Alignments for a candidate for gatA in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Hydrogenophaga taeniospiralis NBRC 102512

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_068169809.1 HTA01S_RS09260 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_001592305.1:WP_068169809.1
          Length = 497

 Score =  450 bits (1158), Expect = e-131
 Identities = 240/481 (49%), Positives = 320/481 (66%), Gaps = 18/481 (3%)

Query: 22  ISDLVDESYKRIQAV------DDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMP 75
           I+D    S + +QA+         + A+LA +E+   A AK  D  V    E G L G+P
Sbjct: 18  IADGKTSSVEAVQALLARAKQHQSLGAYLAFNEDLTLAQAKAADARV-ATGERGPLLGVP 76

Query: 76  IGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTEN 135
           +  KD  VT+G  TT  SK+L  +   +DATVV  L  A AVT+GKLN DEFAMGS  +N
Sbjct: 77  LAHKDIFVTQGFPTTAGSKMLAGYQSPFDATVVANLAQAGAVTLGKLNCDEFAMGSGNDN 136

Query: 136 SAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTY 195
           SAY    NPW+   VPGGSSGGSAAAVAA  VP + G+DTGGSIRQPASF G+ G+KPTY
Sbjct: 137 SAYAPVHNPWDTARVPGGSSGGSAAAVAARLVPAATGTDTGGSIRQPASFTGITGIKPTY 196

Query: 196 GRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVD-KMDSTSANVDVPDFL----- 249
           GR SRYG+VAFASSLDQ GP+ R+  D A LL A++G D   DSTS +    D+      
Sbjct: 197 GRCSRYGMVAFASSLDQAGPMARSAADCATLLTAMAGPDIDRDSTSLDHPAEDYTRLLGQ 256

Query: 250 ----SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYA 305
               +S    +KGL+I +PKE+ GEG   +   +V AAL   E LGAT  ++SLP ++ +
Sbjct: 257 PREGASAAQPLKGLRIGLPKEFFGEGCAPDVLTAVRAALAEYEKLGATLVDISLPRTELS 316

Query: 306 LATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFA 365
           +  YY+++ +EAS+NL+RFDG+++G+R    D+L D+YK++R+EGFG E +RRIM+GT+ 
Sbjct: 317 IPVYYIIAPAEASSNLSRFDGVKFGHRAAKFDDLTDMYKKSRSEGFGPEAQRRIMIGTYV 376

Query: 366 LSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAND 425
           LS GYYDAYY KAQ++R LI +DF+  F + DVI GP  PT A+KIGE + DP+  Y  D
Sbjct: 377 LSHGYYDAYYLKAQQIRRLIAQDFQSAFTQCDVIAGPVAPTVAWKIGEKSDDPVANYLAD 436

Query: 426 ILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484
           I T+  +LAG+PG+SVP G  A  +P+GLQ++G +F E  + + AHAF+QATD H+  P 
Sbjct: 437 IYTLSTSLAGLPGMSVPAGFGAAHMPVGLQLVGNYFKEGELLQTAHAFQQATDWHERAPA 496

Query: 485 L 485
           L
Sbjct: 497 L 497


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: 577
Number of extensions: 19
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: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
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_068169809.1 HTA01S_RS09260 (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.30140.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-171  557.2   0.0   1.7e-171  557.0   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068169809.1  HTA01S_RS09260 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068169809.1  HTA01S_RS09260 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 !  557.0   0.0  1.7e-171  1.7e-171       3     465 ..      16     489 ..      14     490 .. 0.97

  Alignments for each domain:
  == domain 1  score: 557.0 bits;  conditional E-value: 1.7e-171
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               +++ + ++s++e+++++l+r +++++ + a+l+++++ +l++ak+ d++va  e  +l g+p+a Kd +
  lcl|NCBI__GCF_001592305.1:WP_068169809.1  16 TTIADGKTSSVEAVQALLARAKQHQS-LGAYLAFNEDLTLAQAKAADARVAtGErGPLLGVPLAHKDIF 83 
                                               578889999****************9.***********************985646************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138
                                               ++++++tt++Sk+L +y+sp+datVv +l +aga+++Gk N DEFamGs+  +Sa+ +++nP++++rvp
  lcl|NCBI__GCF_001592305.1:WP_068169809.1  84 VTQGFPTTAGSKMLAGYQSPFDATVVANLAQAGAVTLGKLNCDEFAMGSGNDNSAYAPVHNPWDTARVP 152
                                               ********************************************************************* PP

                                 TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207
                                               GGSsgGsaaavaa lvp a g+DTGgSiRqPAsf+g+ G+KPtYG+ SRyG+va+asSldq G++a++ 
  lcl|NCBI__GCF_001592305.1:WP_068169809.1 153 GGSSGGSAAAVAARLVPAATGTDTGGSIRQPASFTGITGIKPTYGRCSRYGMVAFASSLDQAGPMARSA 221
                                               ********************************************************************* PP

                                 TIGR00132 208 edialvldvisgkD.kkDstslevkveelleelkk.........dlkglkvgvvkelseesldkevkek 266
                                                d a +l +++g D  +Dstsl+ + e++++ l +          lkgl++g+ ke+++e++  +v ++
  lcl|NCBI__GCF_001592305.1:WP_068169809.1 222 ADCATLLTAMAGPDiDRDSTSLDHPAEDYTRLLGQpregasaaqPLKGLRIGLPKEFFGEGCAPDVLTA 290
                                               **************569**********9987544333355555579*********************** PP

                                 TIGR00132 267 fekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRs 335
                                               ++++l + e+lga++v++slp+ +l++++Yyii+p+Eassnl+r+dg+++G+r+ + ++l+++y+k+Rs
  lcl|NCBI__GCF_001592305.1:WP_068169809.1 291 VRAALAEYEKLGATLVDISLPRTELSIPVYYIIAPAEASSNLSRFDGVKFGHRAAKFDDLTDMYKKSRS 359
                                               ********************************************************************* PP

                                 TIGR00132 336 egfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaed 404
                                               egfg e +rRim+G+y+ls++yyd+yy+kAq++r+li+++f+ +f+++Dvi++p+apt+a k+gek +d
  lcl|NCBI__GCF_001592305.1:WP_068169809.1 360 EGFGPEAQRRIMIGTYVLSHGYYDAYYLKAQQIRRLIAQDFQSAFTQCDVIAGPVAPTVAWKIGEKSDD 428
                                               ********************************************************************* PP

                                 TIGR00132 405 plemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               p+++yl+D++t+  +laGlp++svP+g     +p+Glq++g++f++ +ll+ a+a++qa+d
  lcl|NCBI__GCF_001592305.1:WP_068169809.1 429 PVANYLADIYTLSTSLAGLPGMSVPAGFGAAHMPVGLQLVGNYFKEGELLQTAHAFQQATD 489
                                               *********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (497 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: 12.69
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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