Alignments for a candidate for gatB in Methylohalobius crimeensis 10Ki

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylohalobius crimeensis 10Ki

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_022949812.1 H035_RS0115175 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000421465.1:WP_022949812.1
          Length = 478

 Score =  481 bits (1237), Expect = e-140
 Identities = 242/475 (50%), Positives = 332/475 (69%), Gaps = 3/475 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+HV+L+T SK+FS +   +GA PNS    IDL  PGVLPV+N+ AV  A+
Sbjct: 1   MEWEPVIGLEIHVQLQTKSKIFSGASTAYGAAPNSQACAIDLGMPGVLPVLNEAAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120
           +  +A+   IA  S F RKNYFYPD PK YQISQ++ P+   G++ I +DG  KRIGITR
Sbjct: 61  KFGLAVEAHIAPRSVFARKNYFYPDLPKGYQISQYELPVVGKGHLMIHLDGLEKRIGITR 120

Query: 121 LHMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTG 178
            H+EEDAGKS H+  + +  +DLNR GTPL+EIVSEPD+RSP+EA AY++KL  ++ Y G
Sbjct: 121 AHLEEDAGKSLHEDFHGMTGIDLNRAGTPLLEIVSEPDMRSPEEAVAYMKKLHQLVVYLG 180

Query: 179 VSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG 238
           + D  ++EGS RCDAN+S+RP G+EKFGT+AE+KN+NSF +V + + YE +RQ E L SG
Sbjct: 181 ICDGNLQEGSFRCDANVSVRPTGEEKFGTRAEIKNVNSFRFVERAISYEIERQIELLESG 240

Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298
           G + QETR +D    +T  MR KE ++DYRYFP+PD++PL IDD + E VR+ +PELP+ 
Sbjct: 241 GTVVQETRLYDAVKDETRSMRAKEEANDYRYFPDPDLLPLVIDDGFVEAVRRELPELPEA 300

Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIE-HGADVKLTSNWLMGGVNEYLNKNQV 357
           +  +++++ GL  YDA VLT ++ +SD+FE TIE  G D KL +NW+M  V   LNK  +
Sbjct: 301 KYHRFIDQYGLKPYDAEVLTASRPLSDYFEKTIELSGGDPKLCANWVMVEVAGALNKAGL 360

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

Query: 418 LLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           +   ++E + NN   V  Y  GK K  GF VGQ+MKA+ G+ANPQ VN+LLK +L
Sbjct: 421 IEGIIDEIIANNPNQVAQYLAGKDKLFGFFVGQVMKATSGKANPQQVNELLKAKL 475


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: 19
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_022949812.1 H035_RS0115175 (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.19596.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-184  599.0   0.0   3.3e-184  598.8   0.0    1.0  1  lcl|NCBI__GCF_000421465.1:WP_022949812.1  H035_RS0115175 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022949812.1  H035_RS0115175 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 !  598.8   0.0  3.3e-184  3.3e-184       3     480 ..       2     475 ..       1     476 [. 0.98

  Alignments for each domain:
  == domain 1  score: 598.8 bits;  conditional E-value: 3.3e-184
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               e+e viGlE+Hvql+tksK+F+ +s+ +    pN++ c+++lg+PG+lPvlN+ av++A+k +la++++
  lcl|NCBI__GCF_000421465.1:WP_022949812.1   2 EWEPVIGLEIHVQLQTKSKIFSGASTAYGA-APNSQACAIDLGMPGVLPVLNEAAVRMAVKFGLAVEAH 69 
                                               7889************************99.9************************************* PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                +++ svF+RK+YfYpDlPkgyqi+q++lP++ +G+l i+l++ ek+igi+r hlEeD+gks ++    
  lcl|NCBI__GCF_000421465.1:WP_022949812.1  70 -IAPRSVFARKNYFYPDLPKGYQISQYELPVVGKGHLMIHLDGLEKRIGITRAHLEEDAGKSLHEDF-- 135
                                               .668************************************************************944.. PP

                                 TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209
                                               + ++ +D+NR+g+PLlEiV++Pd++s++ea+a++kkl+q++ yl+i dg+l+eGs+R+D+Nvs+r+ G+
  lcl|NCBI__GCF_000421465.1:WP_022949812.1 136 HGMTGIDLNRAGTPLLEIVSEPDMRSPEEAVAYMKKLHQLVVYLGICDGNLQEGSFRCDANVSVRPTGE 204
                                               5899***************************************************************** PP

                                 TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278
                                               ek+gtr+EiKN+ns++ +e+ai+yEieRq++ll++g +v+qetr +d  k  t s+R Kee++DYRYfp
  lcl|NCBI__GCF_000421465.1:WP_022949812.1 205 EKFGTRAEIKNVNSFRFVERAISYEIERQIELLESGGTVVQETRLYDAVKDETRSMRAKEEANDYRYFP 273
                                               ********************************************************************* PP

                                 TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkli.kepk 346
                                               +Pdl p++id+ +v+  v+ +lpelPeak +r+  +ygl+ +da+vl++ + l d+fe+  +l+ ++pk
  lcl|NCBI__GCF_000421465.1:WP_022949812.1 274 DPDLLPLVIDDGFVEA-VRRELPELPEAKYHRFIDQYGLKPYDAEVLTASRPLSDYFEKTIELSgGDPK 341
                                               *************999.*****************************************9877651688* PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               l +nW++ e++g Lnk  ++++ + +++e la l+k i +++is+k+ak+++e + e  k++++lie++
  lcl|NCBI__GCF_000421465.1:WP_022949812.1 342 LCANWVMVEVAGALNKAGLDITRTPVTAERLAGLLKRIADNTISGKIAKQVFELMWESDKEADALIEEK 410
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl qi+d+ ++  i++e+i++np++v +y++gk+k+++f+vGqvmk t+g+a+p++v++llk +l
  lcl|NCBI__GCF_000421465.1:WP_022949812.1 411 GLKQITDTGAIEGIIDEIIANNPNQVAQYLAGKDKLFGFFVGQVMKATSGKANPQQVNELLKAKL 475
                                               **************************************************************988 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: 7.03
//
[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