Alignments for a candidate for gatA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Echvi_4078 Echvi_4078 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Cola:Echvi_4078
          Length = 475

 Score =  404 bits (1039), Expect = e-117
 Identities = 224/466 (48%), Positives = 301/466 (64%), Gaps = 5/466 (1%)

Query: 6   HKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGR 65
           H   E+K+ +  KE     +V    K IQ     + AF+ + E+ A   A+++D+ +   
Sbjct: 5   HSFDEIKRSLENKETDCKAIVHYYLKNIQT-KAHLNAFVEVYEQSALEQAEKVDQKIKAG 63

Query: 66  SEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMD 125
           +  G L GM IG+KD +         SSKILE F   + AT VQ+L D +A+ IG+LN D
Sbjct: 64  TA-GKLAGMVIGIKDVLCYADHEVNASSKILEGFQSQFTATAVQKLIDEDAIIIGRLNCD 122

Query: 126 EFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASF 185
           EF MGSS EN+ +    N  +   VPGGSSGGSA AV A     SLG+DTGGS+RQPA+F
Sbjct: 123 EFGMGSSNENTVHGKVLNALDEGRVPGGSSGGSAVAVQANLCTTSLGTDTGGSVRQPAAF 182

Query: 186 CGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDV 245
            G+VG+KPTY RVSR+GL+A+ASS D IG  +  V+DNA +L+ I+G D  DST +   V
Sbjct: 183 TGLVGIKPTYSRVSRFGLIAYASSFDTIGVFSTNVKDNALVLEVIAGQDDNDSTVSRKAV 242

Query: 246 PDFLSSLTGDIKGLKIAVPKEYL-GEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           P +   L  D + +K+A  KE +  E +    +E  L  L  L+  G   EEV  P  +Y
Sbjct: 243 PHYSEQLQLD-RPVKVAYLKETIESEALQPAIKEHTLDILDKLKEEGHQVEEVDFPLLEY 301

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364
            L TYY+L+++EAS+NL+RFDG++YGYRT NA NL  +YK TR+EGFG EVKRRIMLGTF
Sbjct: 302 VLPTYYILTTAEASSNLSRFDGVKYGYRTPNAHNLESMYKLTRSEGFGEEVKRRIMLGTF 361

Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424
            LS+ YYDAY+ KAQKVR LIK+  ED+  K+D IV PTTP+ AFK GE++ DP+ MY  
Sbjct: 362 VLSASYYDAYFTKAQKVRRLIKEFTEDLLNKFDYIVLPTTPSTAFKFGEHSDDPVAMYLE 421

Query: 425 DILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVA 469
           D+ T+  +++GVP IS+P G   +GLP+GLQ+I   F E+ +Y  A
Sbjct: 422 DLYTVQASVSGVPAISIPNGKDENGLPIGLQVITNSFKEAELYAFA 467


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: 583
Number of extensions: 22
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: 475
Length adjustment: 34
Effective length of query: 451
Effective length of database: 441
Effective search space:   198891
Effective search space used:   198891
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: 51 (24.3 bits)

Align candidate Echvi_4078 Echvi_4078 (aspartyl/glutamyl-tRNA(Asn/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.21766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   4.6e-171  555.6   1.3   5.6e-171  555.3   1.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4078  Echvi_4078 aspartyl/glutamyl-tRN


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4078  Echvi_4078 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.3   1.3  5.6e-171  5.6e-171       2     460 ..      11     470 ..      10     474 .. 0.97

  Alignments for each domain:
  == domain 1  score: 555.3 bits;  conditional E-value: 5.6e-171
                            TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkd 73 
                                          k+ l++ke+  k++++ +l++i+++ + +naf+ev +++al++a+k+d+k++  +  klag++i++Kd+++  d
  lcl|FitnessBrowser__Cola:Echvi_4078  11 KRSLENKETDCKAIVHYYLKNIQTKAH-LNAFVEVYEQSALEQAEKVDQKIKaGTaGKLAGMVIGIKDVLCYAD 83 
                                          5678999***************99888.***********************975536***************** PP

                            TIGR00132  74 iettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaa 147
                                           e+ ++SkiLe+++s + at v++l +++a+iiG+ N DEF+mGss e+ ++g + n  +e rvpGGSsgGsa 
  lcl|FitnessBrowser__Cola:Echvi_4078  84 HEVNASSKILEGFQSQFTATAVQKLIDEDAIIIGRLNCDEFGMGSSNENTVHGKVLNALDEGRVPGGSSGGSAV 157
                                          ************************************************************************** PP

                            TIGR00132 148 avaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkD 221
                                          av a+l+  +lg+DTGgS+RqPA+f+g vG+KPtY +vSR+Gl+ayasS+d+iG+++ +v+d alvl+vi+g+D
  lcl|FitnessBrowser__Cola:Echvi_4078 158 AVQANLCTTSLGTDTGGSVRQPAAFTGLVGIKPTYSRVSRFGLIAYASSFDTIGVFSTNVKDNALVLEVIAGQD 231
                                          ************************************************************************** PP

                            TIGR00132 222 kkDstslevkveelleelkkdlkglkvgvvkelse.esldkevkekfekllekleelgaeivevslpsvklala 294
                                           +Dst    +v+++ e+l+   + +kv+++ke +e e l+ ++ke+  ++l+kl+e+g++++ev++p ++++l+
  lcl|FitnessBrowser__Cola:Echvi_4078 232 DNDSTVSRKAVPHYSEQLQL-DRPVKVAYLKETIEsEALQPAIKEHTLDILDKLKEEGHQVEEVDFPLLEYVLP 304
                                          ****************9999.9**********877256899********************************* PP

                            TIGR00132 295 iYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkv 368
                                          +Yyi++++Eassnl+r+dg++yG+r+ ++++l+ +y+ tRsegfgeevkrRimlG+++ls+ yyd+y++kAqkv
  lcl|FitnessBrowser__Cola:Echvi_4078 305 TYYILTTAEASSNLSRFDGVKYGYRTPNAHNLESMYKLTRSEGFGEEVKRRIMLGTFVLSASYYDAYFTKAQKV 378
                                          ************************************************************************** PP

                            TIGR00132 369 rtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlq 442
                                          r+li++  e+l+++ D iv pt+p +afk+ge+ +dp++myl+D++tv a+++G+pais+P gk+e+glpiGlq
  lcl|FitnessBrowser__Cola:Echvi_4078 379 RRLIKEFTEDLLNKFDYIVLPTTPSTAFKFGEHSDDPVAMYLEDLYTVQASVSGVPAISIPNGKDENGLPIGLQ 452
                                          ************************************************************************** PP

                            TIGR00132 443 iigkafddkkllsvakal 460
                                          +i+++f++ +l+ +a  l
  lcl|FitnessBrowser__Cola:Echvi_4078 453 VITNSFKEAELYAFADYL 470
                                          ************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (475 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: 7.41
//
[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