Alignments for a candidate for gatA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Dechlorosoma suillum PS

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Dsui_0886 Dsui_0886 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__PS:Dsui_0886
          Length = 489

 Score =  476 bits (1226), Expect = e-139
 Identities = 241/486 (49%), Positives = 328/486 (67%), Gaps = 6/486 (1%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  + EL Q +  K+I   +L      RI  ++  + A+++   ER+ A AK  D  +
Sbjct: 1   MLNSSLKELAQALAGKKISSVELTQLYLDRINRLNPAINAYVSTQPERSLAQAKAADARL 60

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
               + G L G+P+  KD    +G  TTC SK+L NF   YDATV+Q+   A AV +GK 
Sbjct: 61  -AAGDAGPLTGIPLAQKDIFCAEGWLTTCGSKMLANFVSPYDATVIQKFDAAGAVNLGKT 119

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS E S +   KNPW+   VPGGSSGGSAAAVAA   P + G+DTGGSIRQP
Sbjct: 120 NMDEFAMGSSNETSFFGPVKNPWDQSRVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQP 179

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           A+ C + GLKPTYG VSR+G++AFASSLDQ GP+ R+ ED   LL A++G D  DSTS  
Sbjct: 180 AALCNLTGLKPTYGVVSRWGMIAFASSLDQAGPMARSAEDCGLLLNAMAGFDPKDSTSLE 239

Query: 243 VDVPDFLSSLTGD-----IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
             V D+   L        + GLK+ +PKE+ GEG       ++ AA++  + LGA   EV
Sbjct: 240 RPVEDYTRELNAPASAKPLAGLKVGLPKEFFGEGCDAAVMAAIQAAIEQYKALGAEMVEV 299

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLP+ K ++  YY+++ +EAS+NL+RFDG+RYGYR    D+L D+Y ++RA+GFG EVKR
Sbjct: 300 SLPNMKLSVPAYYVIAPAEASSNLSRFDGVRYGYRASEYDSLDDMYAKSRAQGFGAEVKR 359

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
           RI++GT+ LS GYYDAYY +AQ++R LI +DF   F++ DVI+GPT+P+ AFK+G+   D
Sbjct: 360 RILIGTYVLSHGYYDAYYLQAQRIRRLIAEDFVAAFKQCDVILGPTSPSTAFKLGDKAGD 419

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477
           P+ MY +DI TI VNLAG+PG+S+PCG A+GLP+GLQ+IG +FDE+ +  VAH ++Q TD
Sbjct: 420 PVQMYLSDIYTIAVNLAGLPGMSLPCGFAEGLPVGLQLIGNYFDEARLLNVAHRYQQVTD 479

Query: 478 HHKAKP 483
            H   P
Sbjct: 480 WHGRAP 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: 585
Number of extensions: 18
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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 Dsui_0886 Dsui_0886 (glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit)
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.16203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.6e-190  619.0   0.0   2.9e-190  618.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0886  Dsui_0886 glutamyl-tRNA(Gln) and


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0886  Dsui_0886 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.8   0.0  2.9e-190  2.9e-190       2     465 ..      10     479 ..       9     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 618.8 bits;  conditional E-value: 2.9e-190
                         TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiet 76 
                                       +++l  k++s++e+++ +l+ri++ +  ina++++++e++l++ak+ d+++a  +  +l+gip+a Kd ++ +++ t
  lcl|FitnessBrowser__PS:Dsui_0886  10 AQALAGKKISSVELTQLYLDRINRLNPAINAYVSTQPERSLAQAKAADARLAaGDaGPLTGIPLAQKDIFCAEGWLT 86 
                                       5788899*******************************************9975536******************** PP

                         TIGR00132  77 tcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadl 153
                                       tc+Sk+L n+vspydatV+++  +aga+ +GktN+DEFamGss etS+fg++knP++++rvpGGSsgGsaaavaa l
  lcl|FitnessBrowser__PS:Dsui_0886  87 TCGSKMLANFVSPYDATVIQKFDAAGAVNLGKTNMDEFAMGSSNETSFFGPVKNPWDQSRVPGGSSGGSAAAVAARL 163
                                       ***************************************************************************** PP

                         TIGR00132 154 vplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslev 230
                                       +p a g+DTGgSiRqPA++c+  GlKPtYG+vSR+G++a+asSldq G++a++ ed  l+l++++g D kDstsle 
  lcl|FitnessBrowser__PS:Dsui_0886 164 APAATGTDTGGSIRQPAALCNLTGLKPTYGVVSRWGMIAFASSLDQAGPMARSAEDCGLLLNAMAGFDPKDSTSLER 240
                                       ***************************************************************************** PP

                         TIGR00132 231 kveelleelkk.....dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisps 302
                                       +ve++++el++      l glkvg+ ke+++e++d +v++++++++e+ ++lgae+vevslp++kl++++Yy+i+p+
  lcl|FitnessBrowser__PS:Dsui_0886 241 PVEDYTRELNApasakPLAGLKVGLPKEFFGEGCDAAVMAAIQAAIEQYKALGAEMVEVSLPNMKLSVPAYYVIAPA 317
                                       *******99887755557799******************************************************** PP

                         TIGR00132 303 EassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefekl 379
                                       Eassnl+r+dg+ryG+r++e++sl+++yak+R++gfg+evkrRi++G+y+ls++yyd+yy++Aq++r+li+++f  +
  lcl|FitnessBrowser__PS:Dsui_0886 318 EASSNLSRFDGVRYGYRASEYDSLDDMYAKSRAQGFGAEVKRRILIGTYVLSHGYYDAYYLQAQRIRRLIAEDFVAA 394
                                       ***************************************************************************** PP

                         TIGR00132 380 feevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsv 456
                                       f+++Dvi++pt+p +afklg+ka dp++mylsD++t+ +nlaGlp++s+P+g + +glp+Glq+ig++fd+ +ll+v
  lcl|FitnessBrowser__PS:Dsui_0886 395 FKQCDVILGPTSPSTAFKLGDKAGDPVQMYLSDIYTIAVNLAGLPGMSLPCGFA-EGLPVGLQLIGNYFDEARLLNV 470
                                       ******************************************************.7********************* PP

                         TIGR00132 457 akaleqald 465
                                       a+ ++q +d
  lcl|FitnessBrowser__PS:Dsui_0886 471 AHRYQQVTD 479
                                       ****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.11
//
[ok]

This GapMind analysis is from Apr 09 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