Alignments for a candidate for gatA in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfobacca acetoxidans DSM 11109

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013705468.1 DESAC_RS02335 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000195295.1:WP_013705468.1
          Length = 487

 Score =  557 bits (1436), Expect = e-163
 Identities = 282/480 (58%), Positives = 365/480 (76%), Gaps = 4/480 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV-DGRS 66
           I +L  L+ + EI   +L      RI   DD +  ++ ++ ++A A A+E    +  GR+
Sbjct: 10  IQQLHPLMLRGEISPVELTQGFLDRISQFDDTLHCYITVEAQQALAQAQEATRRLASGRA 69

Query: 67  EHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDE 126
               L G+P+ +KD IVT+GLRTTC+S+ LEN+ P YDATV+ RL++A AV +GK+NMDE
Sbjct: 70  TP--LTGIPLAIKDLIVTQGLRTTCASRSLENYVPPYDATVMHRLREAGAVILGKVNMDE 127

Query: 127 FAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFC 186
           FAMGSSTENSA+  T+NPW LD +PGGSSGGSAAAVAA     SLGSDTGGSIRQPAS C
Sbjct: 128 FAMGSSTENSAFGATRNPWRLDCIPGGSSGGSAAAVAADLCLASLGSDTGGSIRQPASHC 187

Query: 187 GVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVP 246
           GVVGLKPTYGRVSR+GLVAFASSLDQIGPIT+ V D A LLQ ++G D  DSTSA V  P
Sbjct: 188 GVVGLKPTYGRVSRFGLVAFASSLDQIGPITKDVADCALLLQFLAGYDPKDSTSAPVPTP 247

Query: 247 DFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYAL 306
           D+  +L  DIKGLKI VP+EY   G+ +E  ++V AAL+  +GLGA   EVSLPH++YA+
Sbjct: 248 DYSQALNQDIKGLKIGVPQEYFIAGMEEEVEQAVRAALETFKGLGAELVEVSLPHTQYAV 307

Query: 307 ATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFAL 366
           A YYL++++EAS+NLAR+DG++YG+R   A++L+D+Y  TRA+G G EV+RRIMLGT+AL
Sbjct: 308 AVYYLIATAEASSNLARYDGVKYGFRAAEANDLMDMYCATRAQGLGAEVRRRIMLGTYAL 367

Query: 367 SSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDI 426
           S+GYYDAYYKKA +VRTLI++DF++VF+   ++  P  PT AF++GE   DPLTMY +DI
Sbjct: 368 SAGYYDAYYKKASQVRTLIRRDFDEVFQTCQIVATPVAPTTAFRLGEKMDDPLTMYLSDI 427

Query: 427 LTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
            TI  NLAG+PGISVPCGL + GLP+GLQ++ +HFDEST+ + AHAFEQA+  H  KP +
Sbjct: 428 FTISANLAGIPGISVPCGLNSGGLPIGLQLLARHFDESTLLKAAHAFEQASTFHLLKPPI 487


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: 614
Number of extensions: 24
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: 487
Length adjustment: 34
Effective length of query: 451
Effective length of database: 453
Effective search space:   204303
Effective search space used:   204303
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_013705468.1 DESAC_RS02335 (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.21970.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-201  654.2   0.0   6.5e-201  654.0   0.0    1.0  1  lcl|NCBI__GCF_000195295.1:WP_013705468.1  DESAC_RS02335 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_013705468.1  DESAC_RS02335 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 !  654.0   0.0  6.5e-201  6.5e-201       5     463 ..      17     477 ..      13     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 654.0 bits;  conditional E-value: 6.5e-201
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               + + e+s +e+++ +l+ri++++d+++ +++v++++al++a++ ++++a  + ++l+gip+a+Kd i++
  lcl|NCBI__GCF_000195295.1:WP_013705468.1  17 MLRGEISPVELTQGFLDRISQFDDTLHCYITVEAQQALAQAQEATRRLAsGRaTPLTGIPLAIKDLIVT 85 
                                               66789999***************************************9974447*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140
                                               ++++ttcaS+ Lenyv+pydatV++rl+eaga+i+Gk N+DEFamGsste+Safg+t+nP+  + +pGG
  lcl|NCBI__GCF_000195295.1:WP_013705468.1  86 QGLRTTCASRSLENYVPPYDATVMHRLREAGAVILGKVNMDEFAMGSSTENSAFGATRNPWRLDCIPGG 154
                                               ********************************************************************* PP

                                 TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209
                                               SsgGsaaavaadl+  +lgsDTGgSiRqPAs+cgvvGlKPtYG+vSR+Glva+asSldqiG+++k+v d
  lcl|NCBI__GCF_000195295.1:WP_013705468.1 155 SSGGSAAAVAADLCLASLGSDTGGSIRQPASHCGVVGLKPTYGRVSRFGLVAFASSLDQIGPITKDVAD 223
                                               ********************************************************************* PP

                                 TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278
                                                al+l+ ++g+D kDsts+ v+++++ ++l++d+kglk+gv +e++  ++++ev+++++++le+++ lg
  lcl|NCBI__GCF_000195295.1:WP_013705468.1 224 CALLLQFLAGYDPKDSTSAPVPTPDYSQALNQDIKGLKIGVPQEYFIAGMEEEVEQAVRAALETFKGLG 292
                                               ********************************************************************* PP

                                 TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347
                                               ae+vevslp+ ++a+a+Yy+i+++Eassnlarydg++yG r+ e+++l+++y +tR++g+g+ev+rRim
  lcl|NCBI__GCF_000195295.1:WP_013705468.1 293 AELVEVSLPHTQYAVAVYYLIATAEASSNLARYDGVKYGFRAAEANDLMDMYCATRAQGLGAEVRRRIM 361
                                               ********************************************************************* PP

                                 TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416
                                               lG+yals++yyd+yykkA +vrtli+++f+++f+ + ++++p+apt+af+lgek++dpl+mylsD++t+
  lcl|NCBI__GCF_000195295.1:WP_013705468.1 362 LGTYALSAGYYDAYYKKASQVRTLIRRDFDEVFQTCQIVATPVAPTTAFRLGEKMDDPLTMYLSDIFTI 430
                                               ********************************************************************* PP

                                 TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                                anlaG+p+isvP+g ++ glpiGlq+ +++fd+++ll++a+a+eqa
  lcl|NCBI__GCF_000195295.1:WP_013705468.1 431 SANLAGIPGISVPCGLNSGGLPIGLQLLARHFDESTLLKAAHAFEQA 477
                                               *********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (487 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: 12.01
//
[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