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

GapMind for catabolism of small carbon sources

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

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 5209978 Shew_2426 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__PV4:5209978
          Length = 436

 Score =  629 bits (1621), Expect = 0.0
 Identities = 312/436 (71%), Positives = 367/436 (84%)

Query: 1   MGQVLPLVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIE 60
           M ++  +   +GDRIAIV GLRTPFA+QATAFHG+ A+D+GKMVV ELL+RSE+  + IE
Sbjct: 1   MSELQQVRNAKGDRIAIVMGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKEIE 60

Query: 61  QLVFGQVVQMPEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRA 120
           QLV+GQVVQMP APNIAREIVLGTGMNV TDAYSV+RACATSFQ+  NVAES+M G I  
Sbjct: 61  QLVYGQVVQMPAAPNIAREIVLGTGMNVSTDAYSVTRACATSFQSTVNVAESIMTGNIEI 120

Query: 121 GIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYST 180
           GIAGGADSSSVLPIGVSKKLA  LVD+NKAR+  Q+  +  RL L+DL+PVPPAVAEYST
Sbjct: 121 GIAGGADSSSVLPIGVSKKLAHALVDLNKARSFGQKWAIIRRLGLKDLLPVPPAVAEYST 180

Query: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVE 240
           GL MG TAEQMAKTY I+R  QDALAHRSH  A + W  G L++EVM A +PPYK  +  
Sbjct: 181 GLSMGQTAEQMAKTYNISRADQDALAHRSHTLATETWDSGHLRDEVMVAHVPPYKSFIDR 240

Query: 241 DNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY 300
           DNNIR NSSL  YAKLRPAFDRKHG+VTAANSTPLTDGA+AV+LM+ESRAK LG  P+GY
Sbjct: 241 DNNIRENSSLDSYAKLRPAFDRKHGSVTAANSTPLTDGASAVLLMSESRAKALGYEPIGY 300

Query: 301 LRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSE 360
           ++SYAF+AIDVWQDML+GP+++TPLAL+RAG+ + DLTLI+MHEAFAAQTLAN+Q+  S+
Sbjct: 301 IKSYAFSAIDVWQDMLMGPSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASK 360

Query: 361 RFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT 420
           +FA+E LGR  A GE+D +KFNVLGGS+AYGHPFAATG R+ITQ   EL+RRGGG GL T
Sbjct: 361 KFAKEKLGRDRAIGEIDMTKFNVLGGSLAYGHPFAATGTRLITQVCRELKRRGGGTGLAT 420

Query: 421 ACAAGGLGAAMVLEAE 436
           ACAAGGLGAAM++E E
Sbjct: 421 ACAAGGLGAAMIVEVE 436


Lambda     K      H
   0.319    0.133    0.377 

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: 604
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
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: 51 (24.3 bits)

Align candidate 5209978 Shew_2426 (3-ketoacyl-CoA thiolase (RefSeq))
to HMM TIGR02446 (fadI: acetyl-CoA C-acyltransferase FadI (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/TIGR02446.hmm
# target sequence database:        /tmp/gapView.32003.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02446  [M=430]
Accession:   TIGR02446
Description: FadI: acetyl-CoA C-acyltransferase FadI
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.7e-273  891.1   3.9   7.6e-273  890.9   3.9    1.0  1  lcl|FitnessBrowser__PV4:5209978  Shew_2426 3-ketoacyl-CoA thiolas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209978  Shew_2426 3-ketoacyl-CoA thiolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  890.9   3.9  7.6e-273  7.6e-273       1     430 []       7     436 .]       7     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 890.9 bits;  conditional E-value: 7.6e-273
                        TIGR02446   1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapniareivlgt 78 
                                      v++++g+riaiv glrtpfa+qatafhg++a+d+gkmvv+ell+rse+d+k ieqlv+gqvvqmp+apniareivlgt
  lcl|FitnessBrowser__PV4:5209978   7 VRNAKGDRIAIVMGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKEIEQLVYGQVVQMPAAPNIAREIVLGT 84 
                                      6799************************************************************************** PP

                        TIGR02446  79 gmnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdlnkartlgqklkvlsr 156
                                      gmnv+tdaysvtracatsfqs+vnvaesim+g+ieigiaggadsssvlpigvskkla+alvdlnkar++gqk  +++r
  lcl|FitnessBrowser__PV4:5209978  85 GMNVSTDAYSVTRACATSFQSTVNVAESIMTGNIEIGIAGGADSSSVLPIGVSKKLAHALVDLNKARSFGQKWAIIRR 162
                                      ****************************************************************************** PP

                        TIGR02446 157 lglkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawadgklkeevmtafvepykkfiae 234
                                      lglkdllpvppavaeystglsmgqtaeqmakty+i+ra+qdalahrshtla+++w +g+l++evm+a+v+pyk fi +
  lcl|FitnessBrowser__PV4:5209978 163 LGLKDLLPVPPAVAEYSTGLSMGQTAEQMAKTYNISRADQDALAHRSHTLATETWDSGHLRDEVMVAHVPPYKSFIDR 240
                                      ****************************************************************************** PP

                        TIGR02446 235 dnnirenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegrakelgleilgyirsyaftaidveqdmllg 312
                                      dnnirenssl++yaklrpafdrk+gsvtaanstpltdga+av+lmse+rak+lg+e++gyi+syaf+aidv+qdml+g
  lcl|FitnessBrowser__PV4:5209978 241 DNNIRENSSLDSYAKLRPAFDRKHGSVTAANSTPLTDGASAVLLMSESRAKALGYEPIGYIKSYAFSAIDVWQDMLMG 318
                                      ****************************************************************************** PP

                        TIGR02446 313 psyatplalkraglelsdltlidmheafaaqtlanvkllasekfaeeklgrakaigeidmskfnvlggsiayghpfaa 390
                                      psyatplalkrag+el+dltli+mheafaaqtlan++++as+kfa+eklgr++aigeidm kfnvlggs+ayghpfaa
  lcl|FitnessBrowser__PV4:5209978 319 PSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAKEKLGRDRAIGEIDMTKFNVLGGSLAYGHPFAA 396
                                      ****************************************************************************** PP

                        TIGR02446 391 tgarlitqtlrelkrrggglglatacaagglgaamileve 430
                                      tg+rlitq++relkrrggg+glatacaagglgaami+eve
  lcl|FitnessBrowser__PV4:5209978 397 TGTRLITQVCRELKRRGGGTGLATACAAGGLGAAMIVEVE 436
                                      **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (430 nodes)
Target sequences:                          1  (436 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: 11.04
//
[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