Alignments for a candidate for gatA in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methylosarcina fibrata AML-C10

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_020562001.1 A3OW_RS0103280 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000372865.1:WP_020562001.1
          Length = 483

 Score =  510 bits (1314), Expect = e-149
 Identities = 256/482 (53%), Positives = 339/482 (70%), Gaps = 2/482 (0%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           ++D  ITEL Q +   E    +L     +RI+    ++ A++ + EERA A AKE D+ +
Sbjct: 1   MYDRSITELAQGLRSGEFSSRELTLAFLERIER-HPEINAYITVTEERALADAKEADDRL 59

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
             R E  LL G+PI  KD   T+G++T+C SK+L+NF   YDATVV++ ++A AV +GKL
Sbjct: 60  -ARGEGSLLTGIPIAHKDIFCTEGVKTSCGSKMLDNFIAPYDATVVEKFKEAGAVMLGKL 118

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS E S Y   +NPW ++ VPGGSSGGSAAAVAA     + G+DTGGSIRQP
Sbjct: 119 NMDEFAMGSSNETSHYGAVRNPWGINKVPGGSSGGSAAAVAARLAAAATGTDTGGSIRQP 178

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           AS CG+ GLKPTYGRVSRYG++A+ASSLDQ GP+ R+  D A LLQ ++G D+ DSTS +
Sbjct: 179 ASHCGITGLKPTYGRVSRYGMIAYASSLDQGGPMARSAHDAAVLLQTMAGFDEKDSTSVD 238

Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHS 302
           + VPD+ + L  D+KGLKI +P+E+ G+G+ +E    + AA+     LGA   EVS+P  
Sbjct: 239 LPVPDYTAGLNADLKGLKIGLPREFFGDGLSREVAAVIEAAVNEYRKLGAEIREVSMPDL 298

Query: 303 KYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLG 362
             A+  YY+++ +E SANL+RFDG+R+GYR  N  +L DLY ++R EGFG EVKRRI++G
Sbjct: 299 NLAIPAYYVIAPAECSANLSRFDGVRFGYRCQNPSDLTDLYTRSRGEGFGKEVKRRILMG 358

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           T+ALS+GYYDAYY KAQKVR LI  DF+  F + DV++GP  PT AF IGE   DP+ MY
Sbjct: 359 TYALSAGYYDAYYVKAQKVRRLISDDFKKTFAQVDVLMGPVAPTTAFGIGEKMGDPVEMY 418

Query: 423 ANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482
            +DI TI VNLAG+P +SVP G A G P+GLQIIG +F E  +  +AH F++ TD H+  
Sbjct: 419 LSDIYTIAVNLAGLPAMSVPAGFASGQPVGLQIIGNYFTEPRLLNIAHQFQRMTDWHQQL 478

Query: 483 PE 484
           PE
Sbjct: 479 PE 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: 604
Number of extensions: 25
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: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
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_020562001.1 A3OW_RS0103280 (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.13067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-192  624.9   0.0   4.8e-192  624.7   0.0    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020562001.1  A3OW_RS0103280 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020562001.1  A3OW_RS0103280 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 !  624.7   0.0  4.8e-192  4.8e-192       5     465 ..      13     473 ..       9     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 624.7 bits;  conditional E-value: 4.8e-192
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l + e+s++e++ ++lerie++ + ina+++vt+e+al+ ak+ d+++a  e ++l+gipia Kd +++
  lcl|NCBI__GCF_000372865.1:WP_020562001.1  13 LRSGEFSSRELTLAFLERIERHPE-INAYITVTEERALADAKEADDRLArGEgSLLTGIPIAHKDIFCT 80 
                                               6677889999************99.***********************976657*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140
                                               ++++t+c+Sk+L+n+++pydatVve+ keaga+++Gk N+DEFamGss etS +g+++nP+  ++vpGG
  lcl|NCBI__GCF_000372865.1:WP_020562001.1  81 EGVKTSCGSKMLDNFIAPYDATVVEKFKEAGAVMLGKLNMDEFAMGSSNETSHYGAVRNPWGINKVPGG 149
                                               ********************************************************************* PP

                                 TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209
                                               SsgGsaaavaa l+  a g+DTGgSiRqPAs+cg+ GlKPtYG+vSRyG++ayasSldq G++a++ +d
  lcl|NCBI__GCF_000372865.1:WP_020562001.1 150 SSGGSAAAVAARLAAAATGTDTGGSIRQPASHCGITGLKPTYGRVSRYGMIAYASSLDQGGPMARSAHD 218
                                               ********************************************************************* PP

                                 TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278
                                               +a++l++++g D+kDsts++ +v++++  l++dlkglk+g+ +e+++++l++ev++ +e+++++ ++lg
  lcl|NCBI__GCF_000372865.1:WP_020562001.1 219 AAVLLQTMAGFDEKDSTSVDLPVPDYTAGLNADLKGLKIGLPREFFGDGLSREVAAVIEAAVNEYRKLG 287
                                               ********************************************************************* PP

                                 TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347
                                               aei evs+p+++la+++Yy+i+p+E s+nl+r+dg+r+G+r +++++l++ly+++R egfg+evkrRi+
  lcl|NCBI__GCF_000372865.1:WP_020562001.1 288 AEIREVSMPDLNLAIPAYYVIAPAECSANLSRFDGVRFGYRCQNPSDLTDLYTRSRGEGFGKEVKRRIL 356
                                               ********************************************************************* PP

                                 TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416
                                               +G+yals++yyd+yy kAqkvr+li d+f+k f +vDv+++p+apt+af +gek+ dp+emylsD++t+
  lcl|NCBI__GCF_000372865.1:WP_020562001.1 357 MGTYALSAGYYDAYYVKAQKVRRLISDDFKKTFAQVDVLMGPVAPTTAFGIGEKMGDPVEMYLSDIYTI 425
                                               ********************************************************************* PP

                                 TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                                +nlaGlpa+svP+g + +g+p+Glqiig++f + +ll++a+++++ +d
  lcl|NCBI__GCF_000372865.1:WP_020562001.1 426 AVNLAGLPAMSVPAGFA-SGQPVGLQIIGNYFTEPRLLNIAHQFQRMTD 473
                                               *****************.6*************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (483 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: 00:00:00.02
# Mc/sec: 7.74
//
[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