Alignments for a candidate for kbl in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Shewanella oneidensis MR-1

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 203743 SO4674 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file)

Query= reanno::ANA3:7026975
         (397 letters)



>FitnessBrowser__MR1:203743
          Length = 397

 Score =  775 bits (2001), Expect = 0.0
 Identities = 394/397 (99%), Positives = 396/397 (99%)

Query: 1   MASTSFYAQINQQLADVKAEGLYKSERVIASPQQTAIQVNHQEVVNFCANNYLGLANHPE 60
           MASTSFYAQINQQLADVKAEGLYKSER+IASPQQTAIQVNHQEVVNFCANNYLGLANHPE
Sbjct: 1   MASTSFYAQINQQLADVKAEGLYKSERIIASPQQTAIQVNHQEVVNFCANNYLGLANHPE 60

Query: 61  LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120
           LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE
Sbjct: 61  LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120

Query: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180
           TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT
Sbjct: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180

Query: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITG 240
           DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVG NGRGSHEHCGVMGRVDIITG
Sbjct: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGQNGRGSHEHCGVMGRVDIITG 240

Query: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300
           TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE
Sbjct: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300

Query: 301 AVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV 360
           +VWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV
Sbjct: 301 SVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV 360

Query: 361 PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
           PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII
Sbjct: 361 PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397


Lambda     K      H
   0.321    0.134    0.385 

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: 664
Number of extensions: 18
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 203743 SO4674 (2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file))
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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/TIGR01822.hmm
# target sequence database:        /tmp/gapView.17208.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     4e-212  690.2   4.2   4.5e-212  690.0   4.2    1.0  1  lcl|FitnessBrowser__MR1:203743  SO4674 2-amino-3-ketobutyrate co


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203743  SO4674 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.0   4.2  4.5e-212  4.5e-212       1     393 []       6     397 .]       6     397 .] 0.99

  Alignments for each domain:
  == domain 1  score: 690.0 bits;  conditional E-value: 4.5e-212
                       TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrfic 79 
                                     ++a+++++l  ++++Gl+k+erii+spq++ i+v + +ev+nfcannylGl++hpe+i+aa+++ld+hGfG++svrfic
  lcl|FitnessBrowser__MR1:203743   6 FYAQINQQLADVKAEGLYKSERIIASPQQTAIQV-NHQEVVNFCANNYLGLANHPELIKAAQQGLDSHGFGMASVRFIC 83 
                                     678999****************************.789***************************************** PP

                       TIGR01822  80 GtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadledle 158
                                     Gtqd+hk+le+ l+eflg+ed+ily+scfdan+Glfe+ll +edaiisdalnhasiidGvrlckakr+ry+n+d++dle
  lcl|FitnessBrowser__MR1:203743  84 GTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFETLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLE 162
                                     ******************************************************************************* PP

                       TIGR01822 159 aklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkvdiitgt 237
                                     ++l +a+aagar  liatdGvfsmdG+ia+l+ +c+la+ky+alv+vd++ha+Gf+G++GrGs+e ++v+++vdiitgt
  lcl|FitnessBrowser__MR1:203743 163 TQLIAAKAAGARNILIATDGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGQNGRGSHEHCGVMGRVDIITGT 241
                                     ******************************************************************************* PP

                       TIGR01822 238 lGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrekleaaGfdv 316
                                     lGkalGGasGGft++kkev+++lrqrsrpylfsnslap++v+asi+vle+l++++ lr++++en+ryfrek++aaGf++
  lcl|FitnessBrowser__MR1:203743 242 LGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRESVWENSRYFREKMSAAGFTL 320
                                     ******************************************************************************* PP

                       TIGR01822 317 kpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                      +a+haiipvm++dakla+++a+rll e iyviGf++pvvpkGqarir+q+saah++eqldka+eaf+++ +e+ +i
  lcl|FitnessBrowser__MR1:203743 321 GGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVVPKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
                                     *************************************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (397 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.54
//
[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