Alignments for a candidate for gatA in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Halomonas desiderata SP1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_086509865.1 BZY95_RS10430 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_002151265.1:WP_086509865.1
          Length = 486

 Score =  512 bits (1319), Expect = e-150
 Identities = 256/484 (52%), Positives = 345/484 (71%), Gaps = 4/484 (0%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEA- 61
           + D  + EL + +   +    +L      RI  +D ++ +F+ +  E+A A A   D A 
Sbjct: 1   MHDKTLAELTRSLDAGDFSSRELTQHLLGRIDRLDGELNSFITVTHEQALAAADAADAAR 60

Query: 62  VDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGK 121
             GR+  G L G+P+ +KD   T+ ++TT  S++L++F   YDATVV++L+ A  V++GK
Sbjct: 61  AAGRA--GTLTGLPLALKDIFCTQDVKTTAGSRMLDSFIAPYDATVVEKLKAAGTVSLGK 118

Query: 122 LNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
            NMDEFAMGSS ENS Y   KNPW+   VPGGSSGGSAAAVAAG VP ++G+DTGGSIRQ
Sbjct: 119 TNMDEFAMGSSNENSHYGPVKNPWDFTAVPGGSSGGSAAAVAAGLVPAAIGTDTGGSIRQ 178

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+FCG+ GLKPTYGRVSRYG++A+ASSLDQ GP+ R+ ED A LL A++G D  DST  
Sbjct: 179 PAAFCGITGLKPTYGRVSRYGMIAYASSLDQAGPMARSAEDCALLLNAMAGHDLRDSTCV 238

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
              VPD+   L   + GLKI +P EY G+G+  +   +V  A+KV E LGA+  EVSLPH
Sbjct: 239 QRGVPDYTEELGTALSGLKIGLPSEYFGDGLDPQVEAAVREAIKVFESLGASVREVSLPH 298

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIML 361
           + YA+  YY+++ +EAS+NL+R+DG+R+G+R  N  +LIDLYK++RAEGFG+EVKRRI++
Sbjct: 299 THYAIPAYYVIAPAEASSNLSRYDGVRFGHRCANPVDLIDLYKRSRAEGFGDEVKRRILI 358

Query: 362 GTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTM 421
           GT  LS G++DAYYKKAQ+VR LI++DF D FE+ DV++GP +PTPAF +G N KDP+ M
Sbjct: 359 GTHTLSEGFFDAYYKKAQQVRRLIRQDFLDAFEEVDVLMGPASPTPAFDLGAN-KDPVQM 417

Query: 422 YANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKA 481
           Y  DI TI +NLAG+PG+SVP G     P+GLQI+G HF ES +  VAH F+ ATD H+ 
Sbjct: 418 YLQDIYTIAINLAGIPGMSVPAGFVGKRPVGLQILGSHFTESRLLNVAHQFQLATDWHRQ 477

Query: 482 KPEL 485
           +P L
Sbjct: 478 RPAL 481


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: 582
Number of extensions: 23
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: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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_086509865.1 BZY95_RS10430 (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.8814.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-185  601.8   0.0   4.8e-185  601.7   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509865.1  BZY95_RS10430 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509865.1  BZY95_RS10430 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 !  601.7   0.0  4.8e-185  4.8e-185       5     464 ..      13     472 ..       9     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 601.7 bits;  conditional E-value: 4.8e-185
                                 TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 
                                               l++ ++s++e+++++l ri++ + ++n+f++vt+e+al++a++ d++ a  +  +l+g+p+a+Kd +++
  lcl|NCBI__GCF_002151265.1:WP_086509865.1  13 LDAGDFSSRELTQHLLGRIDRLDGELNSFITVTHEQALAAADAADAARAaGRaGTLTGLPLALKDIFCT 81 
                                               5666788999***********************************998875536*************** PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140
                                               +d++tt++S++L+ +++pydatVve+lk+ag++ +GktN+DEFamGss e+S +g++knP++ + vpGG
  lcl|NCBI__GCF_002151265.1:WP_086509865.1  82 QDVKTTAGSRMLDSFIAPYDATVVEKLKAAGTVSLGKTNMDEFAMGSSNENSHYGPVKNPWDFTAVPGG 150
                                               ********************************************************************* PP

                                 TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209
                                               SsgGsaaavaa+lvp a+g+DTGgSiRqPA+fcg+ GlKPtYG+vSRyG++ayasSldq G++a++ ed
  lcl|NCBI__GCF_002151265.1:WP_086509865.1 151 SSGGSAAAVAAGLVPAAIGTDTGGSIRQPAAFCGITGLKPTYGRVSRYGMIAYASSLDQAGPMARSAED 219
                                               ********************************************************************* PP

                                 TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278
                                                al+l++++g+D +Dst ++  v++++eel + l glk+g+  e+++++ld +v+++++++++++e+lg
  lcl|NCBI__GCF_002151265.1:WP_086509865.1 220 CALLLNAMAGHDLRDSTCVQRGVPDYTEELGTALSGLKIGLPSEYFGDGLDPQVEAAVREAIKVFESLG 288
                                               ********************************************************************* PP

                                 TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347
                                               a + evslp+ ++a+++Yy+i+p+Eassnl+rydg+r+G+r  ++ +l +ly+++R+egfg+evkrRi+
  lcl|NCBI__GCF_002151265.1:WP_086509865.1 289 ASVREVSLPHTHYAIPAYYVIAPAEASSNLSRYDGVRFGHRCANPVDLIDLYKRSRAEGFGDEVKRRIL 357
                                               ********************************************************************* PP

                                 TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416
                                               +G+++ls++ +d+yykkAq+vr+li+++f ++feevDv+++p++pt af lg++++ p++myl+D++t+
  lcl|NCBI__GCF_002151265.1:WP_086509865.1 358 IGTHTLSEGFFDAYYKKAQQVRRLIRQDFLDAFEEVDVLMGPASPTPAFDLGANKD-PVQMYLQDIYTI 425
                                               *****************************************************999.************ PP

                                 TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                                +nlaG+p++svP+g      p+Glqi g +f +++ll+va++++ a+
  lcl|NCBI__GCF_002151265.1:WP_086509865.1 426 AINLAGIPGMSVPAGFV-GKRPVGLQILGSHFTESRLLNVAHQFQLAT 472
                                               *****************.599*********************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (486 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: 7.84
//
[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