Alignments for a candidate for gatA in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Pyrolobus fumarii 1A

Align Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial; Glu-AdT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_048192208.1 PYRFU_RS01485 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::Q9LI77
         (537 letters)



>NCBI__GCF_000223395.1:WP_048192208.1
          Length = 486

 Score =  331 bits (849), Expect = 3e-95
 Identities = 208/482 (43%), Positives = 286/482 (59%), Gaps = 29/482 (6%)

Query: 53  LLSGETTAVEIAKSYLSRIRLTEPQLKCF--LHVSENVLKDAQEIDQRIAKGEELGPLAG 110
           LLSGE +  E        IR +E  L  F  L   E+V K+ + + +R ++G+ L PLAG
Sbjct: 2   LLSGELSVDEYVARIYEVIRKSEC-LNAFITLRKQEDVEKELRSVVERASRGDNL-PLAG 59

Query: 111 VLIGVKDNICTQGMPSTAASRILEHYRPPFDATAVKKIKELGGIVVGKTNMDEFGMGSTT 170
           VL+ VKDNI T+G+ +T ASR+LE + PP++AT V+++   G +++GKTNMDEF MGST+
Sbjct: 60  VLVAVKDNIVTKGLRTTCASRMLEEFIPPYNATVVERLVRAGAVILGKTNMDEFAMGSTS 119

Query: 171 EASAFQVTANPWDLSRVPGGSSGGSAAAVAARQCMVSLGSDTGGSVRQPASFCGVVGLKP 230
           E SA+    NPW  SRVPGGSSGGSA A A     V+LGSDTGGS+R PA++ GV GLKP
Sbjct: 120 ELSAYGPVGNPWCPSRVPGGSSGGSAVAAAIGAGGVALGSDTGGSIRLPAAWSGVYGLKP 179

Query: 231 TYGRVSRFGLMAYASSLDVIGCFGSTVADAGMLLHAISGYDRFDSTSSKQDVPEFQSQFL 290
           TYG VSR+GL+AYA SL+ IG       D  M++  I+G+D  DST+            L
Sbjct: 180 TYGLVSRYGLVAYADSLEQIGPLARHPRDIAMVMEVIAGFDERDSTT------------L 227

Query: 291 SVDHFESKPLNGV--KVGIIRETLE-DGVDSGVRSATQEAASHL-EALGCILTEVSLPS- 345
            +  +   P   V  ++ I+R+ LE  GVD  V    ++    L E+LG  + EV L S 
Sbjct: 228 RIGGWRELPSRPVRPRIAILRDLLEHPGVDERVAKVVEKMVYRLSESLGWDIGEVKLGSE 287

Query: 346 -FSLGLPAYYVIASSESSSNLSRYDGVRY---GNQVMAEELNKLYECSRGEGFGGEVKMR 401
              L LPAYYVIA SE+SSNL+RY G+ Y   G +++       +     + FG EVK R
Sbjct: 288 ILDLALPAYYVIAMSEASSNLARYTGILYGPPGRKIVDNVPWTRWFSEVRKLFGWEVKRR 347

Query: 402 ILMGTYALSAGYYDAYYKRAQQVRTLIRKDFKAALEQNDILISPAAPSAAYKIGEKKDDP 461
           I MG +ALSAGY DA Y++A  +R  ++      L+  D ++ P+  S   + GE   DP
Sbjct: 348 IFMGAFALSAGYRDALYEKALIIRRRVKDAVLRVLKNWDAVVLPSCVSPPPRKGEAIGDP 407

Query: 462 LAMYAGDIMTVNVNLAGLPAMVLPCGLVEGGPSGLPVGLQMIGAAFDEEKLLKVGHIFEQ 521
           L MYA D+  V  NLAG+PA+ +P G V+    GLPVG Q+I    ++  L+++    E 
Sbjct: 408 LRMYALDLANVIANLAGVPALAVPAGTVD----GLPVGAQLISQPLNDRLLVELAIEIED 463

