Alignments for a candidate for gatA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Pedobacter sp. GW460-11-11-14-LB5

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate CA265_RS19010 CA265_RS19010 aspartyl/glutamyl-tRNA amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Pedo557:CA265_RS19010
          Length = 472

 Score =  422 bits (1084), Expect = e-122
 Identities = 227/467 (48%), Positives = 317/467 (67%), Gaps = 5/467 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + E++ LI +K++ + DL+   +K+I+  ++ + AF  +    A   AK + + ++   +
Sbjct: 7   LKEIQALISQKQLTLPDLLAYYFKQIEN-NEHLNAFNEVFFLSAEVQAKAIQQKIE-EGK 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L GM IG+KDNI  K    T SSK+LE F   Y +TVVQRL   +A+ IG+LN DEF
Sbjct: 65  QGKLAGMVIGIKDNICYKDHIVTASSKMLEGFVSPYSSTVVQRLLQEDAIIIGRLNCDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMG S E S Y + KN  N D VPGGSSGGSA AV A     +LG+DTGGS+RQPA+FCG
Sbjct: 125 AMGGSNETSYYGVAKNAANPDLVPGGSSGGSAVAVQADMCLSALGTDTGGSVRQPAAFCG 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
            +GLKPTYGR+SRYG++A+ASS DQ+GPIT +VED A LLQ ++G D  DST + V VPD
Sbjct: 185 QIGLKPTYGRISRYGVIAYASSFDQVGPITSSVEDAALLLQVLAGEDDYDSTVSPVAVPD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYL-GEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYAL 306
           + + L  + K  KIAV KE +  E +  E + ++L +++ L+  G T E VS     Y +
Sbjct: 245 YPAHL-NEHKKQKIAVLKETIESEALDSEIKSAILRSIEQLKADGHTVEYVSFDLLDYLV 303

Query: 307 ATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFAL 366
             YY+L+++EAS+NL+R+DG+ YG+R   A +L +LYK +RAEGFG EVKRRI+LGTF L
Sbjct: 304 PAYYILTTAEASSNLSRYDGVHYGHRNLEAKSLNELYKLSRAEGFGEEVKRRILLGTFVL 363

Query: 367 SSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDI 426
           S+GYYDAYY+KAQ+VR LI++  + +F+ YD+I+ P  PT AFKIG+N +D + MY  DI
Sbjct: 364 SAGYYDAYYQKAQQVRRLIREKMDVLFQDYDLILSPVAPTAAFKIGDNVQDAIVMYMADI 423

Query: 427 LTIPVNLAGVPGISVPCG-LADGLPLGLQIIGKHFDESTVYRVAHAF 472
            T+  +L+G P I++P G   +GLPL +Q   KHF+E  +   + AF
Sbjct: 424 FTVLPSLSGNPAIALPIGNNTEGLPLSIQFTAKHFEEDKLLAFSQAF 470


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: 552
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: 472
Length adjustment: 34
Effective length of query: 451
Effective length of database: 438
Effective search space:   197538
Effective search space used:   197538
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 CA265_RS19010 CA265_RS19010 (aspartyl/glutamyl-tRNA amidotransferase subunit A)
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.3469397.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   2.9e-174  566.1   0.3   3.3e-174  565.9   0.3    1.0  1  FitnessBrowser__Pedo557:CA265_RS19010  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Pedo557:CA265_RS19010  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.9   0.3  3.3e-174  3.3e-174       2     460 ..      11     470 ..      10     472 .] 0.98

  Alignments for each domain:
  == domain 1  score: 565.9 bits;  conditional E-value: 3.3e-174
                              TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kekklagipiavKdniav 71 
                                            ++l+ +k++++ ++l  + ++ie++++ +naf ev   +a  +ak++++k++  k+ klag++i++Kdni+ 
  FitnessBrowser__Pedo557:CA265_RS19010  11 QALISQKQLTLPDLLAYYFKQIENNEH-LNAFNEVFFLSAEVQAKAIQQKIEegKQGKLAGMVIGIKDNICY 81 
                                            78899******************9998.***********************964446*************** PP

                              TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsg 143
                                            kd  +t++Sk+Le++vspy++tVv+rl +++a+iiG+ N DEFamG+s etS++gv kn +n + vpGGSsg
  FitnessBrowser__Pedo557:CA265_RS19010  82 KDHIVTASSKMLEGFVSPYSSTVVQRLLQEDAIIIGRLNCDEFAMGGSNETSYYGVAKNAANPDLVPGGSSG 153
                                            ************************************************************************ PP

                              TIGR00132 144 GsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvld 215
                                            Gsa av ad++  alg+DTGgS+RqPA+fcg +GlKPtYG++SRyG++ayasS+dq+G+++ +ved+al+l+
  FitnessBrowser__Pedo557:CA265_RS19010 154 GSAVAVQADMCLSALGTDTGGSVRQPAAFCGQIGLKPTYGRISRYGVIAYASSFDQVGPITSSVEDAALLLQ 225
                                            ************************************************************************ PP

                              TIGR00132 216 visgkDkkDstslevkveelleelkkdlkglkvgvvkelse.esldkevkekfekllekleelgaeivevsl 286
                                            v++g D  Dst   v+v+++  +l++ +k+ k++v+ke +e e ld+e+k+++ + +e+l++ g++++ vs+
  FitnessBrowser__Pedo557:CA265_RS19010 226 VLAGEDDYDSTVSPVAVPDYPAHLNE-HKKQKIAVLKETIEsEALDSEIKSAILRSIEQLKADGHTVEYVSF 296
                                            **************************.999********8772568*************************** PP

                              TIGR00132 287 psvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyy 358
                                            + +++ +++Yyi++++Eassnl+rydg+ yG+r  e+ksl+ely+ +R+egfgeevkrRi+lG+++ls++yy
  FitnessBrowser__Pedo557:CA265_RS19010 297 DLLDYLVPAYYILTTAEASSNLSRYDGVHYGHRNLEAKSLNELYKLSRAEGFGEEVKRRILLGTFVLSAGYY 368
                                            ************************************************************************ PP

                              TIGR00132 359 dkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPl 430
                                            d+yy+kAq+vr+li+++++ lf+++D+i+sp+apt afk+g++ +d++ my++D++tv  +l+G+pai++P+
  FitnessBrowser__Pedo557:CA265_RS19010 369 DAYYQKAQQVRRLIREKMDVLFQDYDLILSPVAPTAAFKIGDNVQDAIVMYMADIFTVLPSLSGNPAIALPI 440
                                            ************************************************************************ PP

                              TIGR00132 431 gkkekglpiGlqiigkafddkkllsvakal 460
                                            g++++glp+ +q+++k+f+++kll +++a+
  FitnessBrowser__Pedo557:CA265_RS19010 441 GNNTEGLPLSIQFTAKHFEEDKLLAFSQAF 470
                                            **************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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: 00:00:00.01
# Mc/sec: 20.52
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Protein sequences (fasta format)
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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