Alignments for a candidate for gatB in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Burkholderia vietnamiensis G4

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011886343.1 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000016205.1:WP_011886343.1
          Length = 490

 Score =  447 bits (1149), Expect = e-130
 Identities = 233/486 (47%), Positives = 329/486 (67%), Gaps = 16/486 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLE H +L T SK+FS +P  FGAEPN+    +DLA PGVLPV+N+ AV+ A+R 
Sbjct: 4   WEVVIGLETHAQLSTVSKIFSGAPTQFGAEPNTQACPVDLALPGVLPVLNRGAVERAIRF 63

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKR------- 115
            +A+   IA  S F RKNYFYPD PK YQISQ++ P+ + G I I+V    K        
Sbjct: 64  GLAIGSTIAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEKAGKPAYEK 123

Query: 116 -IGITRLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRS 172
            + +TR H+EEDAGKS H+    +  +DLNR GTPL+EIV+EP++RS  EA AY + L +
Sbjct: 124 TVNLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHA 183

Query: 173 IIQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQE 232
           ++ + G+ D  M+EGS RCDAN+S+RP GQEKFGT+AE+KNLNSF ++ + + YE +RQ 
Sbjct: 184 LVVWLGICDGNMQEGSFRCDANVSVRPVGQEKFGTRAEIKNLNSFRFLEEAINYEVRRQI 243

Query: 233 EELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTI 292
           E +  GGE+ QETR +D    +T  MR KE + DYRYFP+PD++PL I   W ERV+  +
Sbjct: 244 ELIEDGGEVVQETRLYDPDKRETRSMRSKEDAHDYRYFPDPDLMPLVIGQDWIERVQAGM 303

Query: 293 PELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEH--GADVKLTSNWLMGGVNE 350
           PELP   + ++V++ G+ AYDA VLT +K M+ +FE+ +     A+ K+ +NWLMG V+ 
Sbjct: 304 PELPAAIQQRFVDQYGVSAYDAGVLTSSKAMAAYFEAVVAKAGAANAKIAANWLMGDVSS 363

Query: 351 YLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVF----PELAAKGGNAKQIMED 406
            LN++ +E+    ++   LA +++ I DGT+S+KIAK++F     E A   G A +I++ 
Sbjct: 364 QLNRDGIEIDAIPVSAAQLALVLQRIADGTISNKIAKEIFATIWDEKATDEGAADRIIDA 423

Query: 407 NGLVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQ 466
            GL QISD   L   ++E L  N +SVE+++ GK KA   L+GQ MKA+KG+ANPQ VN+
Sbjct: 424 KGLKQISDTGALEAIIDEVLAANAKSVEEFRAGKEKAFNALIGQAMKATKGKANPQQVNE 483

Query: 467 LLKQEL 472
           LLK++L
Sbjct: 484 LLKKKL 489


Lambda     K      H
   0.313    0.133    0.373 

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: 602
Number of extensions: 29
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: 475
Length of database: 490
Length adjustment: 34
Effective length of query: 441
Effective length of database: 456
Effective search space:   201096
Effective search space used:   201096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_011886343.1 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B)
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.29336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-174  565.4   0.0   5.1e-174  565.2   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011886343.1  aspartyl/glutamyl-tRNA(Asn/Gln) 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011886343.1  aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.2   0.0  5.1e-174  5.1e-174       1     480 [.       1     489 [.       1     490 [] 0.98

  Alignments for each domain:
  == domain 1  score: 565.2 bits;  conditional E-value: 5.1e-174
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               ++++e+viGlE+H ql t sK+F+ +++++   +pNt+ cpv+l+lPG+lPvlN+ av+ A+  +la++
  lcl|NCBI__GCF_000016205.1:WP_011886343.1   1 MTQWEVVIGLETHAQLSTVSKIFSGAPTQFGA-EPNTQACPVDLALPGVLPVLNRGAVERAIRFGLAIG 68 
                                               6789**************************99.************************************ PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke........keigierlhlEeDt 130
                                               s  +++ s+F+RK+YfYpDlPkgyqi+q+++P++++G+++i++ ++e        k+++++r hlEeD+
  lcl|NCBI__GCF_000016205.1:WP_011886343.1  69 ST-IAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEkagkpayeKTVNLTRAHLEEDA 136
                                               **.668************************************999888999****************** PP

                                 TIGR00133 131 gksqykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvD 199
                                               gks ++    + ++ +D+NR+g+PLlEiVt+P+++sa ea+a+ k l++++ +l+i dg+++eGs+R+D
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 137 GKSLHED--FAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHALVVWLGICDGNMQEGSFRCD 203
                                               *****94..4789******************************************************** PP

                                 TIGR00133 200 vNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkK 268
                                               +Nvs+r++Gqek+gtr+EiKNlns++ +e+ai+yE+ Rq++l+++g ev+qetr +d  k  t s+R+K
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 204 ANVSVRPVGQEKFGTRAEIKNLNSFRFLEEAINYEVRRQIELIEDGGEVVQETRLYDPDKRETRSMRSK 272
                                               ********************************************************************* PP

                                 TIGR00133 269 eeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafee 337
                                               e+++DYRYfp+Pdl+p++i ++++++ v++ +pelP a ++r++ +yg+s++da vl+s + ++ +fe 
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 273 EDAHDYRYFPDPDLMPLVIGQDWIER-VQAGMPELPAAIQQRFVDQYGVSAYDAGVLTSSKAMAAYFEA 340
                                               *************************9.****************************************** PP

                                 TIGR00133 338 vvklikep..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen 404
                                               vv  ++ +  k a+nW++ ++ ++Ln+  i++ +  +++ +la +++ i +g+is+k+ake++ ++ ++
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 341 VVAKAGAAnaKIAANWLMGDVSSQLNRDGIEIDAIPVSAAQLALVLQRIADGTISNKIAKEIFATIWDE 409
                                               998876655699******************************************************999 PP

                                 TIGR00133 405 ....kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradp 469
                                                   ++ ++++i+++gl qisd+ +l +i++ev++ n+k+ve++++gkeka++ l+Gq+mk tkg+a+p
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 410 katdEGAADRIIDAKGLKQISDTGALEAIIDEVLAANAKSVEEFRAGKEKAFNALIGQAMKATKGKANP 478
                                               88878899************************************************************* PP

                                 TIGR00133 470 kevekllkell 480
                                               ++v++llk++l
  lcl|NCBI__GCF_000016205.1:WP_011886343.1 479 QQVNELLKKKL 489
                                               ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 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: 00:00:00.03
# Mc/sec: 7.59
//
[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