GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Thioalkalivibrio halophilus HL17

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_077244139.1 B1A74_RS06555 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_001995255.1:WP_077244139.1
          Length = 478

 Score =  488 bits (1257), Expect = e-142
 Identities = 240/477 (50%), Positives = 337/477 (70%), Gaps = 3/477 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +ETVIGLE+H +L T SK+FS +P  +GAEPN     +DL  PGVLPV+N+  V+ A+
Sbjct: 1   MEWETVIGLEIHAQLNTVSKIFSGAPTAYGAEPNRQACPVDLGMPGVLPVLNRGVVERAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +AL+ E+A  S F RKNYFYPD PK YQISQF+ PI  +G++DIE+ DG TKRIG+T
Sbjct: 61  MLGLALDAEVAGRSVFARKNYFYPDLPKGYQISQFELPIVASGHLDIELEDGSTKRIGVT 120

Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+G  ++  +DLNR GTPL+EIVSEPD+RS KEA AY++KL S+++Y 
Sbjct: 121 RAHLEEDAGKSLHEGFEAMTGIDLNRAGTPLVEIVSEPDLRSAKEAVAYMKKLHSLVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
            + D  M+EGS RCDAN+S+RP GQ +FGT+AELKNLNSF +V + + +E +RQ + +  
Sbjct: 181 DICDGNMQEGSFRCDANVSIRPKGQAEFGTRAELKNLNSFRFVERAINFEIERQIDVIEG 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG + QETR +D    +T  MR KE ++DYRYFP+PD++P+ +D  + E +R  +PELPD
Sbjct: 241 GGRVVQETRLYDPDRDETRSMRTKEEANDYRYFPDPDLLPVEVDQDFIEEIRGRLPELPD 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
            ++ ++V E  LP YDA VLT T+EM DF+E+ +      KL +NW+MG  +  LN+++V
Sbjct: 301 AKRERFVREYELPEYDAGVLTATREMGDFYEAVVRGCNAPKLAANWVMGEFSAALNRSEV 360

Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417
           EL +  +    LAG++  I+D T+S KIAK+VF  +    G+A  ++E  GL QI+D   
Sbjct: 361 ELAEAPVDAGALAGLLARIQDETISGKIAKEVFEAMWNGEGDADSVIEAKGLKQITDTGA 420

Query: 418 LLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELDK 474
           +   ++E + NN + +E YK GK K  GF VGQ+MKA++G+ANP  VN+ LK+ LD+
Sbjct: 421 IDAIIDEVIANNPKQLEQYKGGKDKLFGFFVGQVMKATQGKANPAQVNERLKERLDQ 477


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: 636
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: 475
Length of database: 478
Length adjustment: 33
Effective length of query: 442
Effective length of database: 445
Effective search space:   196690
Effective search space used:   196690
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_077244139.1 B1A74_RS06555 (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.1774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.3e-185  601.0   0.0   8.3e-185  600.8   0.0    1.0  1  lcl|NCBI__GCF_001995255.1:WP_077244139.1  B1A74_RS06555 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001995255.1:WP_077244139.1  B1A74_RS06555 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.8   0.0  8.3e-185  8.3e-185       2     480 ..       1     475 [.       1     476 [. 0.99

  Alignments for each domain:
  == domain 1  score: 600.8 bits;  conditional E-value: 8.3e-185
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e viGlE+H qlnt sK+F+ +++ +   +pN++ cpv+lg+PG+lPvlN+ +v+ A++l+lal++
  lcl|NCBI__GCF_001995255.1:WP_077244139.1   1 MEWETVIGLEIHAQLNTVSKIFSGAPTAYGA-EPNRQACPVDLGMPGVLPVLNRGVVERAVMLGLALDA 68 
                                               57899************************99.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                               + v+  svF+RK+YfYpDlPkgyqi+q++lPi+  G+l+iele+++ k+ig++r hlEeD+gks +++ 
  lcl|NCBI__GCF_001995255.1:WP_077244139.1  69 E-VAGRSVFARKNYFYPDLPKGYQISQFELPIVASGHLDIELEDGStKRIGVTRAHLEEDAGKSLHEGF 136
                                               *.557************************************998766********************87 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                               +   ++ +D+NR+g+PL+EiV++Pdl+sakea+a++kkl++++ryl+i dg+++eGs+R+D+Nvsir+k
  lcl|NCBI__GCF_001995255.1:WP_077244139.1 137 E--AMTGIDLNRAGTPLVEIVSEPDLRSAKEAVAYMKKLHSLVRYLDICDGNMQEGSFRCDANVSIRPK 203
                                               5..799*************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               Gq ++gtr+E+KNlns++ +e+ai++EieRq+++++ g  v+qetr +d  +  t s+R Kee++DYRY
  lcl|NCBI__GCF_001995255.1:WP_077244139.1 204 GQAEFGTRAELKNLNSFRFVERAINFEIERQIDVIEGGGRVVQETRLYDPDRDETRSMRTKEEANDYRY 272
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fp+Pdl p+e+d+++++e ++++lpelP+akr+r+++ey+l e+da vl++ +e+ d +e vv+  + p
  lcl|NCBI__GCF_001995255.1:WP_077244139.1 273 FPDPDLLPVEVDQDFIEE-IRGRLPELPDAKRERFVREYELPEYDAGVLTATREMGDFYEAVVRGCNAP 340
                                               ******************.************************************************** PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               kla+nW++ e+ + Ln+++++laea +++ +la l++ i++++is+k+ake++e + + ++d++++ie+
  lcl|NCBI__GCF_001995255.1:WP_077244139.1 341 KLAANWVMGEFSAALNRSEVELAEAPVDAGALAGLLARIQDETISGKIAKEVFEAMWNGEGDADSVIEA 409
                                               ********************************************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +gl qi+d+ ++ +i++evi++npk++e+yk gk+k+++f+vGqvmk t+g+a+p++v++ lke+l
  lcl|NCBI__GCF_001995255.1:WP_077244139.1 410 KGLKQITDTGAIDAIIDEVIANNPKQLEQYKGGKDKLFGFFVGQVMKATQGKANPAQVNERLKERL 475
                                               ****************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 00:00:00.03
# Mc/sec: 7.65
//
[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:

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:

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:

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:

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