Alignments for a candidate for gatA in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Nitratiruptor tergarcus DSM 16512

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_084276351.1 B8779_RS08965 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900176045.1:WP_084276351.1
          Length = 443

 Score =  415 bits (1066), Expect = e-120
 Identities = 223/404 (55%), Positives = 285/404 (70%), Gaps = 10/404 (2%)

Query: 73  GMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSS 132
           G+PI +KDNI   G   TC+SKIL+ +   YDATV+++L+ A     G+ NMDEFAMGS+
Sbjct: 44  GVPIAIKDNIQVDGWEVTCASKILQGYIAPYDATVIEKLKSAGCAPFGRTNMDEFAMGST 103

Query: 133 TENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLK 192
           TE+S Y  T NP +   VPGGSSGGSAA VAAG    +LGSDTGGSIRQPA+FCG+VG+K
Sbjct: 104 TESSCYGKTLNPRDPSRVPGGSSGGSAAVVAAGIAIAALGSDTGGSIRQPAAFCGIVGMK 163

Query: 193 PTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSL 252
           PTYGRVSRYGL A+ SSLDQIGP+T+ VED   L   I+GVD+ DSTSA V    F   +
Sbjct: 164 PTYGRVSRYGLAAYGSSLDQIGPMTQNVEDAIILYNMIAGVDERDSTSARV---PFEPVV 220

Query: 253 TGDIKGLKIAVPKEYLGEGVG--KEARESVLAALKVLEGLGATWEEVSLPHSKYALATYY 310
               + L I V   Y+ +     ++A +  +AALK     G    EVSL  +KY +A+YY
Sbjct: 221 PNADRKLTIGVVPNYVKDASAAVQKAYDKAVAALK---EAGHEIVEVSLMDAKYDIASYY 277

Query: 311 LLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGY 370
           + + +EAS NL+R+DG+RYGYR + A NL ++YK+TR+EGFG EVKRRI+LGTF LSSGY
Sbjct: 278 ITAMAEASTNLSRYDGVRYGYRAE-ASNLKEMYKKTRSEGFGEEVKRRILLGTFVLSSGY 336

Query: 371 YDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIP 430
           YDAYY KAQ+VR LIK ++  VFEK D+I+ P  P  A+K GE  K PL MY +D+ TI 
Sbjct: 337 YDAYYIKAQRVRHLIKDEYSKVFEKVDLILSPVAPDVAYKFGE-LKSPLEMYLSDVYTIG 395

Query: 431 VNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
           VNLAG+P IS+P    +GLP+GLQ+IGK FDE T++  A + E+
Sbjct: 396 VNLAGLPAISLPVDEHEGLPVGLQLIGKAFDEQTLFDGAMSLER 439


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: 622
Number of extensions: 33
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: 485
Length of database: 443
Length adjustment: 33
Effective length of query: 452
Effective length of database: 410
Effective search space:   185320
Effective search space used:   185320
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 WP_084276351.1 B8779_RS08965 (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.6421.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-182  592.9   0.7   2.7e-182  592.6   0.7    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084276351.1  B8779_RS08965 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084276351.1  B8779_RS08965 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 !  592.6   0.7  2.7e-182  2.7e-182      13     462 ..       5     439 ..       1     442 [. 0.92

  Alignments for each domain:
  == domain 1  score: 592.6 bits;  conditional E-value: 2.7e-182
                                 TIGR00132  13 kevleeilerieavkdkinaflevtkekalkkakkldkkvakekklagipiavKdniavkdiettcaSk 81 
                                               ke+l+  +e++e++k++   +++ +k     + k+l++ +a ++   g+pia+Kdni+v ++e+tcaSk
  lcl|NCBI__GCF_900176045.1:WP_084276351.1   5 KEALQLPKEELEEIKKD---LIKKAK-----EQKELNAYIALDSAGEGVPIAIKDNIQVDGWEVTCASK 65 
                                               55555555555555552...222222.....2233333333334678********************** PP

                                 TIGR00132  82 iLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaava 150
                                               iL++y++pydatV+e+lk+ag + +G+tN+DEFamGs+te+S++g t nP++ +rvpGGSsgGsaa+va
  lcl|NCBI__GCF_900176045.1:WP_084276351.1  66 ILQGYIAPYDATVIEKLKSAGCAPFGRTNMDEFAMGSTTESSCYGKTLNPRDPSRVPGGSSGGSAAVVA 134
                                               ********************************************************************* PP

                                 TIGR00132 151 adlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisg 219
                                               a+++  algsDTGgSiRqPA+fcg+vG+KPtYG+vSRyGl+ay sSldqiG+++++ved+ ++ ++i+g
  lcl|NCBI__GCF_900176045.1:WP_084276351.1 135 AGIAIAALGSDTGGSIRQPAAFCGIVGMKPTYGRVSRYGLAAYGSSLDQIGPMTQNVEDAIILYNMIAG 203
                                               ********************************************************************* PP

                                 TIGR00132 220 kDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslps 288
                                               +D++Dsts+ v+ e ++ ++    ++l +gvv ++ ++ ++ +v+++++k++ +l+e g+eivevsl +
  lcl|NCBI__GCF_900176045.1:WP_084276351.1 204 VDERDSTSARVPFEPVVPNA---DRKLTIGVVPNYVKD-ASAAVQKAYDKAVAALKEAGHEIVEVSLMD 268
                                               ***********998666554...469************.****************************** PP

                                 TIGR00132 289 vklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskey 357
                                                k+ +a Yyi +++Eas+nl+rydg+ryG+r+e  + lke+y+ktRsegfgeevkrRi+lG+++ls++y
  lcl|NCBI__GCF_900176045.1:WP_084276351.1 269 AKYDIASYYITAMAEASTNLSRYDGVRYGYRAEASN-LKEMYKKTRSEGFGEEVKRRILLGTFVLSSGY 336
                                               ********************************9999.******************************** PP

                                 TIGR00132 358 ydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpai 426
                                               yd+yy+kAq+vr+li+de++k+fe+vD+i+sp+ap +a k+ge ++ plemylsDv+t+ +nlaGlpai
  lcl|NCBI__GCF_900176045.1:WP_084276351.1 337 YDAYYIKAQRVRHLIKDEYSKVFEKVDLILSPVAPDVAYKFGELKS-PLEMYLSDVYTIGVNLAGLPAI 404
                                               *******************************************999.********************** PP

                                 TIGR00132 427 svPlgkkekglpiGlqiigkafddkkllsvakaleq 462
                                               s+P+ ++ +glp+Glq+igkafd+++l++ a +le+
  lcl|NCBI__GCF_900176045.1:WP_084276351.1 405 SLPVDEH-EGLPVGLQLIGKAFDEQTLFDGAMSLER 439
                                               ******9.7*******************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (443 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: 11.82
//
[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