Alignments for a candidate for gatB in Maridesulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Maridesulfovibrio bastinii DSM 16055

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_027180111.1 G496_RS0115770 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000429985.1:WP_027180111.1
          Length = 481

 Score =  472 bits (1215), Expect = e-137
 Identities = 237/479 (49%), Positives = 327/479 (68%), Gaps = 6/479 (1%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           + FETVIGLEVH +LKTKSKIF    T FG + N     I  G PGVLPVLN++ VE+A 
Sbjct: 2   VQFETVIGLEVHAQLKTKSKIFCGCSTEFGKDPNENVCEICSGMPGVLPVLNEKVVEYAA 61

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKT-----KR 115
           K  +A NC +   + F RKNYFYPD PK YQISQF+ PI E+G ++I +G  T     KR
Sbjct: 62  KMGLATNCTVNKKSVFARKNYFYPDLPKGYQISQFELPICEHGHVDIVLGADTDNPVTKR 121

Query: 116 IGITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSI 174
           +G+TR+H+EEDAGK  H+  +  S VD NR G PL+EIVSEPD+R+ EEA AYL+ L+SI
Sbjct: 122 VGLTRIHIEEDAGKNIHSAAENASYVDLNRTGVPLIEIVSEPDMRSAEEAVAYLKTLRSI 181

Query: 175 IQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQ 234
           + Y G+ D  MEEGS RCDAN+S+RP+GQEEFGT+ ELKNLNSF  VQK +++E  RQ  
Sbjct: 182 LLYLGICDGNMEEGSFRCDANVSVRPMGQEEFGTRAELKNLNSFRHVQKAIQYEVGRQID 241

Query: 235 VLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIP 294
           ++  G  + QETR YD A   T  MR KE + DYRYFP+PDLV + +DDEW    +  +P
Sbjct: 242 LVEDGEKVIQETRLYDAAKNITQSMRGKEEAHDYRYFPDPDLVPIVLDDEWLGDWQMQLP 301

Query: 295 ELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLN 354
           ELP ER++R+ ++ G +  DA  LT  KE+AD++E  V+   E K+ +NW+MG+    ++
Sbjct: 302 ELPAERKQRFEDDYGLSLQDAEFLTSEKELADYYEAAVENYNEPKKVANWIMGDFVHEVH 361

Query: 355 AEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQIS 414
                +A+ +  PE LA +++++++  IS+KI K +F ++  +G D EK VKEKGLVQIS
Sbjct: 362 QSDVSIAETSFKPELLAKLVRMVDEDQISNKIGKDIFPDIFAEGLDPEKYVKEKGLVQIS 421

Query: 415 DEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEI 473
           D   L  +V + L  NP  +E +K GK + + F +GQIM+ +KGQANP +V+K++ +++
Sbjct: 422 DSSALEAVVDQVLAENPDEVEAYKGGKKKLVSFFMGQIMRKTKGQANPGIVSKMIQQKL 480


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: 653
Number of extensions: 32
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: 481
Length adjustment: 34
Effective length of query: 442
Effective length of database: 447
Effective search space:   197574
Effective search space used:   197574
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_027180111.1 G496_RS0115770 (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.1318439.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-191  621.5   0.0   4.8e-191  621.3   0.0    1.0  1  NCBI__GCF_000429985.1:WP_027180111.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429985.1:WP_027180111.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.3   0.0  4.8e-191  4.8e-191       1     480 [.       1     480 [.       1     481 [] 0.98

  Alignments for each domain:
  == domain 1  score: 621.3 bits;  conditional E-value: 4.8e-191
                             TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                           ++++e viGlEvH ql tksK+Fc cs+e+ +  pN+nvc +c g+PG+lPvlN+++v+ A k++la+n+ ++
  NCBI__GCF_000429985.1:WP_027180111.1   1 MVQFETVIGLEVHAQLKTKSKIFCGCSTEFGK-DPNENVCEICSGMPGVLPVLNEKVVEYAAKMGLATNCTVN 72 
                                           6799***************************9.9*************************************66 PP

                             TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgksqykesdkd 141
                                            ++svF+RK+YfYpDlPkgyqi+q++lPi+e+G+++i l ++      k++g++r+h+EeD+gk+ +     +
  NCBI__GCF_000429985.1:WP_027180111.1  73 -KKSVFARKNYFYPDLPKGYQISQFELPICEHGHVDIVLGADTdnpvtKRVGLTRIHIEEDAGKNIHSAA--E 142
                                           .6***********************************99887788999*******************976..5 PP

                             TIGR00133 142 kqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegt 214
                                           + s+vD+NR+gvPL+EiV++Pd++sa+ea+a+lk lr+il yl+i dg++eeGs+R+D+Nvs+r++Gqe++gt
  NCBI__GCF_000429985.1:WP_027180111.1 143 NASYVDLNRTGVPLIEIVSEPDMRSAEEAVAYLKTLRSILLYLGICDGNMEEGSFRCDANVSVRPMGQEEFGT 215
                                           8************************************************************************ PP

                             TIGR00133 215 rvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppiei 287
                                           r+E+KNlns++ ++kai+yE+ Rq++l+++ge+v qetr +d +k+it s+R Kee++DYRYfp+Pdl+pi++
  NCBI__GCF_000429985.1:WP_027180111.1 216 RAELKNLNSFRHVQKAIQYEVGRQIDLVEDGEKVIQETRLYDAAKNITQSMRGKEEAHDYRYFPDPDLVPIVL 288
                                           ************************************************************************* PP

                             TIGR00133 288 deevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeL 360
                                           d+e++ + ++ +lpelP ++++r++ +ygls +da+ l+s++el+d++e +v++ +epk+++nWi+ +++ e+
  NCBI__GCF_000429985.1:WP_027180111.1 289 DDEWLGD-WQMQLPELPAERKQRFEDDYGLSLQDAEFLTSEKELADYYEAAVENYNEPKKVANWIMGDFVHEV 360
                                           ****988.***************************************************************** PP

                             TIGR00133 361 nkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveev 433
                                           +++++s+ae+ +kpe la+l+++++e++is+k++k+++  ++ ++ dp+k ++++gl+qisd ++l ++v++v
  NCBI__GCF_000429985.1:WP_027180111.1 361 HQSDVSIAETSFKPELLAKLVRMVDEDQISNKIGKDIFPDIFAEGLDPEKYVKEKGLVQISDSSALEAVVDQV 433
                                           ************************************************************************* PP

                             TIGR00133 434 ikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           ++enp+eve yk gk+k++ f++Gq+m+ktkg+a+p  v k+++++l
  NCBI__GCF_000429985.1:WP_027180111.1 434 LAENPDEVEAYKGGKKKLVSFFMGQIMRKTKGQANPGIVSKMIQQKL 480
                                           *******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.10
//
[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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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