Alignments for a candidate for gatB in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Thioalkalivibrio denitrificans ALJD

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_077279617.1 B1C78_RS13075 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_002000365.1:WP_077279617.1
          Length = 477

 Score =  477 bits (1227), Expect = e-139
 Identities = 241/476 (50%), Positives = 335/476 (70%), Gaps = 4/476 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +ETVIGLEVH +L T SK+FS +   +GA PNS    +DL  PGVLPV+N+ AV  A+
Sbjct: 1   MDWETVIGLEVHAQLATKSKIFSGASTAYGAAPNSQACAVDLGLPGVLPVLNREAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
           +  +A++ EIA  S F RKNYFYPD PK YQISQ++ P+   G I+IE+ DGETK IGIT
Sbjct: 61  KFGLAIDAEIAPRSVFARKNYFYPDLPKGYQISQYELPVVGLGRIEIELEDGETKTIGIT 120

Query: 120 RLHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+  + +  +DLNR GTPL+EIVSEPD+RS KEA AYL+KL ++++Y 
Sbjct: 121 RAHLEEDAGKSLHEDFHGMSGIDLNRAGTPLLEIVSEPDMRSAKEAVAYLKKLHALVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
            + D  M+EGS RCDAN+S+R  G EKFGT+AE+KN+NSF +V + + +E +RQ + L  
Sbjct: 181 EICDGNMQEGSFRCDANVSVRRKGTEKFGTRAEIKNINSFRFVERAINFEVERQIDILEG 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG + QETR FD   G+T  MR KE ++DYRYFP+PD++PL ID  + E VR T+PELPD
Sbjct: 241 GGAVVQETRLFDPDKGETRSMRSKEEANDYRYFPDPDLLPLEIDSGFIEAVRGTLPELPD 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEH-GADVKLTSNWLMGGVNEYLNKNQ 356
           E+K +++   GL AYDA VLT ++EM D++E+ ++  G   KL +NW+MG ++  LNK+ 
Sbjct: 301 EKKHRFMTHYGLSAYDAGVLTASREMGDYYEAVVKACGGHAKLAANWVMGELSAALNKDN 360

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
            E+ ++ ++ E L  M+  IED T+S KIAK VF  +    G+A +++E  GL QI+D  
Sbjct: 361 REITESPVSAEALGRMLARIEDNTISGKIAKDVFEAMWNGEGSADEVIEKKGLKQITDTG 420

Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   +++ + +N   +E Y+ GK K  GF VGQ+MKA+ G+ANP  VN LLK++L
Sbjct: 421 AIETIIDKVIADNPSQLEQYRAGKDKLFGFFVGQVMKATGGKANPAQVNDLLKRKL 476


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: 627
Number of extensions: 27
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: 475
Length of database: 477
Length adjustment: 33
Effective length of query: 442
Effective length of database: 444
Effective search space:   196248
Effective search space used:   196248
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_077279617.1 B1C78_RS13075 (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.2579739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-183  596.7   0.0   1.6e-183  596.5   0.0    1.0  1  NCBI__GCF_002000365.1:WP_077279617.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002000365.1:WP_077279617.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.5   0.0  1.6e-183  1.6e-183       2     480 ..       1     476 [.       1     477 [] 0.98

  Alignments for each domain:
  == domain 1  score: 596.5 bits;  conditional E-value: 1.6e-183
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +++e viGlEvH ql tksK+F+ +s+ +    pN++ c+v+lglPG+lPvlN+eav++A+k +la++++ ++
  NCBI__GCF_002000365.1:WP_077279617.1   1 MDWETVIGLEVHAQLATKSKIFSGASTAYGA-APNSQACAVDLGLPGVLPVLNREAVRMAVKFGLAIDAE-IA 71 
                                           57899************************99.9*************************************.66 PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslv 146
                                           + svF+RK+YfYpDlPkgyqi+q++lP++  G++eiele++e k+igi+r hlEeD+gks ++    + +s +
  NCBI__GCF_002000365.1:WP_077279617.1  72 PRSVFARKNYFYPDLPKGYQISQYELPVVGLGRIEIELEDGEtKTIGITRAHLEEDAGKSLHEDF--HGMSGI 142
                                           8*************************************99877*******************944..689*** PP

                             TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiK 219
                                           D+NR+g+PLlEiV++Pd++sakea+a+lkkl++++rylei dg+++eGs+R+D+Nvs+r kG+ek+gtr+EiK
  NCBI__GCF_002000365.1:WP_077279617.1 143 DLNRAGTPLLEIVSEPDMRSAKEAVAYLKKLHALVRYLEICDGNMQEGSFRCDANVSVRRKGTEKFGTRAEIK 215
                                           ************************************************************************* PP

                             TIGR00133 220 NlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevv 292
                                           N+ns++ +e+ai++E+eRq+++l+ g  v+qetr fd  k  t s+R+Kee++DYRYfp+Pdl p+eid  ++
  NCBI__GCF_002000365.1:WP_077279617.1 216 NINSFRFVERAINFEVERQIDILEGGGAVVQETRLFDPDKGETRSMRSKEEANDYRYFPDPDLLPLEIDSGFI 288
                                           ************************************************************************* PP

                             TIGR00133 293 kekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.klavnWileellgeLnkkk 364
                                           +  v+++lpelP++k++r++++ygls++da vl++ +e+ d++e vvk+ + + kla+nW++ el + Lnk +
  NCBI__GCF_002000365.1:WP_077279617.1 289 EA-VRGTLPELPDEKKHRFMTHYGLSAYDAGVLTASREMGDYYEAVVKACGGHaKLAANWVMGELSAALNKDN 360
                                           99.********************************************9976554******************* PP

                             TIGR00133 365 islaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveeviken 437
                                            +++e+ +++e+l ++++ i++++is+k+ak+++e + + +++++++iek+gl qi+d+ ++  i+++vi++n
  NCBI__GCF_002000365.1:WP_077279617.1 361 REITESPVSAEALGRMLARIEDNTISGKIAKDVFEAMWNGEGSADEVIEKKGLKQITDTGAIETIIDKVIADN 433
                                           ************************************************************************* PP

                             TIGR00133 438 pkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           p ++e+y++gk+k+++f+vGqvmk t g+a+p++v+ llk +l
  NCBI__GCF_002000365.1:WP_077279617.1 434 PSQLEQYRAGKDKLFGFFVGQVMKATGGKANPAQVNDLLKRKL 476
                                           ****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (477 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: 19.40
//
[ok]

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