Alignments for a candidate for gatB in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thauera aminoaromatica S2

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_004301670.1 C665_RS05040 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000310185.1:WP_004301670.1
          Length = 486

 Score =  435 bits (1119), Expect = e-126
 Identities = 224/479 (46%), Positives = 326/479 (68%), Gaps = 9/479 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLEVH +L T SK+FS +   FGAEPN   + +D+A PGVLPV+N+ AV+ A+R 
Sbjct: 6   WEVVIGLEVHAQLDTASKIFSGASTAFGAEPNRQASAVDIALPGVLPVLNRGAVERAIRF 65

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGET---KRIGI 118
            +A+   +A +S F RKNYFYPD PK YQISQ D P+   G I I V +GE+   K + +
Sbjct: 66  GLAIGAHVAEKSVFARKNYFYPDLPKGYQISQMDLPVVVGGTITIRVGEGESAYEKTVRL 125

Query: 119 TRLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176
           TR H+EEDAGKS H+  + +  +DLNR GTPL+EIVSEPD+RS  EA AY   L +++++
Sbjct: 126 TRAHLEEDAGKSLHEDFHGMTGIDLNRAGTPLLEIVSEPDMRSSAEAVAYARTLHALVRW 185

Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236
             + D  M+EGS RCDAN+S+R  G  +FGT+ E+KNLNSF ++++ ++YE + Q + L 
Sbjct: 186 IDICDGNMQEGSFRCDANVSVRRKGATEFGTRREIKNLNSFRFLQQAIDYEVQWQIDTLE 245

Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
            GG I Q T  FD  TG+T +MR KE + DYRYFP+PD++PL I   WK RV+  +PELP
Sbjct: 246 DGGRIEQATVLFDPDTGETRMMRSKEDAHDYRYFPDPDLLPLMIAPEWKARVQAEMPELP 305

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIE--HGADVKLTSNWLMGGVNEYLNK 354
              K +++++ GL AYDA  LT +KE++DF+++T+     A  K  +NW+MG +   LNK
Sbjct: 306 GAMKGRFMDDWGLSAYDATTLTASKEVADFYQATVSAAGAALAKPCANWVMGELAARLNK 365

Query: 355 NQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPEL-AAKGGNAKQIMEDNGLVQIS 413
            ++++  + ++P  LAG++  I D T+S+ IA+KVF  L   +G  A ++++  GL Q++
Sbjct: 366 AELDVAASPVSPAQLAGLVARIADNTISNAIARKVFEALWNGEGATADEVIDKQGLRQVT 425

Query: 414 DEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           D   +   ++E L  N++SVE+++ GK KA   LVGQ+MKASKG+A P  VN LL+++L
Sbjct: 426 DTGAIEAMIDEVLAANQKSVEEFRAGKEKAFNALVGQVMKASKGKAGPAQVNALLRKKL 484


Lambda     K      H
   0.313    0.133    0.373 

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: 580
Number of extensions: 22
Number of successful extensions: 5
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: 475
Length of database: 486
Length adjustment: 34
Effective length of query: 441
Effective length of database: 452
Effective search space:   199332
Effective search space used:   199332
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_004301670.1 C665_RS05040 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.567881.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-164  533.9   0.0   1.9e-164  533.7   0.0    1.0  1  NCBI__GCF_000310185.1:WP_004301670.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000310185.1:WP_004301670.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.7   0.0  1.9e-164  1.9e-164       3     480 ..       5     484 ..       3     485 .. 0.97

  Alignments for each domain:
  == domain 1  score: 533.7 bits;  conditional E-value: 1.9e-164
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++e+viGlEvH ql+t+sK+F+ +s+ +   +pN++ ++v+++lPG+lPvlN+ av+ A+  +la++++ v+e
  NCBI__GCF_000310185.1:WP_004301670.1   5 DWEVVIGLEVHAQLDTASKIFSGASTAFGA-EPNRQASAVDIALPGVLPVLNRGAVERAIRFGLAIGAH-VAE 75 
                                           789*************************99.**************************************.668 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke....keigierlhlEeDtgksqykesdkdkqs 144
                                           +svF+RK+YfYpDlPkgyqi+q dlP++ +G+++i + e+e    k+++++r hlEeD+gks ++    + ++
  NCBI__GCF_000310185.1:WP_004301670.1  76 KSVFARKNYFYPDLPKGYQISQMDLPVVVGGTITIRVGEGEsayeKTVRLTRAHLEEDAGKSLHEDF--HGMT 146
                                           ************************************999888899*******************944..5899 PP

                             TIGR00133 145 lvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvE 217
                                            +D+NR+g+PLlEiV++Pd++s+ ea+a+ + l++++r+++i dg+++eGs+R+D+Nvs+r kG +++gtr E
  NCBI__GCF_000310185.1:WP_004301670.1 147 GIDLNRAGTPLLEIVSEPDMRSSAEAVAYARTLHALVRWIDICDGNMQEGSFRCDANVSVRRKGATEFGTRRE 219
                                           ************************************************************************* PP

                             TIGR00133 218 iKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieidee 290
                                           iKNlns++ +++ai+yE++ q++ l++g  ++q+t  fd  +  t ++R+Ke+++DYRYfp+Pdl p+ i++e
  NCBI__GCF_000310185.1:WP_004301670.1 220 IKNLNSFRFLQQAIDYEVQWQIDTLEDGGRIEQATVLFDPDTGETRMMRSKEDAHDYRYFPDPDLLPLMIAPE 292
                                           ************************************************************************* PP

                             TIGR00133 291 vvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep..klavnWileellgeLn 361
                                           +   +v++++pelP a++ r++ + gls++da +l++ +e++d ++  v++++ +  k  +nW++ el+++Ln
  NCBI__GCF_000310185.1:WP_004301670.1 293 WKA-RVQAEMPELPGAMKGRFMDDWGLSAYDATTLTASKEVADFYQATVSAAGAAlaKPCANWVMGELAARLN 364
                                           955.5*********************************************999988899************** PP

                             TIGR00133 362 kkkislaeallkpeelaeliklikegkisqksakelleellen.kkdpkklieklgliqisdekelvkiveev 433
                                           k ++++a++ ++p +la l++ i +++is+ +a++++e l +  +  ++++i+k+gl q++d+ ++ ++++ev
  NCBI__GCF_000310185.1:WP_004301670.1 365 KAELDVAASPVSPAQLAGLVARIADNTISNAIARKVFEALWNGeGATADEVIDKQGLRQVTDTGAIEAMIDEV 437
                                           **************************************9998658999************************* PP

                             TIGR00133 434 ikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           ++ n+k+ve++++gkeka++ lvGqvmk +kg+a p++v++ll+++l
  NCBI__GCF_000310185.1:WP_004301670.1 438 LAANQKSVEEFRAGKEKAFNALVGQVMKASKGKAGPAQVNALLRKKL 484
                                           *******************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 17.80
//
[ok]

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

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Steps (tab-delimited)
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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