Alignments for a candidate for gatA in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfotalea psychrophila LSv54

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011187888.1 DP_RS03210 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000025945.1:WP_011187888.1
          Length = 485

 Score =  491 bits (1264), Expect = e-143
 Identities = 246/475 (51%), Positives = 332/475 (69%), Gaps = 2/475 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M  ++  I E    +   +I   +L     +RI  V+D+V+ F+ +DEE A A AK  D+
Sbjct: 1   MKAYELSIEEAAAKLRAGDISSVELTQSCLQRIGDVEDRVKGFITVDEEGALAQAKAADK 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
           A+    E   L G+P+ +KD +  K L  TC SK+LE F   Y+AT+V +LQ A AV +G
Sbjct: 61  ALQN-GETNPLCGIPMSIKDLLAVKDLPMTCGSKMLEKFIAPYNATIVDKLQGAGAVNLG 119

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K+ MDEFAMGS++E  A+ + +NPW    V GGSSGGSA  VAA E  FS+G+DTGGSIR
Sbjct: 120 KVTMDEFAMGSTSETCAFGVPQNPWKEGYVAGGSSGGSAVTVAAQECFFSIGTDTGGSIR 179

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPA+ CGVVG+KPTYGRVSRYGL AFASSLDQ GP+ RTV D A ++ +I G D MDSTS
Sbjct: 180 QPAALCGVVGMKPTYGRVSRYGLTAFASSLDQAGPLCRTVADTALVMNSICGYDPMDSTS 239

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
            N +VPD+ +SL   +KGL+I +PKEY  +G+  E  + V  A+ VL   GA   +VSLP
Sbjct: 240 INQEVPDYTASLVEGVKGLRIGIPKEYFAKGLDSEVEKVVRNAIAVLASAGAEIVDVSLP 299

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H++Y +A YYL++ +EAS NL+R+DG  YGYR   +  L D+YK TR+ GFG+EVK+RI+
Sbjct: 300 HTEYCVAVYYLIAPAEASTNLSRYDGALYGYRDLESKTLEDMYKDTRSAGFGDEVKKRIL 359

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           +GT+ALSSGYYDAYYKKA +VRTLI +DF++ +   DV++ P TPTPA+K+G  + DPL 
Sbjct: 360 IGTYALSSGYYDAYYKKASQVRTLIIEDFKNAYRSCDVLLSPVTPTPAWKLGAKSDDPLA 419

Query: 421 MYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQ 474
           +Y +DI+T+  NLAG+PG+SVP G   DGLP+G+Q+ G HF E  + +VA+  E+
Sbjct: 420 IYLSDIMTVSANLAGIPGMSVPGGFTEDGLPVGIQLQGSHFQEEILLKVAYNLEK 474


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: 594
Number of extensions: 26
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: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
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_011187888.1 DP_RS03210 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.15559.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-186  607.1   0.0   1.2e-186  606.9   0.0    1.0  1  lcl|NCBI__GCF_000025945.1:WP_011187888.1  DP_RS03210 Asp-tRNA(Asn)/Glu-tRN


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_011187888.1  DP_RS03210 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.9   0.0  1.2e-186  1.2e-186       4     464 ..      14     476 ..      11     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 606.9 bits;  conditional E-value: 1.2e-186
                                 TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdnia 70 
                                               +l + ++s++e+++++l+ri  v+d+++ f++v++e al++ak+ dk+++  e ++l gip+++Kd +a
  lcl|NCBI__GCF_000025945.1:WP_011187888.1  14 KLRAGDISSVELTQSCLQRIGDVEDRVKGFITVDEEGALAQAKAADKALQnGEtNPLCGIPMSIKDLLA 82 
                                               566778999***************************************9975546************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139
                                               vkd+++tc+Sk+Le +++py+at+v +l+ aga+ +Gk  +DEFamGs++et afgv +nP++e +v+G
  lcl|NCBI__GCF_000025945.1:WP_011187888.1  83 VKDLPMTCGSKMLEKFIAPYNATIVDKLQGAGAVNLGKVTMDEFAMGSTSETCAFGVPQNPWKEGYVAG 151
                                               ********************************************************************* PP

                                 TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                               GSsgGsa +vaa+++ +++g+DTGgSiRqPA++cgvvG+KPtYG+vSRyGl+a+asSldq G+l ++v 
  lcl|NCBI__GCF_000025945.1:WP_011187888.1 152 GSSGGSAVTVAAQECFFSIGTDTGGSIRQPAALCGVVGMKPTYGRVSRYGLTAFASSLDQAGPLCRTVA 220
                                               ********************************************************************* PP

                                 TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleel 277
                                               d+alv++ i+g+D +Dsts++ +v++++ +l + +kgl++g+ ke++ ++ld+ev++ +++++ +l + 
  lcl|NCBI__GCF_000025945.1:WP_011187888.1 221 DTALVMNSICGYDPMDSTSINQEVPDYTASLVEGVKGLRIGIPKEYFAKGLDSEVEKVVRNAIAVLASA 289
                                               ********************************************************************* PP

                                 TIGR00132 278 gaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRi 346
                                               gaeiv+vslp+ ++++a+Yy+i+p+Eas+nl+rydg  yG+r  e k l+++y+ tRs+gfg+evk+Ri
  lcl|NCBI__GCF_000025945.1:WP_011187888.1 290 GAEIVDVSLPHTEYCVAVYYLIAPAEASTNLSRYDGALYGYRDLESKTLEDMYKDTRSAGFGDEVKKRI 358
                                               ********************************************************************* PP

                                 TIGR00132 347 mlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvlt 415
                                               ++G+yals++yyd+yykkA +vrtlii++f+++++++Dv++sp++pt a klg+k +dpl+ ylsD++t
  lcl|NCBI__GCF_000025945.1:WP_011187888.1 359 LIGTYALSSGYYDAYYKKASQVRTLIIEDFKNAYRSCDVLLSPVTPTPAWKLGAKSDDPLAIYLSDIMT 427
                                               ********************************************************************* PP

                                 TIGR00132 416 vpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                               v anlaG+p++svP g +e+glp+G+q++g +f+++ ll+va++le++l
  lcl|NCBI__GCF_000025945.1:WP_011187888.1 428 VSANLAGIPGMSVPGGFTEDGLPVGIQLQGSHFQEEILLKVAYNLEKLL 476
                                               *********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (485 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.53
//
[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