Alignments for a candidate for kbl in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Shewanella amazonensis SB2B

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 6935883 Sama_0098 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq)

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



>FitnessBrowser__SB2B:6935883
          Length = 397

 Score =  692 bits (1785), Expect = 0.0
 Identities = 350/397 (88%), Positives = 367/397 (92%)

Query: 1   MASTSFYAQINQQLADVKAEGLYKSERVIASPQQTAIQVNHQEVVNFCANNYLGLANHPE 60
           MASTSFY QI QQLADVKAEGLYKSERVI SPQQ AI+V   EV+NFCANNYLGLANHPE
Sbjct: 1   MASTSFYEQIKQQLADVKAEGLYKSERVIVSPQQAAIKVGGDEVINFCANNYLGLANHPE 60

Query: 61  LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120
           L+KAAQ GL  HGFGMASVRFICGTQDIHKQLEA LSEFLG EDTILYSSCFDANAGLFE
Sbjct: 61  LVKAAQAGLADHGFGMASVRFICGTQDIHKQLEAKLSEFLGTEDTILYSSCFDANAGLFE 120

Query: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180
           TLL  EDAI+SDALNHASIIDGVRLCKA RFRYANNDMADLETQL AA+ AGAR+ILIAT
Sbjct: 121 TLLGPEDAIVSDALNHASIIDGVRLCKAMRFRYANNDMADLETQLKAAREAGARHILIAT 180

Query: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITG 240
           DGVFSMDGVIANL+GVCDLAD+YGALVMVDDSHAVGF+G NGRG+HE+C VM RVDIITG
Sbjct: 181 DGVFSMDGVIANLKGVCDLADQYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRVDIITG 240

Query: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300
           TLGKALGGASGG+TSGKKEVIDWLRQRSRPYLFSNSLAPSIV ASI VL+MLK GQALRE
Sbjct: 241 TLGKALGGASGGYTSGKKEVIDWLRQRSRPYLFSNSLAPSIVAASIRVLDMLKDGQALRE 300

Query: 301 AVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV 360
           AVWENSRYFREKMSAAGFTL GADHAI+PVM+GDAKLA+DF+ RLL E IYVIGFSFPVV
Sbjct: 301 AVWENSRYFREKMSAAGFTLAGADHAIVPVMLGDAKLAADFSARLLKEDIYVIGFSFPVV 360

Query: 361 PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
           PKGQARIRTQMSAAHTR QLDKAIEAFTRI KEM II
Sbjct: 361 PKGQARIRTQMSAAHTRAQLDKAIEAFTRIGKEMGII 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: 582
Number of extensions: 14
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 6935883 Sama_0098 (2-amino-3-ketobutyrate coenzyme A ligase (RefSeq))
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.16713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.6e-215  699.5   3.0   6.3e-215  699.4   3.0    1.0  1  lcl|FitnessBrowser__SB2B:6935883  Sama_0098 2-amino-3-ketobutyrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6935883  Sama_0098 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.4   3.0  6.3e-215  6.3e-215       1     393 []       6     397 .]       6     397 .] 0.99

  Alignments for each domain:
  == domain 1  score: 699.4 bits;  conditional E-value: 6.3e-215
                         TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrf 77 
                                       ++++++++l  ++++Gl+k+er+i+spq+a i+v  G ev+nfcannylGl++hpe+++aa+++l +hGfG++svrf
  lcl|FitnessBrowser__SB2B:6935883   6 FYEQIKQQLADVKAEGLYKSERVIVSPQQAAIKV-GGDEVINFCANNYLGLANHPELVKAAQAGLADHGFGMASVRF 81 
                                       67899*****************************.99**************************************** PP

                         TIGR01822  78 icGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadl 154
                                       icGtqd+hk+le+kl+eflgted+ily+scfdan+Glfe+llg+edai+sdalnhasiidGvrlcka r+ry+n+d+
  lcl|FitnessBrowser__SB2B:6935883  82 ICGTQDIHKQLEAKLSEFLGTEDTILYSSCFDANAGLFETLLGPEDAIVSDALNHASIIDGVRLCKAMRFRYANNDM 158
                                       ***************************************************************************** PP

                         TIGR01822 155 edleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkv 231
                                       +dle++lk+ar+agar+ liatdGvfsmdG+ia+l+ +c+la++y+alv+vd++ha+Gf+G++GrG++e++dv+d+v
  lcl|FitnessBrowser__SB2B:6935883 159 ADLETQLKAAREAGARHILIATDGVFSMDGVIANLKGVCDLADQYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRV 235
                                       ***************************************************************************** PP

                         TIGR01822 232 diitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrek 308
                                       diitgtlGkalGGasGG+t++kkev+++lrqrsrpylfsnslap++v+asi+vl++l++++ lr+ ++en+ryfrek
  lcl|FitnessBrowser__SB2B:6935883 236 DIITGTLGKALGGASGGYTSGKKEVIDWLRQRSRPYLFSNSLAPSIVAASIRVLDMLKDGQALREAVWENSRYFREK 312
                                       ***************************************************************************** PP

                         TIGR01822 309 leaaGfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvk 385
                                       ++aaGf++++a+hai+pvml+dakla ++++rll+e iyviGf++pvvpkGqarir+q+saah+++qldka+eaf++
  lcl|FitnessBrowser__SB2B:6935883 313 MSAAGFTLAGADHAIVPVMLGDAKLAADFSARLLKEDIYVIGFSFPVVPKGQARIRTQMSAAHTRAQLDKAIEAFTR 389
                                       ***************************************************************************** PP

                         TIGR01822 386 vGrelgvi 393
                                       +G+e+g+i
  lcl|FitnessBrowser__SB2B:6935883 390 IGKEMGII 397
                                       *****997 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: 10.68
//
[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