Alignments for a candidate for gatA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfovibrio vulgaris Miyazaki F

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate 8502127 DvMF_2838 aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq)

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Miya:8502127
          Length = 501

 Score =  484 bits (1245), Expect = e-141
 Identities = 247/472 (52%), Positives = 332/472 (70%), Gaps = 6/472 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + E++  + ++E+    +      RI A +  + A L    E A A A+ LD A  G   
Sbjct: 13  LAEVRDRLARRELTAEQVTAACLDRITATEPAIAALLVTRGEGALAEARALDAA--GPDP 70

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L+G+P+ VKD + T G RTTC S+IL +F P YDA  V +L++A AV +GK NMDEF
Sbjct: 71  AKPLWGVPLTVKDALTTAGTRTTCGSRILGDFTPHYDAFAVGKLREAGAVILGKTNMDEF 130

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTENSA+  T+NPWN+  VPGGSSGGSAA+VAAG+   SLG+DTGGSIRQPAS CG
Sbjct: 131 AMGSSTENSAFGPTRNPWNVARVPGGSSGGSAASVAAGQCFGSLGTDTGGSIRQPASLCG 190

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
            VGLKPTYGRVSR+GLVA+ SSLDQIGP+TRTVED A LL  I+G D  D+TSA + V D
Sbjct: 191 CVGLKPTYGRVSRFGLVAYGSSLDQIGPLTRTVEDAALLLSVIAGHDPRDATSATLPVDD 250

Query: 248 FLSSLTG--DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYA 305
           ++ +L    D+ G++I VP+E+ GEG+  E   +  AAL    GLGAT  +V LPH+ Y+
Sbjct: 251 YMGALASRKDLSGVRIGVPREFRGEGIDPEVSAACEAALDTARGLGATIVDVELPHTPYS 310

Query: 306 LATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFA 365
           +A YY+++ +EAS+NLARFDG+RYG R ++  +L DLY ++RAEGFG+EV+RRIMLGT+ 
Sbjct: 311 IAAYYIIAPAEASSNLARFDGVRYGRRAESPRDLADLYVRSRAEGFGDEVQRRIMLGTYV 370

Query: 366 LSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAND 425
           LSSGYYDAYY+KA +VR LI++D+E    + DV+ GP +P  A+ +GE T DPL MY  D
Sbjct: 371 LSSGYYDAYYRKAAQVRRLIREDYEKALSRCDVLCGPASPVTAWGLGELTSDPLKMYMMD 430

Query: 426 ILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           + T+ +NLAG+PG+ +P G+    G+P+GLQ++G+ F E  +   A+    A
Sbjct: 431 VFTLSLNLAGLPGLCIPVGMGSRSGMPVGLQMLGRAFGEGDLLAAANVLSGA 482


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: 592
Number of extensions: 30
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: 501
Length adjustment: 34
Effective length of query: 451
Effective length of database: 467
Effective search space:   210617
Effective search space used:   210617
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 8502127 DvMF_2838 (aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq))
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.19691.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.3e-181  587.9   0.0   8.3e-181  587.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8502127  DvMF_2838 aspartyl/glutamyl-tRNA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502127  DvMF_2838 aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.7   0.0  8.3e-181  8.3e-181       2     462 ..      17     481 ..      16     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 587.7 bits;  conditional E-value: 8.3e-181
                         TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkvake.kklagipiavKdniavkdiett 77 
                                       ++ l ++e+++++v+ ++l+ri a++  i a+l ++ e al++a++ld++  +  k+l g+p++vKd +++ +++tt
  lcl|FitnessBrowser__Miya:8502127  17 RDRLARRELTAEQVTAACLDRITATEPAIAALLVTRGEGALAEARALDAAGPDPaKPLWGVPLTVKDALTTAGTRTT 93 
                                       5678999******************************************8876658********************* PP

                         TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadlv 154
                                       c+S+iL ++++ yda  v +l+eaga+i+GktN+DEFamGsste+Safg+t+nP+n +rvpGGSsgGsaa+vaa+++
  lcl|FitnessBrowser__Miya:8502127  94 CGSRILGDFTPHYDAFAVGKLREAGAVILGKTNMDEFAMGSSTENSAFGPTRNPWNVARVPGGSSGGSAASVAAGQC 170
                                       ***************************************************************************** PP

                         TIGR00132 155 plalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslevk 231
                                         +lg+DTGgSiRqPAs+cg+vGlKPtYG+vSR+Glvay sSldqiG+l+++ved+al+l+vi+g+D +D ts+  +
  lcl|FitnessBrowser__Miya:8502127 171 FGSLGTDTGGSIRQPASLCGCVGLKPTYGRVSRFGLVAYGSSLDQIGPLTRTVEDAALLLSVIAGHDPRDATSATLP 247
                                       ***************************************************************************** PP

                         TIGR00132 232 veelleelkk..dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEass 306
                                       v++++ +l++  dl g+++gv +e+++e++d ev+++ e++l++ + lga+iv+v+lp+  +++a+Yyii+p+Eass
  lcl|FitnessBrowser__Miya:8502127 248 VDDYMGALASrkDLSGVRIGVPREFRGEGIDPEVSAACEAALDTARGLGATIVDVELPHTPYSIAAYYIIAPAEASS 324
                                       ****99887666999************************************************************** PP

                         TIGR00132 307 nlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeev 383
                                       nlar+dg+ryG+r+e +++l +ly+++R+egfg+ev+rRimlG+y+ls++yyd+yy kA +vr+li++++ek+++ +
  lcl|FitnessBrowser__Miya:8502127 325 NLARFDGVRYGRRAESPRDLADLYVRSRAEGFGDEVQRRIMLGTYVLSSGYYDAYYRKAAQVRRLIREDYEKALSRC 401
                                       ***************************************************************************** PP

                         TIGR00132 384 DvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkke.kglpiGlqiigkafddkkllsvaka 459
                                       Dv+ +p++p++a  lge ++dpl+my+ Dv+t+ +nlaGlp++ +P+g+ + +g+p+Glq+ g+af +  ll +a+ 
  lcl|FitnessBrowser__Miya:8502127 402 DVLCGPASPVTAWGLGELTSDPLKMYMMDVFTLSLNLAGLPGLCIPVGMGSrSGMPVGLQMLGRAFGEGDLLAAANV 478
                                       ************************************************97769*******************99988 PP

                         TIGR00132 460 leq 462
                                       l+ 
  lcl|FitnessBrowser__Miya:8502127 479 LSG 481
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (501 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: 10.57
//
[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