Alignments for a candidate for gatB in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Rhodomicrobium vannielii ATCC 17100

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_013419229.1 RVAN_RS07950 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000166055.1:WP_013419229.1
          Length = 491

 Score =  422 bits (1084), Expect = e-122
 Identities = 214/472 (45%), Positives = 316/472 (66%), Gaps = 5/472 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E ++G+EVH ++ +++K+FS + A FG EPNS+ +++D A PG+LPV+N   V  A+R 
Sbjct: 17  WEVIVGMEVHAQVLSNAKLFSGASAAFGGEPNSHVSLVDAAMPGMLPVINVECVKQAIRT 76

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122
            + L  +I   S FDRKNYFYPD P+ YQISQF  PI   G + +++   +  +GI RLH
Sbjct: 77  GLGLKAQINRRSVFDRKNYFYPDLPQGYQISQFKFPIVGEGIVTVDLKEYSFDVGIERLH 136

Query: 123 MEEDAGKSTH--KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180
           +E+DAGKS H    ++S VDLNR G  L+EIVS+PDIRS +EA AY+ KLR+I++Y G  
Sbjct: 137 LEQDAGKSLHDQDPDHSYVDLNRSGVALMEIVSKPDIRSSEEAKAYITKLRTILRYLGTC 196

Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240
           D  MEEGSLR D N+S+R  G    GT+ E+KN+NS  ++ + +EYE +RQ + +  GG 
Sbjct: 197 DGNMEEGSLRADVNVSVRKLG-APLGTRCEIKNVNSIRFIGQAIEYEARRQIDVIEDGGT 255

Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300
           I QETR FD  +GKT  MR KE + DYRYFP+PD++PL + +A+ E +++ +PELPDE++
Sbjct: 256 IKQETRLFDAKSGKTRPMRSKEEAHDYRYFPDPDLLPLEVSEAFVEDLKKVLPELPDEKR 315

Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360
           A++++E  L AYDA VL L +  +DF+E T+  G D KL +NW+MG     LNK   ++ 
Sbjct: 316 ARFMSEYALSAYDAGVLILDRASADFYE-TVARGRDPKLAANWMMGDFFAALNKTGKDIT 374

Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLK 420
           ++ ++   L  +I LI    +S +IAK+VF  +  KGG    I+E+ GL Q++D   + K
Sbjct: 375 ESPISAAQLGELIDLISSDVISGRIAKEVFEIMLDKGGTPGAIVEERGLKQVTDTGAIEK 434

Query: 421 FVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            V+E +  N + VE  +  K K + + VGQ+M+A+ G+ANP  VN LL+Q+L
Sbjct: 435 VVDEIIAANPKQVEQVQT-KPKTLSWFVGQVMRATGGKANPDAVNALLRQKL 485


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: 639
Number of extensions: 33
Number of successful extensions: 5
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: 491
Length adjustment: 34
Effective length of query: 441
Effective length of database: 457
Effective search space:   201537
Effective search space used:   201537
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: 52 (24.6 bits)

Align candidate WP_013419229.1 RVAN_RS07950 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.19385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.8e-168  544.8   0.0   9.5e-168  544.5   0.0    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013419229.1  RVAN_RS07950 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013419229.1  RVAN_RS07950 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.5   0.0  9.5e-168  9.5e-168       4     480 ..      17     485 ..      15     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 544.5 bits;  conditional E-value: 9.5e-168
                                 TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                               +e+++G+EvH q+  ++KlF+ +s  +   +pN++v+ v+ ++PG lPv+N e vk+A+  +l l+++i
  lcl|NCBI__GCF_000166055.1:WP_013419229.1  17 WEVIVGMEVHAQVLSNAKLFSGASAAFGG-EPNSHVSLVDAAMPGMLPVINVECVKQAIRTGLGLKAQI 84 
                                               689**************************.**************************************7 PP

                                 TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkd 141
                                               ++  svFdRK+YfYpDlP+gyqi+q+++Pi+ +G ++++l+e +  +gierlhlE+D+gks + ++  +
  lcl|NCBI__GCF_000166055.1:WP_013419229.1  85 NR-RSVFDRKNYFYPDLPQGYQISQFKFPIVGEGIVTVDLKEYSFDVGIERLHLEQDAGKSLHDQD--P 150
                                               75.9***********************************************************966..7 PP

                                 TIGR00133 142 kqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqe 210
                                               ++s+vD+NRsgv L+EiV+kPd++s++ea+a++ klr+ilryl+  dg++eeGs+R+DvNvs+r  G  
  lcl|NCBI__GCF_000166055.1:WP_013419229.1 151 DHSYVDLNRSGVALMEIVSKPDIRSSEEAKAYITKLRTILRYLGTCDGNMEEGSLRADVNVSVRKLG-A 218
                                               9***************************************************************666.5 PP

                                 TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpe 279
                                                 gtr EiKN+ns++ i +aieyE  Rq++++++g ++kqetr fd k+ +t  +R+Kee++DYRYfp+
  lcl|NCBI__GCF_000166055.1:WP_013419229.1 219 PLGTRCEIKNVNSIRFIGQAIEYEARRQIDVIEDGGTIKQETRLFDAKSGKTRPMRSKEEAHDYRYFPD 287
                                               799****************************************************************** PP

                                 TIGR00133 280 PdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkla 348
                                               Pdl p+e++e +v++ +++ lpelP++kr+r+++ey ls++da vl+ d+  +d +e+v++   +pkla
  lcl|NCBI__GCF_000166055.1:WP_013419229.1 288 PDLLPLEVSEAFVED-LKKVLPELPDEKRARFMSEYALSAYDAGVLILDRASADFYETVARGR-DPKLA 354
                                               *************99.9*************************************999988765.56*** PP

                                 TIGR00133 349 vnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgl 417
                                               +nW++ ++ + Lnk+  +++e+ +++ +l eli+li+ ++is+++ake++e +l++++ p +++e++gl
  lcl|NCBI__GCF_000166055.1:WP_013419229.1 355 ANWMMGDFFAALNKTGKDITESPISAAQLGELIDLISSDVISGRIAKEVFEIMLDKGGTPGAIVEERGL 423
                                               ********************************************************************* PP

                                 TIGR00133 418 iqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                                q++d+ ++ k+v+e+i+ npk+ve+ +  k k+l ++vGqvm+ t g+a+p+ v++ll+++l
  lcl|NCBI__GCF_000166055.1:WP_013419229.1 424 KQVTDTGAIEKVVDEIIAANPKQVEQVQT-KPKTLSWFVGQVMRATGGKANPDAVNALLRQKL 485
                                               ************************99865.677899***********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (491 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: 00:00:00.01
# Mc/sec: 11.84
//
[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