Alignments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_2015 N515DRAFT_2015 branched-chain amino acid aminotransferase

Query= reanno::Dyella79:N515DRAFT_2015
         (305 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2015
          Length = 305

 Score =  622 bits (1605), Expect = 0.0
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MAQQYPEWIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKR 60
           MAQQYPEWIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKR
Sbjct: 1   MAQQYPEWIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKR 60

Query: 61  LYQSAKIYDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAETPIDVAV 120
           LYQSAKIYDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAETPIDVAV
Sbjct: 61  LYQSAKIYDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAETPIDVAV 120

Query: 121 AAWPMGPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGE 180
           AAWPMGPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGE
Sbjct: 121 AAWPMGPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGE 180

Query: 181 GIALANTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDI 240
           GIALANTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDI
Sbjct: 181 GIALANTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDI 240

Query: 241 PREYLYLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWG 300
           PREYLYLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWG
Sbjct: 241 PREYLYLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWG 300

Query: 301 WLEPV 305
           WLEPV
Sbjct: 301 WLEPV 305


Lambda     K      H
   0.320    0.138    0.425 

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: 515
Number of extensions: 15
Number of successful extensions: 1
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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 N515DRAFT_2015 N515DRAFT_2015 (branched-chain amino acid aminotransferase)
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.8767.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.6e-120  386.0   0.0   6.4e-120  385.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015  N515DRAFT_2015 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2015  N515DRAFT_2015 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.8   0.0  6.4e-120  6.4e-120       1     298 []      10     305 .]      10     305 .] 0.99

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 6.4e-120
                                    TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipys 66 
                                                  w +G++ ++++a++hv++halhYG++vfeGiR+Y t++g+aifrl++h++Rly+saki+++ +pys
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015  10 WQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKRLYQSAKIYDMVLPYS 75 
                                                  89**************************************************************** PP

                                    TIGR01122  67 keelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGik 132
                                                  ++++  ++++v+++n+l  aY+Rp++y+G +++gl++  +++++v++aaw++g ylg eale+Gi+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015  76 QDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSA--ETPIDVAVAAWPMGPYLGPEALESGID 139
                                                  ************************************9..889************************ PP

                                    TIGR01122 133 vkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgv 198
                                                  + vss++r a+n+ip+ aka+gnYl+ +l+  ea+r G+ e+i+L + G ++eG+Gen+f+v dgv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015 140 ACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALANTGLLSEGAGENLFLVFDGV 205
                                                  ****************************************************************** PP

                                    TIGR01122 199 lltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrki 264
                                                  l t p s siL+gitr ++i+la+e giev e+ i re ly+ De+ + Gtaae+tPir+vDg+ki
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015 206 LHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYLYLCDELLMCGTAAEITPIRSVDGKKI 271
                                                  ****************************************************************** PP

                                    TIGR01122 265 gegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                                  g+gk+G vt+++qe ff l++gkt+++++wl++v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2015 272 GSGKAGRVTRRMQELFFGLFNGKTNDQWGWLEPV 305
                                                  *******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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: 00:00:00.01
# Mc/sec: 8.77
//
[ok]

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

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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

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