Alignments for a candidate for gatA in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Leptospirillum ferrooxidans C2-3

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_014450045.1 LFE_RS09710 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000284315.1:WP_014450045.1
          Length = 493

 Score =  451 bits (1159), Expect = e-131
 Identities = 230/456 (50%), Positives = 313/456 (68%), Gaps = 2/456 (0%)

Query: 20  IKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVK 79
           + I ++ +    RI + D K+ AFL ++   A+  A++LD      S+  L +G PI +K
Sbjct: 26  VTIEEVTEFCLSRIDSRDGKLGAFLTINPN-AKNRARQLDNRRSELSKRSLFYGYPIAIK 84

Query: 80  DNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYK 139
           DN+  +GL TTC+S+IL N   IY AT V RL  A AV +GK NMDEFAMGSSTENSA  
Sbjct: 85  DNLNIEGLPTTCASRILANHRSIYTATAVSRLLSAGAVVLGKTNMDEFAMGSSTENSAMG 144

Query: 140 LTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVS 199
           +T+NPW+ D VPGGSSGGSA AV+ G  P SLGSDTGGSIRQPA+FCGV+GLKPTYGR+S
Sbjct: 145 ITRNPWDHDRVPGGSSGGSAVAVSGGMAPMSLGSDTGGSIRQPAAFCGVLGLKPTYGRIS 204

Query: 200 RYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGL 259
           R GLVAF+SSLDQIGP  +   D   +   +SG D +D TS+  D  + +      +KG 
Sbjct: 205 RQGLVAFSSSLDQIGPFAQNPLDALHVTVLLSGHDPLDMTSSTRDPLEMVHDYEKPLKGK 264

Query: 260 KIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASA 319
            + +P+E+ GEG+  + RES+  + ++L   G   + V LP ++YA+  YYL+++SEA++
Sbjct: 265 VVGIPEEFWGEGMDPQVRESLEKSRELLVKAGMVLKPVRLPSTQYAVNVYYLIATSEAAS 324

Query: 320 NLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQ 379
           NL+RFDGIRYG R   A +L +LY+++R EGFG EVKRRI+LGTFALS+GY D YY+KAQ
Sbjct: 325 NLSRFDGIRYGERKTGARDLKELYEKSRGEGFGPEVKRRILLGTFALSAGYQDQYYRKAQ 384

Query: 380 KVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAGVPGI 439
           KV+ LI+++F   F + D++  P TPTPAF+ GE   DPL+MY +DI TI  NLAG+P +
Sbjct: 385 KVQALIREEFMRSFSECDLLFAPVTPTPAFRFGEKISDPLSMYLSDIFTISANLAGLPAL 444

Query: 440 SVPC-GLADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
           S P    ++GLP+G Q+IG H+ E  + + A    +
Sbjct: 445 STPSFPTSNGLPVGAQLIGPHWSEGVLLKAASVLHE 480


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: 565
Number of extensions: 21
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: 493
Length adjustment: 34
Effective length of query: 451
Effective length of database: 459
Effective search space:   207009
Effective search space used:   207009
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_014450045.1 LFE_RS09710 (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.3595848.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-171  557.1   0.0     2e-171  556.8   0.0    1.0  1  NCBI__GCF_000284315.1:WP_014450045.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014450045.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.8   0.0    2e-171    2e-171       8     461 ..      24     479 ..      18     483 .. 0.97

  Alignments for each domain:
  == domain 1  score: 556.8 bits;  conditional E-value: 2e-171
                             TIGR00132   8 kevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKdniavkdiett 77 
                                            +v+i+ev+e +l ri++ + k+ afl+++++ a ++a++ld++ +  ++ ++ +g pia+Kdn+++++++tt
  NCBI__GCF_000284315.1:WP_014450045.1  24 GSVTIEEVTEFCLSRIDSRDGKLGAFLTINPN-AKNRARQLDNRRSelSKrSLFYGYPIAIKDNLNIEGLPTT 95 
                                           57899************************998.8888999988877563436999****************** PP

                             TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaava 150
                                           caS+iL n++s+y at v rl +aga+++GktN+DEFamGsste+Sa g+t+nP++++rvpGGSsgGsa av+
  NCBI__GCF_000284315.1:WP_014450045.1  96 CASRILANHRSIYTATAVSRLLSAGAVVLGKTNMDEFAMGSSTENSAMGITRNPWDHDRVPGGSSGGSAVAVS 168
                                           ************************************************************************* PP

                             TIGR00132 151 adlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkk 223
                                            +++p++lgsDTGgSiRqPA+fcgv+GlKPtYG++SR+Glva++sSldqiG++a++  d+  v+  +sg+D  
  NCBI__GCF_000284315.1:WP_014450045.1 169 GGMAPMSLGSDTGGSIRQPAAFCGVLGLKPTYGRISRQGLVAFSSSLDQIGPFAQNPLDALHVTVLLSGHDPL 241
                                           ************************************************************************* PP

                             TIGR00132 224 DstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiY 296
                                           D ts   ++ e++++ +k lkg  vg+ +e+ +e++d +v+e++ek  e l + g+ +++v lps ++a+ +Y
  NCBI__GCF_000284315.1:WP_014450045.1 242 DMTSSTRDPLEMVHDYEKPLKGKVVGIPEEFWGEGMDPQVRESLEKSRELLVKAGMVLKPVRLPSTQYAVNVY 314
                                           *********9*************************************************************** PP

                             TIGR00132 297 yiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvr 369
                                           y+i++sEa+snl+r+dgiryG+r + +++lkely k+R egfg evkrRi+lG++als++y d+yy kAqkv+
  NCBI__GCF_000284315.1:WP_014450045.1 315 YLIATSEAASNLSRFDGIRYGERKTGARDLKELYEKSRGEGFGPEVKRRILLGTFALSAGYQDQYYRKAQKVQ 387
                                           ************************************************************************* PP

                             TIGR00132 370 tliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlq 442
                                            li++ef   f+e+D++++p++pt af++gek +dpl+mylsD++t+ anlaGlpa+s P   +++glp+G q
  NCBI__GCF_000284315.1:WP_014450045.1 388 ALIREEFMRSFSECDLLFAPVTPTPAFRFGEKISDPLSMYLSDIFTISANLAGLPALSTPSFPTSNGLPVGAQ 460
                                           ************************************************************************* PP

                             TIGR00132 443 iigkafddkkllsvakale 461
                                           +ig ++++  ll++a  l+
  NCBI__GCF_000284315.1:WP_014450045.1 461 LIGPHWSEGVLLKAASVLH 479
                                           ************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (493 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.68
//
[ok]

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