Alignments for a candidate for gatA in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Ammonifex degensii KC4

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_015739099.1 ADEG_RS05550 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000024605.1:WP_015739099.1
          Length = 489

 Score =  544 bits (1401), Expect = e-159
 Identities = 281/475 (59%), Positives = 347/475 (73%), Gaps = 1/475 (0%)

Query: 11  LKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGL 70
           L++   +KEI   ++V    +RI+ V+ KV+AFL L EE A   A++LD A+    E G 
Sbjct: 12  LRERFCRKEISAKEIVTAFLERIKQVEPKVKAFLTLCEEEALNQAEQLDRALAYGEEMGP 71

Query: 71  LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMG 130
           L G+P+ +KDN+   G  TTC+SKIL NF P YDATVV+RL++A A+ +GK N+DEFAMG
Sbjct: 72  LAGVPVALKDNLCLSGFPTTCASKILANFYPPYDATVVRRLKEAGAIIVGKTNLDEFAMG 131

Query: 131 SSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVG 190
           SSTENSA+  T NPW+L  VPGGSSGGSAAAVAAGEVP +LGSDTGGSIRQPA+FCGVVG
Sbjct: 132 SSTENSAFHPTANPWDLSRVPGGSSGGSAAAVAAGEVPVALGSDTGGSIRQPAAFCGVVG 191

Query: 191 LKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLS 250
           LKPTYGRVSRYGLVAFASSLDQIGPITR VED A +LQ I+G D  D+TS   +VPD+ S
Sbjct: 192 LKPTYGRVSRYGLVAFASSLDQIGPITRCVEDCALVLQVIAGHDPRDATSIPGEVPDYRS 251

Query: 251 SLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYY 310
           SL  D+KG+K+ +P+EYLGEG+  E R  V      L  LGA  +  SLPH+KYAL  YY
Sbjct: 252 SLISDLKGMKVGIPREYLGEGIAPEVRAVVEEVAAKLADLGAQVDYTSLPHTKYALPAYY 311

Query: 311 LLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGY 370
           L++ +EAS+NLAR+DG+RYG R   A    D    TR EGFG EVKRRIMLGT+ALS+GY
Sbjct: 312 LVAPAEASSNLARYDGVRYGLRVP-AKEAKDSMALTRKEGFGPEVKRRIMLGTYALSAGY 370

Query: 371 YDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIP 430
           Y+AYY KA KVRTLIK+DF++ F  +D ++ PTTPTPAF++GE   DPLTMY +DI T+ 
Sbjct: 371 YEAYYLKALKVRTLIKRDFDEAFAHFDCLLTPTTPTPAFRMGEKLADPLTMYFSDICTLA 430

Query: 431 VNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           VNLAG+P ISVP G    LP+G+Q I     E  ++RVA+A EQ       +P L
Sbjct: 431 VNLAGLPAISVPAGKVGHLPVGVQFIAPPLKEDKLFRVAYALEQVVGFPSWRPPL 485


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: 629
Number of extensions: 27
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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_015739099.1 ADEG_RS05550 (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.6394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-198  643.6   0.0     1e-197  643.4   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015739099.1  ADEG_RS05550 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015739099.1  ADEG_RS05550 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.4   0.0    1e-197    1e-197       2     464 ..      13     476 ..      12     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 643.4 bits;  conditional E-value: 1e-197
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               +e   +ke+s+ke+++++leri++v+ k++afl++++e+al++a++ld+++a  +e  +lag+p+a+Kd
  lcl|NCBI__GCF_000024605.1:WP_015739099.1  13 RERFCRKEISAKEIVTAFLERIKQVEPKVKAFLTLCEEEALNQAEQLDRALAygEEmGPLAGVPVALKD 81 
                                               5667899********************************************9976656*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               n++  +++ttcaSkiL n+ +pydatVv+rlkeaga+i+GktNlDEFamGsste+Saf +t+nP++ +r
  lcl|NCBI__GCF_000024605.1:WP_015739099.1  82 NLCLSGFPTTCASKILANFYPPYDATVVRRLKEAGAIIVGKTNLDEFAMGSSTENSAFHPTANPWDLSR 150
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaavaa++vp+algsDTGgSiRqPA+fcgvvGlKPtYG+vSRyGlva+asSldqiG++++
  lcl|NCBI__GCF_000024605.1:WP_015739099.1 151 VPGGSSGGSAAAVAAGEVPVALGSDTGGSIRQPAAFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITR 219
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                                ved alvl+vi+g+D +D ts+  +v+++ ++l +dlkg+kvg+ +e+ +e++  ev++ +e++  kl
  lcl|NCBI__GCF_000024605.1:WP_015739099.1 220 CVEDCALVLQVIAGHDPRDATSIPGEVPDYRSSLISDLKGMKVGIPREYLGEGIAPEVRAVVEEVAAKL 288
                                               ********************************************************************* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevk 343
                                                +lga++   slp+ k+al++Yy+++p+Eassnlarydg+ryG rv  ++ +k+ +a tR+egfg evk
  lcl|NCBI__GCF_000024605.1:WP_015739099.1 289 ADLGAQVDYTSLPHTKYALPAYYLVAPAEASSNLARYDGVRYGLRVPAKE-AKDSMALTRKEGFGPEVK 356
                                               **********************************************9998.9***************** PP

                                 TIGR00132 344 rRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsD 412
                                               rRimlG+yals++yy++yy+kA kvrtli+++f+++f + D +++pt+pt af++gek +dpl+my sD
  lcl|NCBI__GCF_000024605.1:WP_015739099.1 357 RRIMLGTYALSAGYYEAYYLKALKVRTLIKRDFDEAFAHFDCLLTPTTPTPAFRMGEKLADPLTMYFSD 425
                                               ********************************************************************* PP

                                 TIGR00132 413 vltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                               ++t+ +nlaGlpaisvP+gk    lp+G+q+i+  ++++kl++va+aleq +
  lcl|NCBI__GCF_000024605.1:WP_015739099.1 426 ICTLAVNLAGLPAISVPAGKV-GHLPVGVQFIAPPLKEDKLFRVAYALEQVV 476
                                               *********************.69************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.50
//
[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