Alignments for a candidate for gatB in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Denitrovibrio acetiphilus DSM 12809

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_013011690.1 DACET_RS12230 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000025725.1:WP_013011690.1
          Length = 474

 Score =  505 bits (1300), Expect = e-147
 Identities = 253/475 (53%), Positives = 346/475 (72%), Gaps = 2/475 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           MN+E VIGLEVHV++ T+SKIF +    FG+  NT    + LG PGVLPV+N++ +EF +
Sbjct: 1   MNYEPVIGLEVHVQMATESKIFCTCSNKFGSAPNTNVCPVCLGMPGVLPVMNEKVMEFTV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119
           KA +ALNCEI   + F RKNYFYPD PKAYQISQ++ PI ENG+I+IE+  G  KRIGIT
Sbjct: 61  KAGLALNCEIRNKSVFARKNYFYPDLPKAYQISQYELPICENGYIDIELEDGTQKRIGIT 120

Query: 120 RLHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
           R+H+EEDAGKL H+ DG S VD NR GTPL+EIVSEPD+R+ EEA AYL+K+K+I++Y  
Sbjct: 121 RIHIEEDAGKLVHSADG-SGVDLNRTGTPLMEIVSEPDLRSAEEAKAYLQKVKTILKYVE 179

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           VSDC MEEGS+RCDAN+SLRP+G+E+FGT+ E+KN+NSF  V++ +++EEKRQ ++L  G
Sbjct: 180 VSDCNMEEGSMRCDANVSLRPVGREKFGTRAEIKNVNSFKNVERAIKYEEKRQAKLLDEG 239

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             + QETR ++  T  T  MR KE + DYRYFP+PDLV L +++E+ + +K S+PELPD 
Sbjct: 240 GTVVQETRLFNADTGTTASMRGKEDAHDYRYFPDPDLVPLVLENEFIDNIKNSLPELPDA 299

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359
           R KR++EE    AYDA  LT  K  A+FFE  ++     K  SN +M E+  + N +Q E
Sbjct: 300 RMKRFMEEFSLPAYDAAFLTSEKNYAEFFETALKAHNNPKGISNLIMTELMRHANDKQCE 359

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           + +  ++PE LA ++KL++ GTIS  I+KK+F+E++E G     IV+EKG+ Q SDEG L
Sbjct: 360 INEAGISPENLAEIVKLLDSGTISGNISKKLFEEVLESGKKPSVIVEEKGMAQNSDEGEL 419

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIK 474
            K+V + +D NP   E F+ G  +  GF +GQIM+ASKG+ANP +V ++L + IK
Sbjct: 420 EKIVKQVIDANPDETERFRAGDKKLQGFFMGQIMRASKGKANPGVVTQLLNKLIK 474


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: 651
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: 476
Length of database: 474
Length adjustment: 33
Effective length of query: 443
Effective length of database: 441
Effective search space:   195363
Effective search space used:   195363
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_013011690.1 DACET_RS12230 (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.1312239.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.3e-187  607.2   0.3     1e-186  607.1   0.3    1.0  1  NCBI__GCF_000025725.1:WP_013011690.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013011690.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.1   0.3    1e-186    1e-186       2     480 ..       1     473 [.       1     474 [] 0.98

  Alignments for each domain:
  == domain 1  score: 607.1 bits;  conditional E-value: 1e-186
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           ++ye viGlEvHvq+ t+sK+Fc+csn++ +  pNtnvcpvclg+PG+lPv+N++++++ +k +laln++ ++
  NCBI__GCF_000025725.1:WP_013011690.1   1 MNYEPVIGLEVHVQMATESKIFCTCSNKFGS-APNTNVCPVCLGMPGVLPVMNEKVMEFTVKAGLALNCE-IR 71 
                                           689****************************.9*************************************.67 PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslv 146
                                           ++svF+RK+YfYpDlPk+yqi+q++lPi+e+G+++iele++  k+igi+r+h+EeD+gk+++  +     s v
  NCBI__GCF_000025725.1:WP_013011690.1  72 NKSVFARKNYFYPDLPKAYQISQYELPICENGYIDIELEDGTqKRIGITRIHIEEDAGKLVHSAD----GSGV 140
                                           8************************************9886559******************966....599* PP

                             TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiK 219
                                           D+NR+g+PL+EiV++Pdl+sa+ea+a+l+k+++il+y+e+sd+++eeGsmR+D+Nvs+r++G+ek+gtr+EiK
  NCBI__GCF_000025725.1:WP_013011690.1 141 DLNRTGTPLMEIVSEPDLRSAEEAKAYLQKVKTILKYVEVSDCNMEEGSMRCDANVSLRPVGREKFGTRAEIK 213
                                           ************************************************************************* PP

                             TIGR00133 220 NlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevv 292
                                           N+ns+k++e+ai+yE +Rq kll +g +v+qetr f+  + +t s+R Ke+++DYRYfp+Pdl+p+++++e++
  NCBI__GCF_000025725.1:WP_013011690.1 214 NVNSFKNVERAIKYEEKRQAKLLDEGGTVVQETRLFNADTGTTASMRGKEDAHDYRYFPDPDLVPLVLENEFI 286
                                           ************************************************************************* PP

                             TIGR00133 293 kekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkki 365
                                           ++ +++ lpelP+a+ +r+++e+ l ++da  l+s++++++ fe++ k+ ++pk   n i++el+++ n+k++
  NCBI__GCF_000025725.1:WP_013011690.1 287 DN-IKNSLPELPDARMKRFMEEFSLPAYDAAFLTSEKNYAEFFETALKAHNNPKGISNLIMTELMRHANDKQC 358
                                           *9.9********************************************************************* PP

                             TIGR00133 366 slaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenp 438
                                           +++ea ++pe+lae++kl++ g+is+ ++k+l+ee+le +k+p+ ++e++g+ q sde el kiv++vi+ np
  NCBI__GCF_000025725.1:WP_013011690.1 359 EINEAGISPENLAEIVKLLDSGTISGNISKKLFEEVLESGKKPSVIVEEKGMAQNSDEGELEKIVKQVIDANP 431
                                           ************************************************************************* PP

                             TIGR00133 439 kevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +e+e++++g +k+++f++Gq+m+ +kg+a+p  v++ll++l+
  NCBI__GCF_000025725.1:WP_013011690.1 432 DETERFRAGDKKLQGFFMGQIMRASKGKANPGVVTQLLNKLI 473
                                           **************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (474 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.16
//
[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