNLEEGSFRCDANI 203
                                               **976..58************************************************************ PP

                                 TIGR00133 203 sirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKees 271
                                               s+r++Gq+++gtr+E+KN+ns+++i+kai yE++Rq++l+++ge++ qetr +d  k +t s+R K ++
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 204 SVRPMGQKEFGTRAELKNINSFRNIHKAIRYEVARQIDLIEDGEKIIQETRLYDADKGTTHSMRGKADA 272
                                               ********************************************************************* PP

                                 TIGR00133 272 eDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvk 340
                                               +DYRY p+Pdl+p++i ++++ e +++ lpelP +++ r+  +++lseeda+++ s+++++d+fe v  
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 273 HDYRYYPDPDLVPVVIFDDLLGE-WQASLPELPAERKGRFIDDMELSEEDAELISSEKDVADYFEAVLD 340
                                               *******************9988.********************************************* PP

                                 TIGR00133 341 likepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpk 409
                                                 +epk++vnWi  ++l+e+n++ ++++++ ++pe++a+l++l+++++is k++k+++ e++ ++ dp+
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 341 YHNEPKKVVNWIKGDFLREVNQSAMNISDCKFTPEMMAKLVQLVEKDTISIKIGKDIFAEIFADGLDPE 409
                                               ********************************************************************* PP

                                 TIGR00133 410 klieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllke 478
                                               k ++ +gl+qisd + l ++v+++++enp+eve +k gk+k++ f++Gq+m++tkg+a+p  v k++ e
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 410 KYVKDKGLVQISDSSSLEAVVDKILAENPDEVEAFKGGKKKLMSFFMGQIMRETKGKANPGMVSKMISE 478
                                               ********************************************************************* PP

                                 TIGR00133 479 ll 480
                                               +l
  lcl|NCBI__GCF_000425265.1:WP_027720955.1 479 KL 480
                                               98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 8.38
//
[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