Alignments for a candidate for gatA in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfitobacterium hafniense DCB-2

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_015945354.1 DHAF_RS23080 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000021925.1:WP_015945354.1
          Length = 491

 Score =  462 bits (1189), Expect = e-134
 Identities = 244/486 (50%), Positives = 334/486 (68%), Gaps = 4/486 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M L    + +L QL+  KE+   +L     +RI+  D ++QAF+ +  E A A A+ +DE
Sbjct: 1   MQLHTLTVHQLSQLLADKEVSSLELTQAYLERIRQKDHELQAFVTVTGEEALAQARLVDE 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
              G  E   L G+P+ V+DNI T G++TTC+S++L ++ P  DATV+ RL+ A +V IG
Sbjct: 61  QRLGGEELSALAGIPMAVQDNICTAGVKTTCASRMLSHYIPPADATVMGRLKKAGSVLIG 120

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K N+DEF MGSST +SA   T+NP++L  VPGGS GG+AAAVAAGE  F+LGSDTGG IR
Sbjct: 121 KANLDEFGMGSSTGHSACHDTRNPFDLRAVPGGSGGGAAAAVAAGEAAFALGSDTGGDIR 180

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPA+FCGV+GLKPTYG V R GL+++ASSLDQIGP  R ++D A +L+ I G D  DSTS
Sbjct: 181 QPAAFCGVIGLKPTYGYVPRTGLISYASSLDQIGPFARDLKDLALILKTICGHDAGDSTS 240

Query: 241 ANVDVPDFLSSL---TGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
           A ++VPDF  SL   + DIKGLKI +PKEY   GV       +  A+  LE LGA   EV
Sbjct: 241 ALLEVPDFRESLSNDSNDIKGLKIGLPKEYFAAGVSPGVAARLQEAITKLEELGARCVEV 300

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           +LPH++ A A +Y L+ +EAS+NLAR+DG+RYG R +  D + +++ +TR +GFG+ VKR
Sbjct: 301 TLPHTEVAAAAHYALACAEASSNLARYDGVRYGLRVEGED-VQNMFMKTRGQGFGSAVKR 359

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
            IMLGT  LSS +YD YY +A KVRTL  +DF   FE+ D ++ P T T A +  +   +
Sbjct: 360 SIMLGTHVLSSAHYDDYYTQALKVRTLNSQDFAQAFEQVDCLLTPATLTTAPQKSDLAGE 419

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
           PLT+  +   T+P NLAG+P +S+P GL++G+P+GLQ+IG+HFDE T+ RVA+  EQ TD
Sbjct: 420 PLTLVHSHRCTLPANLAGLPALSLPYGLSEGMPVGLQLIGRHFDEQTLLRVAYTLEQNTD 479

Query: 478 HHKAKP 483
             + +P
Sbjct: 480 QTRPQP 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: 583
Number of extensions: 30
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: 491
Length adjustment: 34
Effective length of query: 451
Effective length of database: 457
Effective search space:   206107
Effective search space used:   206107
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_015945354.1 DHAF_RS23080 (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.4629.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-170  551.6   0.0   8.5e-170  551.4   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015945354.1  DHAF_RS23080 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015945354.1  DHAF_RS23080 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 !  551.4   0.0  8.5e-170  8.5e-170       2     465 ..      12     479 ..      11     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 551.4 bits;  conditional E-value: 8.5e-170
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                                +ll +kevs+ e+++++leri +++++++af++vt e+al++a+ +d++    +e + lagip+av d
  lcl|NCBI__GCF_000021925.1:WP_015945354.1  12 SQLLADKEVSSLELTQAYLERIRQKDHELQAFVTVTGEEALAQARLVDEQRLggEElSALAGIPMAVQD 80 
                                               68899********************************************887876667*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               ni++ +++ttcaS++L+ y++p datV+ rlk+ag ++iGk+NlDEF+mGsst +Sa   t+nP + + 
  lcl|NCBI__GCF_000021925.1:WP_015945354.1  81 NICTAGVKTTCASRMLSHYIPPADATVMGRLKKAGSVLIGKANLDEFGMGSSTGHSACHDTRNPFDLRA 149
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGS+gG+aaavaa+++ +algsDTGg iRqPA+fcgv+GlKPtYG v R Gl++yasSldqiG++a+
  lcl|NCBI__GCF_000021925.1:WP_015945354.1 150 VPGGSGGGAAAAVAAGEAAFALGSDTGGDIRQPAAFCGVIGLKPTYGYVPRTGLISYASSLDQIGPFAR 218
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkk...dlkglkvgvvkelseesldkevkekfekll 271
                                               + +d+al+l++i+g+D+ Dsts+  +v+++ e+l +   d+kglk+g+ ke++  +++ +v++++++++
  lcl|NCBI__GCF_000021925.1:WP_015945354.1 219 DLKDLALILKTICGHDAGDSTSALLEVPDFRESLSNdsnDIKGLKIGLPKEYFAAGVSPGVAARLQEAI 287
                                               ****************************9999988767799**************************** PP

                                 TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                                kleelga  vev lp+ ++a a+ y ++ +Eassnlarydg+ryG rve  + ++++++ktR +gfg+
  lcl|NCBI__GCF_000021925.1:WP_015945354.1 288 TKLEELGARCVEVTLPHTEVAAAAHYALACAEASSNLARYDGVRYGLRVEGED-VQNMFMKTRGQGFGS 355
                                               *************************************************9988.*************** PP

                                 TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemy 409
                                                vkr imlG+++ls+  yd yy++A kvrtl  ++f ++fe+vD +++p++ t+a +  + a +pl+  
  lcl|NCBI__GCF_000021925.1:WP_015945354.1 356 AVKRSIMLGTHVLSSAHYDDYYTQALKVRTLNSQDFAQAFEQVDCLLTPATLTTAPQKSDLAGEPLTLV 424
                                               ********************************************************999***9****** PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                                s  +t+panlaGlpa+s+P+g + +g+p+Glq+ig++fd+++ll+va++leq++d
  lcl|NCBI__GCF_000021925.1:WP_015945354.1 425 HSHRCTLPANLAGLPALSLPYGLS-EGMPVGLQLIGRHFDEQTLLRVAYTLEQNTD 479
                                               ************************.7**************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (491 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: 00:00:00.02
# Mc/sec: 7.86
//
[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