Alignments for a candidate for gatB in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfuromonas acetexigens

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_092055667.1 BQ4888_RS07085 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_900111775.1:WP_092055667.1
          Length = 482

 Score =  471 bits (1212), Expect = e-137
 Identities = 235/476 (49%), Positives = 322/476 (67%), Gaps = 6/476 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIGLEVHV+L T +K+F   P  FG  PNS T  + L  PG LPV+NK+ V++A+R 
Sbjct: 5   YEVVIGLEVHVQLTTKTKIFCGCPTEFGQAPNSQTCPVCLGLPGALPVLNKQVVEYAIRT 64

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVD-GETKRIGITRL 121
            +A +  IA  S   RKNYFYPD PK YQISQF+ PI E+G+++IE + G  K IGITR+
Sbjct: 65  GLATHCTIAPRSVMARKNYFYPDLPKGYQISQFELPICEHGHLEIETEEGGPKTIGITRI 124

Query: 122 HMEEDAGKSTHKGE-----YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176
           HMEEDAGK  H         S VDLNR  TPL+EIVSEPD+RS  EA AYL+KL  I+ Y
Sbjct: 125 HMEEDAGKLIHGDTPETVGASFVDLNRACTPLLEIVSEPDMRSSDEAIAYLKKLHQIVVY 184

Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236
            GV D  +E+GS RCDAN+S+RP+GQ++ GT+AELKN+NSF ++++ +EYE +RQ E + 
Sbjct: 185 LGVCDGNLEQGSFRCDANVSIRPWGQKELGTRAELKNINSFRFIKQAIEYEIERQIEVIE 244

Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
            GG++ QETR FD + G T  MR KE + DYRYFP+PD+VP+ +   W E  RQ +PELP
Sbjct: 245 DGGKVVQETRLFDANAGTTRSMRGKEEAHDYRYFPDPDLVPIVVSPEWIESARQELPELP 304

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356
           + ++ ++V E GL  YDA VLT  + M D+F++ +    D K  +NW+MG V   LN   
Sbjct: 305 EAKQERFVREYGLSLYDAEVLTAERAMGDYFDACVRLHDDGKACANWVMGEVQRRLNDEG 364

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           + +    ++PE L GM+K I+D T+S KIAK VF  +   G +A  I+++ GL Q++D  
Sbjct: 365 ISIAKAPVSPELLVGMLKRIDDNTISGKIAKTVFDAMWTSGKSADTIIDEQGLKQVTDTG 424

Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   +++ +  N   VE+Y+ GK K  GF VGQ+MKAS+G+ANP  VN+LLK++L
Sbjct: 425 AIEAIIDQIITANPGQVEEYRGGKEKVFGFFVGQVMKASQGKANPAAVNELLKKKL 480


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: 669
Number of extensions: 30
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: 482
Length adjustment: 34
Effective length of query: 441
Effective length of database: 448
Effective search space:   197568
Effective search space used:   197568
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_092055667.1 BQ4888_RS07085 (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.16839.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-192  626.7   0.0   1.3e-192  626.5   0.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092055667.1  BQ4888_RS07085 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092055667.1  BQ4888_RS07085 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 !  626.5   0.0  1.3e-192  1.3e-192       2     480 ..       3     480 ..       2     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 626.5 bits;  conditional E-value: 1.3e-192
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                                +ye+viGlEvHvql tk+K+Fc c++e+ +  pN+++cpvclglPGalPvlNk++v+ A+  +la+++
  lcl|NCBI__GCF_900111775.1:WP_092055667.1   3 SKYEVVIGLEVHVQLTTKTKIFCGCPTEFGQ-APNSQTCPVCLGLPGALPVLNKQVVEYAIRTGLATHC 70 
                                               589****************************.9************************************ PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                                 +++ sv +RK+YfYpDlPkgyqi+q++lPi+e+G+leie+ee+  k+igi+r+h+EeD+gk+ +  +
  lcl|NCBI__GCF_900111775.1:WP_092055667.1  71 T-IAPRSVMARKNYFYPDLPKGYQISQFELPICEHGHLEIETEEGGpKTIGITRIHMEEDAGKLIHGDT 138
                                               *.668************************************987655*******************988 PP

                                 TIGR00133 139 dk.dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirl 206
                                                +    s+vD+NR+++PLlEiV++Pd++s++ea a+lkkl+qi+ yl++ dg+le+Gs+R+D+Nvsir+
  lcl|NCBI__GCF_900111775.1:WP_092055667.1 139 PEtVGASFVDLNRACTPLLEIVSEPDMRSSDEAIAYLKKLHQIVVYLGVCDGNLEQGSFRCDANVSIRP 207
                                               7746789************************************************************** PP

                                 TIGR00133 207 kGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275
                                                Gq++ gtr+E+KN+ns++ i++aieyEieRq++++++g +v+qetr fd +  +t s+R Kee++DYR
  lcl|NCBI__GCF_900111775.1:WP_092055667.1 208 WGQKELGTRAELKNINSFRFIKQAIEYEIERQIEVIEDGGKVVQETRLFDANAGTTRSMRGKEEAHDYR 276
                                               ********************************************************************* PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               Yfp+Pdl+pi++++e++++  +++lpelPeak++r+++eygls +da+vl++++ + d+f+  v+l ++
  lcl|NCBI__GCF_900111775.1:WP_092055667.1 277 YFPDPDLVPIVVSPEWIES-ARQELPELPEAKQERFVREYGLSLYDAEVLTAERAMGDYFDACVRLHDD 344
                                               ******************9.************************************************* PP

                                 TIGR00133 345 pklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                                k+ +nW++ e++++Ln++ is+a+a ++pe l+ ++k i++++is+k+ak++++ + + +k+++++i+
  lcl|NCBI__GCF_900111775.1:WP_092055667.1 345 GKACANWVMGEVQRRLNDEGISIAKAPVSPELLVGMLKRIDDNTISGKIAKTVFDAMWTSGKSADTIID 413
                                               ********************************************************************* PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ++gl q++d+ ++ +i++++i+ np++ve+y+ gkek+++f+vGqvmk ++g+a+p+ v++llk++l
  lcl|NCBI__GCF_900111775.1:WP_092055667.1 414 EQGLKQVTDTGAIEAIIDQIITANPGQVEEYRGGKEKVFGFFVGQVMKASQGKANPAAVNELLKKKL 480
                                               *****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (482 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.21
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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