GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Shewanella amazonensis SB2B

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)

Query= reanno::SB2B:6935813
         (387 letters)



>FitnessBrowser__SB2B:6935813
          Length = 387

 Score =  758 bits (1958), Expect = 0.0
 Identities = 387/387 (100%), Positives = 387/387 (100%)

Query: 1   MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60
           MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ
Sbjct: 1   MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60

Query: 61  TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120
           TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH
Sbjct: 61  TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120

Query: 121 MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS 180
           MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS
Sbjct: 121 MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS 180

Query: 181 IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA 240
           IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA
Sbjct: 181 IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA 240

Query: 241 LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ 300
           LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ
Sbjct: 241 LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ 300

Query: 301 DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM 360
           DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM
Sbjct: 301 DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM 360

Query: 361 EHKDATLGLATMCIGLGQGIATVFERV 387
           EHKDATLGLATMCIGLGQGIATVFERV
Sbjct: 361 EHKDATLGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.319    0.134    0.384 

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: 723
Number of extensions: 17
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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: 50 (23.9 bits)

Align candidate 6935813 Sama_0031 (3-ketoacyl-CoA thiolase (RefSeq))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

# 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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.18964.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-224  730.3  11.4   2.6e-224  730.2  11.4    1.0  1  lcl|FitnessBrowser__SB2B:6935813  Sama_0031 3-ketoacyl-CoA thiolas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6935813  Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.2  11.4  2.6e-224  2.6e-224       2     385 .]       4     387 .]       3     387 .] 1.00

  Alignments for each domain:
  == domain 1  score: 730.2 bits;  conditional E-value: 2.6e-224
                         TIGR02445   2 vvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevph 78 
                                        vivd++rtpmgrskgg+frn+rae lsa l+k+ll rnp v++  +ed++wgcvqqtleqgfniarna+lla+vp+
  lcl|FitnessBrowser__SB2B:6935813   4 AVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQTLEQGFNIARNASLLAGVPK 80 
                                       79*************************************************************************** PP

                         TIGR02445  79 evaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgkl 155
                                       + +avtvnrlcgssm+alh+a+raimtg ++ ++iggvehmghv+m+hgvdfhpgl+ +vaka+gmmgltaemlgkl
  lcl|FitnessBrowser__SB2B:6935813  81 TAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEHMGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKL 157
                                       ***************************************************************************** PP

                         TIGR02445 156 hgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvt 232
                                       hgisre+qd+fa+rsh+rahaa++eg+f nei  +eg+da+g l ++dydevirpett+e+la lrp+fdp+ngtvt
  lcl|FitnessBrowser__SB2B:6935813 158 HGISREMQDQFAVRSHQRAHAASIEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVT 234
                                       ***************************************************************************** PP

                         TIGR02445 233 agtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneaf 309
                                       agtssalsdga+amlvm ee+a+ lg+++rar+rsmavag+d +imgygpvpat+kal raglsi+d+dv+elneaf
  lcl|FitnessBrowser__SB2B:6935813 235 AGTSSALSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQDMDVIELNEAF 311
                                       ***************************************************************************** PP

                         TIGR02445 310 aaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                       aaq+lp++kdlgl+d++++kvnlnggaialghplgcsgaristtl+nlme+kda+ glatmciglgqgiatvferv
  lcl|FitnessBrowser__SB2B:6935813 312 AAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387
                                       ***************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (387 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.69
//
[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