GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Shewanella loihica PV-4

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 5211293 Shew_3709 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq)

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



>FitnessBrowser__PV4:5211293
          Length = 397

 Score =  726 bits (1873), Expect = 0.0
 Identities = 367/397 (92%), Positives = 383/397 (96%)

Query: 1   MASTSFYAQINQQLADVKAEGLYKSERVIASPQQTAIQVNHQEVVNFCANNYLGLANHPE 60
           MA+TSFY QINQQLA+VKAEGLYKSERVIASPQ+T I+VN  EV+NFCANNYLGLANHPE
Sbjct: 1   MATTSFYDQINQQLAEVKAEGLYKSERVIASPQKTEIEVNGHEVMNFCANNYLGLANHPE 60

Query: 61  LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120
           LI AAQQGL  HGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE
Sbjct: 61  LITAAQQGLSDHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120

Query: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180
           TLLDAEDAI+SDALNHASIIDGVRLCKAKRFRYANNDMADLETQL AAKAAGAR+ILIAT
Sbjct: 121 TLLDAEDAIVSDALNHASIIDGVRLCKAKRFRYANNDMADLETQLQAAKAAGARHILIAT 180

Query: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITG 240
           DGVFSMDGVIANL+GVCDLADKYGALVMVDDSHAVGF+G NGRG+HE+C VM RVDIITG
Sbjct: 181 DGVFSMDGVIANLKGVCDLADKYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRVDIITG 240

Query: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300
           TLGKALGGASGGFTS KKEV+DWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE
Sbjct: 241 TLGKALGGASGGFTSAKKEVVDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300

Query: 301 AVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV 360
           AVWENSRYFREKM+AAGFTLGGADHAIIPVMIGDAKLASDFANRLL E+IYVIGFSFPVV
Sbjct: 301 AVWENSRYFREKMTAAGFTLGGADHAIIPVMIGDAKLASDFANRLLEENIYVIGFSFPVV 360

Query: 361 PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397
           PKGQARIRTQMSAAHTREQLD+AI+AFTRIAKEM II
Sbjct: 361 PKGQARIRTQMSAAHTREQLDRAIDAFTRIAKEMGII 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: 602
Number of extensions: 13
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 5211293 Shew_3709 (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.23928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.4e-215  699.9   3.2     5e-215  699.7   3.2    1.0  1  lcl|FitnessBrowser__PV4:5211293  Shew_3709 2-amino-3-ketobutyrate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211293  Shew_3709 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 !  699.7   3.2    5e-215    5e-215       1     393 []       6     397 .]       6     397 .] 1.00

  Alignments for each domain:
  == domain 1  score: 699.7 bits;  conditional E-value: 5e-215
                        TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrfi 78 
                                      ++++++++l  ++++Gl+k+er+i+spqk++i v +G+ev+nfcannylGl++hpe+i aa+++l +hGfG++svrfi
  lcl|FitnessBrowser__PV4:5211293   6 FYDQINQQLAEVKAEGLYKSERVIASPQKTEIEV-NGHEVMNFCANNYLGLANHPELITAAQQGLSDHGFGMASVRFI 82 
                                      68999*****************************.9****************************************** PP

                        TIGR01822  79 cGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadled 156
                                      cGtqd+hk+le+ l+eflg+ed+ily+scfdan+Glfe+ll +edai+sdalnhasiidGvrlckakr+ry+n+d++d
  lcl|FitnessBrowser__PV4:5211293  83 CGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFETLLDAEDAIVSDALNHASIIDGVRLCKAKRFRYANNDMAD 160
                                      ****************************************************************************** PP

                        TIGR01822 157 leaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkvdii 234
                                      le++l++a+aagar+ liatdGvfsmdG+ia+l+ +c+la+ky+alv+vd++ha+Gf+G++GrG++e++dv+d+vdii
  lcl|FitnessBrowser__PV4:5211293 161 LETQLQAAKAAGARHILIATDGVFSMDGVIANLKGVCDLADKYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRVDII 238
                                      ****************************************************************************** PP

                        TIGR01822 235 tgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrekleaa 312
                                      tgtlGkalGGasGGft+akkevv++lrqrsrpylfsnslap++v+asi+vle+l++++ lr+ ++en+ryfrek++aa
  lcl|FitnessBrowser__PV4:5211293 239 TGTLGKALGGASGGFTSAKKEVVDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALREAVWENSRYFREKMTAA 316
                                      ****************************************************************************** PP

                        TIGR01822 313 GfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrel 390
                                      Gf++ +a+haiipvm++dakla+++a+rllee iyviGf++pvvpkGqarir+q+saah++eqld+a++af+++ +e+
  lcl|FitnessBrowser__PV4:5211293 317 GFTLGGADHAIIPVMIGDAKLASDFANRLLEENIYVIGFSFPVVPKGQARIRTQMSAAHTREQLDRAIDAFTRIAKEM 394
                                      ****************************************************************************** PP

                        TIGR01822 391 gvi 393
                                      g+i
  lcl|FitnessBrowser__PV4:5211293 395 GII 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: 8.00
//
[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:

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:

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:

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:

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