Alignments for a candidate for gatA in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfacinum infernum DSM 9756

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_073040200.1 BUB04_RS13000 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900129305.1:WP_073040200.1
          Length = 487

 Score =  516 bits (1329), Expect = e-151
 Identities = 257/481 (53%), Positives = 347/481 (72%), Gaps = 4/481 (0%)

Query: 6   HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63
           H++T  E +  + +KE  ++++V    +RI+ +D  + ++L +  ++A   A+  D    
Sbjct: 5   HELTIHETRGALLRKEASVTEVVTAYLERIEELDKSLNSYLTVLADQALEQARAYDSGTL 64

Query: 64  GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123
              +  L  G+P+ +KD + T+G+RTTC S+ILENF P +DAT V RL++  A+ +GK N
Sbjct: 65  PLQDKPL-GGVPLALKDVLCTQGVRTTCGSRILENFIPPFDATAVARLKENGAILLGKTN 123

Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183
           MDEFAMGSS ENSAY   +NPW+++ VPGGSSGGSAAAVAA     +LG+DTGGSIRQPA
Sbjct: 124 MDEFAMGSSNENSAYGPVRNPWDMERVPGGSSGGSAAAVAADLCAGALGTDTGGSIRQPA 183

Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243
           SFCGVVG+KPTYGRVSRYGLVAFASSLDQIGPIT+ V D A LLQ ++G D  DST    
Sbjct: 184 SFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITKDVRDAALLLQVVAGHDPRDSTCLEQ 243

Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303
            V D  + L   I+G+ + +PKEY  EG+  E   ++  A  V   LGA   E+SLPH+ 
Sbjct: 244 PVGDLQARLDEPIRGMTLGIPKEYFVEGMDPEVARAMEEAFAVFRDLGARLVEISLPHTD 303

Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363
           Y +A YY+++ +EAS+NLAR+DG++YG+R   A +L+ +Y+++R  GFG EVKRRIMLGT
Sbjct: 304 YGVAAYYIIAPAEASSNLARYDGVKYGFRKQEARDLLTMYRESRNLGFGAEVKRRIMLGT 363

Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423
           ++LS+GYYDAYY+KA +VRTLIK+DF   F+  D I+ P  PTPAFKIGE T+DPL MY 
Sbjct: 364 YSLSAGYYDAYYRKASQVRTLIKQDFIQAFDNCDAIIAPVVPTPAFKIGEKTQDPLQMYL 423

Query: 424 NDILTIPVNLAGVPGISVPCG-LADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAK 482
           +D+LT+P +LAG+PGISVPCG  + GLP+GLQ++G HF E+ V ++AH FE+ TDH   K
Sbjct: 424 SDVLTLPASLAGIPGISVPCGHTSGGLPVGLQVLGPHFGEAVVLQLAHNFEKNTDHGNKK 483

Query: 483 P 483
           P
Sbjct: 484 P 484


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: 656
Number of extensions: 21
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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_073040200.1 BUB04_RS13000 (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.1567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-195  635.2   0.0   3.7e-195  635.0   0.0    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073040200.1  BUB04_RS13000 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073040200.1  BUB04_RS13000 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 !  635.0   0.0  3.7e-195  3.7e-195       4     465 ..      15     478 ..      12     479 .. 0.99

  Alignments for each domain:
  == domain 1  score: 635.0 bits;  conditional E-value: 3.7e-195
                                 TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kekklagipiavKdnia 70 
                                               +l +ke+s++ev++++lerie+ ++++n++l+v +++al++a+++d+ +   ++k+l g+p+a+Kd+++
  lcl|NCBI__GCF_900129305.1:WP_073040200.1  15 ALLRKEASVTEVVTAYLERIEELDKSLNSYLTVLADQALEQARAYDSGTLplQDKPLGGVPLALKDVLC 83 
                                               57899******************************************98875558************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139
                                               +++++ttc+S+iLen+++p+dat v rlke+ga+++GktN+DEFamGss e+Sa+g+++nP++ ervpG
  lcl|NCBI__GCF_900129305.1:WP_073040200.1  84 TQGVRTTCGSRILENFIPPFDATAVARLKENGAILLGKTNMDEFAMGSSNENSAYGPVRNPWDMERVPG 152
                                               ********************************************************************* PP

                                 TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                               GSsgGsaaavaadl+  alg+DTGgSiRqPAsfcgvvG+KPtYG+vSRyGlva+asSldqiG+++k+v 
  lcl|NCBI__GCF_900129305.1:WP_073040200.1 153 GSSGGSAAAVAADLCAGALGTDTGGSIRQPASFCGVVGMKPTYGRVSRYGLVAFASSLDQIGPITKDVR 221
                                               ********************************************************************* PP

                                 TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleel 277
                                               d+al+l+v++g+D +Dst le +v +l  +l + ++g+ +g+ ke++ e++d ev++++e++  ++++l
  lcl|NCBI__GCF_900129305.1:WP_073040200.1 222 DAALLLQVVAGHDPRDSTCLEQPVGDLQARLDEPIRGMTLGIPKEYFVEGMDPEVARAMEEAFAVFRDL 290
                                               ********************************************************************* PP

                                 TIGR00132 278 gaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRi 346
                                               ga +ve+slp+ ++ +a+Yyii+p+Eassnlarydg++yG r +e+++l  +y ++R+ gfg+evkrRi
  lcl|NCBI__GCF_900129305.1:WP_073040200.1 291 GARLVEISLPHTDYGVAAYYIIAPAEASSNLARYDGVKYGFRKQEARDLLTMYRESRNLGFGAEVKRRI 359
                                               ********************************************************************* PP

                                 TIGR00132 347 mlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvlt 415
                                               mlG+y ls++yyd+yy kA +vrtli+++f ++f+++D i++p++pt afk+gek++dpl+mylsDvlt
  lcl|NCBI__GCF_900129305.1:WP_073040200.1 360 MLGTYSLSAGYYDAYYRKASQVRTLIKQDFIQAFDNCDAIIAPVVPTPAFKIGEKTQDPLQMYLSDVLT 428
                                               ********************************************************************* PP

                                 TIGR00132 416 vpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               +pa+laG+p+isvP+g+++ glp+Glq+ g +f +  +l++a+++e+++d
  lcl|NCBI__GCF_900129305.1:WP_073040200.1 429 LPASLAGIPGISVPCGHTSGGLPVGLQVLGPHFGEAVVLQLAHNFEKNTD 478
                                               **********************************************9987 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.94
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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