Alignments for a candidate for gatA in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Chlorobium phaeobacteroides BS1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate 642682954 Cphamn1_0436 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-)

Query= SwissProt::O06491
         (485 letters)



>IMG__ChlphaBS1_FD:642682954
          Length = 477

 Score =  447 bits (1150), Expect = e-130
 Identities = 229/469 (48%), Positives = 320/469 (68%), Gaps = 3/469 (0%)

Query: 11  LKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGL 70
           L++ +  +EI    +V +  +RI+   ++   ++ +  ++A   AKELD  ++   + G 
Sbjct: 9   LRKRLLSREISCETVVLDYLERIRKNHER-NVYITVFNDQALQRAKELDRKLEAGEQPGR 67

Query: 71  LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMG 130
           LFG+P+ VKDN+  K    TC+SKILE +  +Y+AT V+RL   +AV +GK+NMDEFAMG
Sbjct: 68  LFGLPMAVKDNLSVKDASLTCASKILEGYTAVYNATAVERLLKEDAVFLGKVNMDEFAMG 127

Query: 131 SSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVG 190
           SS ENSA+    NP++   VPGGSSGGSAAAVA      +LGSDTGGS+RQPA FC VVG
Sbjct: 128 SSNENSAFGPVPNPYDDSRVPGGSSGGSAAAVAGDLAMVALGSDTGGSVRQPAGFCNVVG 187

Query: 191 LKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLS 250
           LKPTYGR+SRYGLVAF SS DQIG ++R  +D A +L  I+G D  D+TS+   VPD+LS
Sbjct: 188 LKPTYGRISRYGLVAFGSSFDQIGILSRNCDDAALVLGVIAGKDAADTTSSQHVVPDYLS 247

Query: 251 SL-TGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATY 309
            + +  +KG+KI VP+EY  E +      +V   L+ L   GA   +++LP S +A+A Y
Sbjct: 248 EMGSVSLKGMKIGVPEEYFPETLDPGVALAVRNRLEELRDAGAELVDIALPESDHAIAAY 307

Query: 310 YLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSG 369
           Y+L+++EAS+NLARFDG RYGYR+ +A +L  +Y  +R+EGFG EVKRRIMLGT+ LS+G
Sbjct: 308 YILTTAEASSNLARFDGARYGYRSGDASDLSGMYVNSRSEGFGGEVKRRIMLGTYVLSAG 367

Query: 370 YYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTI 429
           YYD YYKKAQ+VR +    +++   K DVI GPT+P P F IG+   +PL MY  D+ T+
Sbjct: 368 YYDTYYKKAQQVRRVFLDRYKEALAKVDVIAGPTSPFPPFGIGDKMDEPLEMYLADVFTV 427

Query: 430 PVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
           P ++AG+P +SVP G    GLP+GLQ+IG  FDE  +  +A   +++ +
Sbjct: 428 PASIAGLPALSVPAGFDRSGLPVGLQLIGDFFDEGKLLGIAREIQRSQE 476


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: 620
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: 477
Length adjustment: 34
Effective length of query: 451
Effective length of database: 443
Effective search space:   199793
Effective search space used:   199793
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: 51 (24.3 bits)

Align candidate 642682954 Cphamn1_0436 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-))
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.2580027.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
     2e-184  599.6   0.0   2.2e-184  599.5   0.0    1.0  1  IMG__ChlphaBS1_FD:642682954  


Domain annotation for each sequence (and alignments):
>> IMG__ChlphaBS1_FD:642682954  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.5   0.0  2.2e-184  2.2e-184       2     463 ..      10     474 ..       9     477 .] 0.98

  Alignments for each domain:
  == domain 1  score: 599.5 bits;  conditional E-value: 2.2e-184
                    TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniavkdiettcaS 80 
                                  ++ l ++e+s + v+ ++leri ++++  n++++v +++al++ak+ld+k++  ++  +l+g+p+avKdn++vkd ++tcaS
  IMG__ChlphaBS1_FD:642682954  10 RKRLLSREISCETVVLDYLERIRKNHE-RNVYITVFNDQALQRAKELDRKLEagEQpGRLFGLPMAVKDNLSVKDASLTCAS 90 
                                  6778899****************9999.9*********************99865545************************ PP

                    TIGR00132  81 kiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadlvplalgsDT 162
                                  kiLe+y+++y+at verl +++a+ +Gk N+DEFamGss e+Safg++ nP +++rvpGGSsgGsaaava dl+ +algsDT
  IMG__ChlphaBS1_FD:642682954  91 KILEGYTAVYNATAVERLLKEDAVFLGKVNMDEFAMGSSNENSAFGPVPNPYDDSRVPGGSSGGSAAAVAGDLAMVALGSDT 172
                                  ********************************************************************************** PP

                    TIGR00132 163 GgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslevkveelleelkk.dl 243
                                  GgS+RqPA fc+vvGlKPtYG++SRyGlva+ sS+dqiGil+++ +d+alvl vi+gkD++D+ts +  v+++l+e+ +  l
  IMG__ChlphaBS1_FD:642682954 173 GGSVRQPAGFCNVVGLKPTYGRISRYGLVAFGSSFDQIGILSRNCDDAALVLGVIAGKDAADTTSSQHVVPDYLSEMGSvSL 254
                                  ***************************************************************************9999899 PP

                    TIGR00132 244 kglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelks 325
                                  kg+k+gv +e++ e+ld +v+ ++++ le+l++ gae+v++ lp+++ a+a+Yyi++++Eassnlar+dg ryG+r  ++++
  IMG__ChlphaBS1_FD:642682954 255 KGMKIGVPEEYFPETLDPGVALAVRNRLEELRDAGAELVDIALPESDHAIAAYYILTTAEASSNLARFDGARYGYRSGDASD 336
                                  ********************************************************************************** PP

                    TIGR00132 326 lkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedple 407
                                  l+ +y+++Rsegfg evkrRimlG+y+ls++yyd yykkAq+vr++  d +++++ +vDvi++pt+p  +f +g+k+++ple
  IMG__ChlphaBS1_FD:642682954 337 LSGMYVNSRSEGFGGEVKRRIMLGTYVLSAGYYDTYYKKAQQVRRVFLDRYKEALAKVDVIAGPTSPFPPFGIGDKMDEPLE 418
                                  ********************************************************************************** PP

                    TIGR00132 408 mylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                  myl+Dv+tvpa++aGlpa+svP+g +++glp+Glq+ig  fd+ kll +a+++++ 
  IMG__ChlphaBS1_FD:642682954 419 MYLADVFTVPASIAGLPALSVPAGFDRSGLPVGLQLIGDFFDEGKLLGIAREIQRS 474
                                  **************************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (477 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.26
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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