Alignments for a candidate for gatA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfovibrio vulgaris Hildenborough

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate 206234 DVU0808 glutamyl-tRNA(Gln) amidotransferase, A subunit

Query= SwissProt::O06491
         (485 letters)



>MicrobesOnline__882:206234
          Length = 489

 Score =  483 bits (1243), Expect = e-141
 Identities = 247/472 (52%), Positives = 335/472 (70%), Gaps = 6/472 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  ++  + ++E++  D V +   RI+  + ++ A L L  E A   A+ LD A  G   
Sbjct: 9   LAAIRDALARREVRAEDAVLDCLARIETTEPRIDALLHLRAEAAIEEARALDAA--GPDA 66

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L+G+P+ VKD + T G  TT  S+ILE+F P YDA  VQRL++A A+ +GK NMDEF
Sbjct: 67  SRPLWGVPVTVKDALTTAGTPTTAGSRILEDFVPFYDAFAVQRLREAGAIILGKNNMDEF 126

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSAYK T+NPW+   VPGGSSGGSAA+VAAG+   SLG+DTGGSIRQPAS CG
Sbjct: 127 AMGSSTENSAYKPTRNPWDTARVPGGSSGGSAASVAAGQCFASLGTDTGGSIRQPASLCG 186

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
            VGLKPTYGRVSRYGL+A+ SSLDQIGP+TRTVED A ++  I+G DK DST A+  V D
Sbjct: 187 CVGLKPTYGRVSRYGLIAYGSSLDQIGPMTRTVEDAAIVMGVIAGHDKRDSTCADRPVED 246

Query: 248 FLSSLTG--DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYA 305
           F ++L    D+ G++I VP E+ GEG+  E   S  AAL     LGAT  +V+LPH+  +
Sbjct: 247 FAAALASRHDLAGVRIGVPAEFWGEGLSPEVATSCRAALDAARDLGATIVDVALPHTPQS 306

Query: 306 LATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFA 365
           +A YY+++S+EAS+NLAR+DG+RYG R    ++L+DLY ++R+EG G+EV+RRIMLGT+ 
Sbjct: 307 IAAYYIVASAEASSNLARYDGVRYGKRAHAPEDLMDLYVRSRSEGLGDEVQRRIMLGTYV 366

Query: 366 LSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAND 425
           LSSGYYDAYY+KA +VR  I +D+ + F   DVI GP +P  A+ +G  T DPL MY  D
Sbjct: 367 LSSGYYDAYYRKAAQVRRRILEDYRNAFATCDVICGPVSPVTAWPLGALTADPLQMYLMD 426

Query: 426 ILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           + T+ +NLAG+PG+S+P GL    G+P+G+Q++G+ FDE+T+  V +   +A
Sbjct: 427 VFTLSLNLAGLPGLSLPVGLGTESGMPVGIQLLGRSFDEATLLSVGNVLSRA 478


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: 614
Number of extensions: 35
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: 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 206234 DVU0808 (glutamyl-tRNA(Gln) 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.16181.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.3e-181  589.6   0.0   2.7e-181  589.3   0.0    1.0  1  lcl|MicrobesOnline__882:206234  DVU0808 glutamyl-tRNA(Gln) amido


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206234  DVU0808 glutamyl-tRNA(Gln) amidotransferase, A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.3   0.0  2.7e-181  2.7e-181       2     463 ..      13     478 ..      12     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 589.3 bits;  conditional E-value: 2.7e-181
                       TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvake.kklagipiavKdniavkdiettca 79 
                                     +++l ++ev++++++ ++l+rie+++ +i+a+l++++e a+++a++ld++  +  ++l g+p++vKd +++ +++tt++
  lcl|MicrobesOnline__882:206234  13 RDALARREVRAEDAVLDCLARIETTEPRIDALLHLRAEAAIEEARALDAAGPDAsRPLWGVPVTVKDALTTAGTPTTAG 91 
                                     678999*******************************************8876636*********************** PP

                       TIGR00132  80 SkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadlvplal 158
                                     S+iLe++v+ yda  v+rl+eaga+i+Gk N+DEFamGsste+Sa+++t+nP++++rvpGGSsgGsaa+vaa+++  +l
  lcl|MicrobesOnline__882:206234  92 SRILEDFVPFYDAFAVQRLREAGAIILGKNNMDEFAMGSSTENSAYKPTRNPWDTARVPGGSSGGSAASVAAGQCFASL 170
                                     ******************************************************************************* PP

                       TIGR00132 159 gsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslevkveelle 237
                                     g+DTGgSiRqPAs+cg+vGlKPtYG+vSRyGl+ay sSldqiG+++++ved+a+v+ vi+g+Dk+Dst ++ +ve++  
  lcl|MicrobesOnline__882:206234 171 GTDTGGSIRQPASLCGCVGLKPTYGRVSRYGLIAYGSSLDQIGPMTRTVEDAAIVMGVIAGHDKRDSTCADRPVEDFAA 249
                                     *****************************************************************************99 PP

                       TIGR00132 238 elkk..dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgi 314
                                     +l++  dl g+++gv  e+ +e+l+ ev+++ +++l++ ++lga+iv+v lp+   ++a+Yyi++++Eassnlarydg+
  lcl|MicrobesOnline__882:206234 250 ALASrhDLAGVRIGVPAEFWGEGLSPEVATSCRAALDAARDLGATIVDVALPHTPQSIAAYYIVASAEASSNLARYDGV 328
                                     98877799*********************************************************************** PP

                       TIGR00132 315 ryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptapt 393
                                     ryGkr++ +++l++ly+++Rseg+g+ev+rRimlG+y+ls++yyd+yy kA +vr+ i ++++++f  +Dvi +p++p+
  lcl|MicrobesOnline__882:206234 329 RYGKRAHAPEDLMDLYVRSRSEGLGDEVQRRIMLGTYVLSSGYYDAYYRKAAQVRRRILEDYRNAFATCDVICGPVSPV 407
                                     ******************************************************************************* PP

                       TIGR00132 394 lafklgekaedplemylsDvltvpanlaGlpaisvPlgkke.kglpiGlqiigkafddkkllsvakaleqa 463
                                     +a  lg+ ++dpl+myl Dv+t+ +nlaGlp++s+P+g  + +g+p+G+q+ g++fd+ +llsv++ l++a
  lcl|MicrobesOnline__882:206234 408 TAWPLGALTADPLQMYLMDVFTLSLNLAGLPGLSLPVGLGTeSGMPVGIQLLGRSFDEATLLSVGNVLSRA 478
                                     *************************************987648*********************9998876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.21
//
[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