Alignments for a candidate for gatB in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Archaeoglobus veneficus SNP6

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013684372.1 ARCVE_RS08530 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= metacyc::MONOMER-13956
         (476 letters)



>NCBI__GCF_000194625.1:WP_013684372.1
          Length = 471

 Score =  378 bits (970), Expect = e-109
 Identities = 202/476 (42%), Positives = 318/476 (66%), Gaps = 18/476 (3%)

Query: 4   ETVIGLEVHVEL-KTKSKIFSSSPTPFG-AEANTQTSVIDLGYPGVLPVLNKEAVEFAMK 61
           + VIGLEVHV+L K  +K+F S P  +  +E NT    + LG PG +PV+N+EAV+ A+K
Sbjct: 3   DVVIGLEVHVQLNKLNTKLFCSCPINYHESEPNTHVCPVCLGMPGAMPVVNREAVKAAIK 62

Query: 62  AAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRL 121
            A+AL+ +I + T FDRKNYFYPD PK +QISQ+D+P+   G++ IEV G+ K+I + R+
Sbjct: 63  VALALHADIQSFTVFDRKNYFYPDLPKGFQISQYDRPLAWGGYVTIEVDGEEKKIALKRI 122

Query: 122 HLEEDAGKLTHTGD----GYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQY 177
           H+EED GKL++ G      YSL+D+NR G PL+EIV+EP + +P+EA  +L KL+ I++Y
Sbjct: 123 HMEEDPGKLSYKGSITTARYSLIDYNRSGVPLLEIVTEPVMHSPKEARLFLNKLRIILEY 182

Query: 178 TGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLL 237
             V D  + EG++R DAN+S++       G + E+KN++SF  V+K L +E  RQ  ++ 
Sbjct: 183 LDVFDGSL-EGAMRVDANVSIKG------GGRVEIKNISSFKGVEKALSYEITRQRNLIR 235

Query: 238 SGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELP 297
            G  +++ETR +DEA   T+ +R KE   DYRYFPEPDLV +Y   E  E VK ++PE+P
Sbjct: 236 RGRAVRRETRHFDEANNITVSLRGKEEEQDYRYFPEPDLVPVY-TSELLEEVKGTLPEMP 294

Query: 298 DERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQ 357
           +E+R+R+I++ G +   A VL L  +MA++FEE V      + A++W++  +   LN   
Sbjct: 295 EEKRERFIKQYGLSDAFAKVLVLDVKMANYFEE-VASVINPRLAASWIVDVLRGELNYRS 353

Query: 358 KE--LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISD 415
            +  +A   L PE +A ++K  E+  I+ K   +V +  +++GG+ ++I++ KGL  I  
Sbjct: 354 WDFGMAFERLKPEEMAKLLKYFEEERITEKGVVEVIRTKLDEGGEIDEIIEAKGLFAI-P 412

Query: 416 EGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLE 471
           +  + +L  EA++NNP+++ED+++GK +A+ FLVGQ+MKA++G+A+P    KI+ E
Sbjct: 413 KSEIERLCREAIENNPKAVEDYRSGKKQALNFLVGQVMKATRGRADPGETAKIMKE 468


Lambda     K      H
   0.314    0.134    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: 625
Number of extensions: 29
Number of successful extensions: 8
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: 476
Length of database: 471
Length adjustment: 33
Effective length of query: 443
Effective length of database: 438
Effective search space:   194034
Effective search space used:   194034
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_013684372.1 ARCVE_RS08530 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.10172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-197  641.3   0.0   4.8e-197  641.1   0.0    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013684372.1  ARCVE_RS08530 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013684372.1  ARCVE_RS08530 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.1   0.0  4.8e-197  4.8e-197       5     480 ..       3     470 ..       1     471 [] 0.98

  Alignments for each domain:
  == domain 1  score: 641.1 bits;  conditional E-value: 4.8e-197
                                 TIGR00133   5 elviGlEvHvqln.tksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                               ++viGlEvHvqln +++KlFc+c+ +++e++pNt+vcpvclg+PGa+Pv+N+eavk+A+k+alal++ i
  lcl|NCBI__GCF_000194625.1:WP_013684372.1   3 DVVIGLEVHVQLNkLNTKLFCSCPINYHESEPNTHVCPVCLGMPGAMPVVNREAVKAAIKVALALHADI 71 
                                               79***********99*****************************************************6 PP

                                 TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk. 140
                                               +  ++vFdRK+YfYpDlPkg+qi+q+d+P+a +G+++ie++++ek+i ++r+h+EeD+gk++yk+s + 
  lcl|NCBI__GCF_000194625.1:WP_013684372.1  72 Q-SFTVFDRKNYFYPDLPKGFQISQYDRPLAWGGYVTIEVDGEEKKIALKRIHMEEDPGKLSYKGSITt 139
                                               5.6***************************************************************987 PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               +++sl+D+NRsgvPLlEiVt+P+++s+kear fl+klr il+yl+++dg l eG+mRvD+Nvsi+    
  lcl|NCBI__GCF_000194625.1:WP_013684372.1 140 ARYSLIDYNRSGVPLLEIVTEPVMHSPKEARLFLNKLRIILEYLDVFDGSL-EGAMRVDANVSIK---- 203
                                               99*************************************************.9************.... PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                                  g rvEiKN++s+k++eka++yEi+Rq +l+++g+ v +etr+fde+++itvslR Kee++DYRYfp
  lcl|NCBI__GCF_000194625.1:WP_013684372.1 204 --GGGRVEIKNISSFKGVEKALSYEITRQRNLIRRGRAVRRETRHFDEANNITVSLRGKEEEQDYRYFP 270
                                               ..99***************************************************************** PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkl 347
                                               ePdl+p+  +e  ++e v+++lpe+Pe+kr+r+ k+ygls+ +akvlv d++++++feev+++i++ +l
  lcl|NCBI__GCF_000194625.1:WP_013684372.1 271 EPDLVPVYTSEL-LEE-VKGTLPEMPEEKRERFIKQYGLSDAFAKVLVLDVKMANYFEEVASVINP-RL 336
                                               ******887776.577.9**********************************************98.9* PP

                                 TIGR00133 348 avnWileellgeLnkkkislaea..llkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               a++Wi++ l+geLn++++++  a   lkpee+a+l+k+++e++i++k + e++++ l+++++++++ie+
  lcl|NCBI__GCF_000194625.1:WP_013684372.1 337 AASWIVDVLRGELNYRSWDFGMAfeRLKPEEMAKLLKYFEEERITEKGVVEVIRTKLDEGGEIDEIIEA 405
                                               *******************9887779******************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +gl++i +  e+ ++++e+i++npk+ve+y+sgk++al+flvGqvmk t+gradp e++k++ke+l
  lcl|NCBI__GCF_000194625.1:WP_013684372.1 406 KGLFAIPKS-EIERLCREAIENNPKAVEDYRSGKKQALNFLVGQVMKATRGRADPGETAKIMKEIL 470
                                               ******987.9*****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (471 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: 00:00:00.02
# Mc/sec: 8.41
//
[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