Query: 522 TL 523
            L
Sbjct: 464 HL 465


Lambda     K      H
   0.316    0.133    0.375 

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: 627
Number of extensions: 29
Number of successful extensions: 4
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: 537
Length of database: 486
Length adjustment: 35
Effective length of query: 502
Effective length of database: 451
Effective search space:   226402
Effective search space used:   226402
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 WP_048192208.1 PYRFU_RS01485 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.25479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-149  482.5   0.0   7.6e-149  482.3   0.0    1.0  1  lcl|NCBI__GCF_000223395.1:WP_048192208.1  PYRFU_RS01485 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000223395.1:WP_048192208.1  PYRFU_RS01485 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.3   0.0  7.6e-149  7.6e-149       7     464 ..       4     465 ..       1     467 [. 0.92

  Alignments for each domain:
  == domain 1  score: 482.3 bits;  conditional E-value: 7.6e-149
                                 TIGR00132   7 kkevsikevleeilerieavkdkinaflevtkekalk.kakkldkkva.kek.klagipiavKdniavk 72 
                                               + e+s+ e + +i+e i + +  +naf++++k++ ++ + +++ ++++  ++ +lag+++avKdni++k
  lcl|NCBI__GCF_000223395.1:WP_048192208.1   4 SGELSVDEYVARIYEVIRKSEC-LNAFITLRKQEDVEkELRSVVERASrGDNlPLAGVLVAVKDNIVTK 71 
                                               5678888999999999998887.******988766550556666666544456**************** PP

                                 TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGS 141
                                               +++ttcaS++Le++++py+atVverl +aga+i+GktN+DEFamGs++e Sa+g++ nP+  +rvpGGS
  lcl|NCBI__GCF_000223395.1:WP_048192208.1  72 GLRTTCASRMLEEFIPPYNATVVERLVRAGAVILGKTNMDEFAMGSTSELSAYGPVGNPWCPSRVPGGS 140
                                               ********************************************************************* PP

                                 TIGR00132 142 sgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedi 210
                                               sgGsa a a +   +algsDTGgSiR PA+++gv+GlKPtYGlvSRyGlvaya Sl+qiG+la++  di
  lcl|NCBI__GCF_000223395.1:WP_048192208.1 141 SGGSAVAAAIGAGGVALGSDTGGSIRLPAAWSGVYGLKPTYGLVSRYGLVAYADSLEQIGPLARHPRDI 209
                                               ********************************************************************* PP

                                 TIGR00132 211 alvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelsee.sldkevkekfekllekle.el 277
                                               a+v++vi+g D++Dst+l +    + +el +   + +++++++l e+ ++d++v++ +ek++ +l  +l
  lcl|NCBI__GCF_000223395.1:WP_048192208.1 210 AMVMEVIAGFDERDSTTLRIGG--W-RELPSRPVRPRIAILRDLLEHpGVDERVAKVVEKMVYRLSeSL 275
                                               ******************9965..3.44444456689******8765389***************6258 PP

                                 TIGR00132 278 gaeivevslp..svklalaiYyiispsEassnlarydgiryG...krveelkslkelyaktRsegfgee 341
                                               g +i ev+l    ++lal++Yy+i++sEassnlary+gi yG   +++ +   +++ +++ R+  fg e
  lcl|NCBI__GCF_000223395.1:WP_048192208.1 276 GWDIGEVKLGseILDLALPAYYVIAMSEASSNLARYTGILYGppgRKIVDNVPWTRWFSEVRKL-FGWE 343
                                               ********986579***************************733356666666*********87.**** PP

                                 TIGR00132 342 vkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyl 410
                                               vkrRi +Ga+als++y d+ y+kA  +r+ ++d++  ++++ D +v p+    + + ge   dpl+my+
  lcl|NCBI__GCF_000223395.1:WP_048192208.1 344 VKRRIFMGAFALSAGYRDALYEKALIIRRRVKDAVLRVLKNWDAVVLPSCVSPPPRKGEAIGDPLRMYA 412
                                               ********************************************************************* PP

                                 TIGR00132 411 sDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                                D+  v+anlaG+pa++vP+g+  +glp+G q+i++ ++d+ l+++a ++e++l
  lcl|NCBI__GCF_000223395.1:WP_048192208.1 413 LDLANVIANLAGVPALAVPAGTV-DGLPVGAQLISQPLNDRLLVELAIEIEDHL 465
                                               ***********************.7**********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (486 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.27
//
[ok]

This GapMind analysis is from Apr 10 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