Alignments for a candidate for gatB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Sinorhizobium meliloti 1021

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate SMc01350 SMc01350 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Smeli:SMc01350
          Length = 516

 Score =  424 bits (1089), Expect = e-123
 Identities = 225/478 (47%), Positives = 314/478 (65%), Gaps = 11/478 (2%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E +IG+EVH ++ ++SK+FS +   FG+EPN+N +++D A PG+LPV+N+  V  A+R 
Sbjct: 38  WEVIIGMEVHAQVLSNSKLFSSASTEFGSEPNANVSLVDAAMPGMLPVINEECVKQAVRT 97

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETK------RI 116
            + L  +I   S FDRKNYFYPD P+ YQISQ+  PI   G I I V  + +       I
Sbjct: 98  GLGLKAKINNRSIFDRKNYFYPDLPQGYQISQYKDPIVGEGKIIISVGPDRQGQFEDVEI 157

Query: 117 GITRLHMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSII 174
           GI RLH+E+DAGKS H      S VDLNR G  L+EIVS+PD+RS  EA AYL KLRSI+
Sbjct: 158 GIERLHLEQDAGKSMHDQHPAMSYVDLNRSGVALMEIVSKPDLRSSDEAKAYLTKLRSIL 217

Query: 175 QYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEE 234
           +Y G  D  M+EGS+R D N+S+R  G E FGT+ E+KN+NS  +V + +EYE +RQ   
Sbjct: 218 RYLGTCDGNMDEGSMRADVNVSVRRPG-EAFGTRCEIKNVNSIRFVGQSIEYEARRQIAI 276

Query: 235 LLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPE 294
           L  GG I QETR FD + G+T  MR KE + DYRYFP+PD++PL  DDA+ E ++  +PE
Sbjct: 277 LEDGGAIDQETRLFDANKGETRSMRSKEEAHDYRYFPDPDLLPLEFDDAFVEALKADLPE 336

Query: 295 LPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNK 354
           LPD++K ++V +LGL  YDA VL   K ++D+FE+  E G D K  +NW++  +   LNK
Sbjct: 337 LPDDKKERFVRDLGLSVYDASVLVSEKAIADYFEAVAE-GRDGKAAANWVINDLLGALNK 395

Query: 355 NQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISD 414
               + +T ++P  L G+I LI+DGT+S K+AK VF  L  +GG+  +I+E  G+ Q++D
Sbjct: 396 AGKTIEETPVSPAQLGGIIDLIKDGTISGKLAKDVFEILWNEGGDPAEIVESRGMKQVTD 455

Query: 415 EATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
              + K V+E +  N   VE  K  K    G+ VGQ+MKA+ G+ANPQ V  L+K +L
Sbjct: 456 TGAIEKAVDEIIAANPDQVEKAK-AKPSLAGWFVGQVMKATGGKANPQAVQALVKSKL 512


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: 722
Number of extensions: 33
Number of successful extensions: 6
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: 516
Length adjustment: 34
Effective length of query: 441
Effective length of database: 482
Effective search space:   212562
Effective search space used:   212562
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 SMc01350 SMc01350 (aspartyl/glutamyl-tRNA amidotransferase 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.9619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.5e-168  545.6   0.0   5.1e-168  545.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01350  SMc01350 aspartyl/glutamyl-tRNA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01350  SMc01350 aspartyl/glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.4   0.0  5.1e-168  5.1e-168       3     480 ..      37     512 ..      35     513 .. 0.97

  Alignments for each domain:
  == domain 1  score: 545.4 bits;  conditional E-value: 5.1e-168
                           TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevs 77 
                                         ++e++iG+EvH q+  +sKlF+++s+e+ + +pN nv+ v+ ++PG lPv+N+e vk+A+  +l l++ki+ + s
  lcl|FitnessBrowser__Smeli:SMc01350  37 DWEVIIGMEVHAQVLSNSKLFSSASTEFGS-EPNANVSLVDAAMPGMLPVINEECVKQAVRTGLGLKAKIN-NRS 109
                                         679***************************.**************************************65.7** PP

                           TIGR00133  78 vFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke......keigierlhlEeDtgksqykesdkdkqslv 146
                                         +FdRK+YfYpDlP+gyqi+q++ Pi+ +Gk+ i++  +        eigierlhlE+D+gks++ ++  + +s+v
  lcl|FitnessBrowser__Smeli:SMc01350 110 IFDRKNYFYPDLPQGYQISQYKDPIVGEGKIIISVGPDRqgqfedVEIGIERLHLEQDAGKSMHDQH--PAMSYV 182
                                         *********************************99776667787789*****************966..79**** PP

                           TIGR00133 147 DfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNl 221
                                         D+NRsgv L+EiV+kPdl+s++ea+a+l klr+ilryl+  dg+++eGsmR+DvNvs+r +  e++gtr EiKN+
  lcl|FitnessBrowser__Smeli:SMc01350 183 DLNRSGVALMEIVSKPDLRSSDEAKAYLTKLRSILRYLGTCDGNMDEGSMRADVNVSVR-RPGEAFGTRCEIKNV 256
                                         ***********************************************************.55678********** PP

                           TIGR00133 222 nslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekv 296
                                         ns++ + + ieyE  Rq+++l++g  + qetr fd +k  t s+R+Kee++DYRYfp+Pdl p+e+d+ +v+  +
  lcl|FitnessBrowser__Smeli:SMc01350 257 NSIRFVGQSIEYEARRQIAILEDGGAIDQETRLFDANKGETRSMRSKEEAHDYRYFPDPDLLPLEFDDAFVEA-L 330
                                         **********************************************************************999.* PP

                           TIGR00133 297 eeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeal 371
                                         ++ lpelP+ k++r+++++gls +da vlvs++ ++d+fe v++  +  k+a+nW++++llg Lnk   +++e+ 
  lcl|FitnessBrowser__Smeli:SMc01350 331 KADLPELPDDKKERFVRDLGLSVYDASVLVSEKAIADYFEAVAEGRDG-KAAANWVINDLLGALNKAGKTIEETP 404
                                         ****************************************99987766.************************** PP

                           TIGR00133 372 lkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyks 446
                                         ++p +l  +i+lik+g+is+k ak+++e l ++++dp +++e +g+ q++d+ ++ k+v+e+i+ np++vek k+
  lcl|FitnessBrowser__Smeli:SMc01350 405 VSPAQLGGIIDLIKDGTISGKLAKDVFEILWNEGGDPAEIVESRGMKQVTDTGAIEKAVDEIIAANPDQVEKAKA 479
                                         ***********************************************************************9875 PP

                           TIGR00133 447 gkekalkflvGqvmkktkgradpkevekllkell 480
                                          k ++ +++vGqvmk t g+a+p+ v++l+k +l
  lcl|FitnessBrowser__Smeli:SMc01350 480 -KPSLAGWFVGQVMKATGGKANPQAVQALVKSKL 512
                                         .67899************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (516 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: 7.40
//
[ok]

This GapMind analysis is from Apr 09 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