Alignments for a candidate for ilvE in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Dechlorosoma suillum PS

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Dsui_3339 Dsui_3339 branched-chain amino acid aminotransferase, group I

Query= reanno::BFirm:BPHYT_RS16285
         (307 letters)



>FitnessBrowser__PS:Dsui_3339
          Length = 306

 Score =  446 bits (1147), Expect = e-130
 Identities = 215/304 (70%), Positives = 254/304 (83%), Gaps = 1/304 (0%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSM+DRDG IW DGKL+ WR+A  H LTH+LHYGM VFEGVRAY+T D GTAIFRLQ+HT
Sbjct: 1   MSMSDRDGFIWQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQT-DKGTAIFRLQDHT 59

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           +RL  SA IFQM +P+  E L  AQ EV+R N LES Y+RP+ + GSEK+GVS KG  +H
Sbjct: 60  QRLARSAHIFQMALPYSQEELNEAQKEVIRANNLESGYIRPLAFYGSEKMGVSPKGAKVH 119

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           V IAAWPWGAYLGE+G+ +GIR+KTSSFTRHHVN++MVRAKASG Y+NSILAN EA+ DG
Sbjct: 120 VIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILANNEALTDG 179

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEA+LLD +GYV EG+GEN F+V NGKLYTPDL+SCL+GITR TVI LA + GI+V+EK
Sbjct: 180 YDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDLTSCLEGITRATVIQLAGEMGIEVVEK 239

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVY  DEAFFTGTAAEVTPIRELDNR IG G RGP+T+ LQ  +FD+VNG+S  +
Sbjct: 240 RITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAH 299

Query: 301 ANWL 304
           A+WL
Sbjct: 300 ADWL 303


Lambda     K      H
   0.319    0.136    0.411 

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: 364
Number of extensions: 6
Number of successful extensions: 2
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: 307
Length of database: 306
Length adjustment: 27
Effective length of query: 280
Effective length of database: 279
Effective search space:    78120
Effective search space used:    78120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate Dsui_3339 Dsui_3339 (branched-chain amino acid aminotransferase, group I)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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.carbon/TIGR01122.hmm
# target sequence database:        /tmp/gapView.4442.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-143  463.2   0.1   1.9e-143  463.0   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_3339  Dsui_3339 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3339  Dsui_3339 branched-chain amino acid aminotransferase, group I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.0   0.1  1.9e-143  1.9e-143       1     298 []      11     306 .]      11     306 .] 0.99

  Alignments for each domain:
  == domain 1  score: 463.0 bits;  conditional E-value: 1.9e-143
                         TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 
                                       w dG+lv++++a++h lth+lhYG++vfeG+RaY+tdkg+aifrl++h++Rl  sa+i+++ +pys+eel+e++kev
  lcl|FitnessBrowser__PS:Dsui_3339  11 WQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQTDKGTAIFRLQDHTQRLARSAHIFQMALPYSQEELNEAQKEV 87 
                                       99*************************************************************************** PP

                         TIGR01122  78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154
                                       +r+nnl+s YiRpl+++G+e++g++p  ++kv+viiaaw+wgaylgee++++Gi++k+ssf+r++vn+ + +aka+g
  lcl|FitnessBrowser__PS:Dsui_3339  88 IRANNLESGYIRPLAFYGSEKMGVSP-KGAKVHVIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASG 163
                                       **************************.6779********************************************** PP

                         TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231
                                       nY+ns+la+ eal+ Gydea+lLd eGyv eG+Genifivk+g+l+tP++ +s+L+gitr +vi+la e+giev+e+
  lcl|FitnessBrowser__PS:Dsui_3339 164 NYMNSILANNEALTDGYDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDL-TSCLEGITRATVIQLAGEMGIEVVEK 239
                                       **************************************************.78************************ PP

                         TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                       ri+r+e+y aDe+f+tGtaaevtPire+D+r+ig g+rGpvtk lqe++fd+v+g+  ++++wl  v
  lcl|FitnessBrowser__PS:Dsui_3339 240 RITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAHADWLAFV 306
                                       ***************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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: 11.57
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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 catabolism of small carbon sources