Alignments for a candidate for fadA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Shewanella amazonensis SB2B

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 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__SB2B:6938035
          Length = 436

 Score =  625 bits (1613), Expect = 0.0
 Identities = 305/426 (71%), Positives = 366/426 (85%)

Query: 11  QGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQM 70
           +G+RIAIVSGLRTPFA+QATAFHG+ A+D+GKMVV ELL+RSE+  +++EQLV+GQVVQM
Sbjct: 11  RGERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQM 70

Query: 71  PEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSS 130
           P APNIAREIVLGTGMNV TDAYSV+RACATSFQ+  N+AES+M G I  GIAGGADSSS
Sbjct: 71  PAAPNIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSS 130

Query: 131 VLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYSTGLRMGDTAEQ 190
           VLPIGVSKKLA  LVD+ KART  Q+L +F RL ++DL+PVPPAVAEYSTGL MG TAEQ
Sbjct: 131 VLPIGVSKKLAHALVDLTKARTFGQKLAIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQ 190

Query: 191 MAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSL 250
           MAKT+GI+R  QDA+AHRSH  AAQ W+ G +K EVM A +PPY Q + +DNNIR +S L
Sbjct: 191 MAKTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPYNQFIEKDNNIRESSDL 250

Query: 251 ADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
           A YAKLRP FDRKHG+VTAANSTPLTDGA+A++LM+E RAK LG  P+GY++SYAF AID
Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310

Query: 311 VWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRA 370
           VW+DML+GP+++TP+AL+RAG+ + DLTLI+MHEAFAAQ LAN+++  S++FA E LG+ 
Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370

Query: 371 HATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAA 430
            A GE+D SKFNVLGGS+AYGHPFAATGAR+ITQ  +EL+RRGGG GL TACAAGGLGAA
Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAA 430

Query: 431 MVLEAE 436
           M+LE E
Sbjct: 431 MILEVE 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: 573
Number of extensions: 9
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 6938035 Sama_2168 (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.2056092.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.7e-269  877.7   8.1   8.7e-269  877.5   8.1    1.0  1  lcl|FitnessBrowser__SB2B:6938035  Sama_2168 3-ketoacyl-CoA thiolas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938035  Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.5   8.1  8.7e-269  8.7e-269       1     430 []       7     436 .]       7     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 877.5 bits;  conditional E-value: 8.7e-269
                         TIGR02446   1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapniareivlg 77 
                                       v++++geriaiv+glrtpfa+qatafhg++a+d+gkmvv+ell+rse+d+kl+eqlv+gqvvqmp+apniareivlg
  lcl|FitnessBrowser__SB2B:6938035   7 VTNARGERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQMPAAPNIAREIVLG 83 
                                       689************************************************************************** PP

                         TIGR02446  78 tgmnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdlnkartlgqklkvl 154
                                       tgmnv tdaysvtracatsfqs+vn+aesim+g+ieigiaggadsssvlpigvskkla+alvdl+kart+gqkl ++
  lcl|FitnessBrowser__SB2B:6938035  84 TGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVLPIGVSKKLAHALVDLTKARTFGQKLAIF 160
                                       ***************************************************************************** PP

                         TIGR02446 155 srlglkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawadgklkeevmtafvepykkf 231
                                       +rlg+kdllpvppavaeystglsmgqtaeqmakt+gi+ra+qda+ahrshtlaaq+wa+g +k+evm+a+v+py++f
  lcl|FitnessBrowser__SB2B:6938035 161 RRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMAKTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPYNQF 237
                                       ***************************************************************************** PP

                         TIGR02446 232 iaednnirenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegrakelgleilgyirsyaftaidveqd 308
                                       i++dnnire s+la+yaklrp fdrk+gsvtaanstpltdga+a++lmsegrak+lg++++gyi+syaf+aidv++d
  lcl|FitnessBrowser__SB2B:6938035 238 IEKDNNIRESSDLASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAIDVWED 314
                                       ***************************************************************************** PP

                         TIGR02446 309 mllgpsyatplalkraglelsdltlidmheafaaqtlanvkllasekfaeeklgrakaigeidmskfnvlggsiayg 385
                                       ml+gpsyatp+alkrag++l+dltli+mheafaaq+lan+k++as+kfaeeklg+++aigeidmskfnvlggs+ayg
  lcl|FitnessBrowser__SB2B:6938035 315 MLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQNRAIGEIDMSKFNVLGGSLAYG 391
                                       ***************************************************************************** PP

                         TIGR02446 386 hpfaatgarlitqtlrelkrrggglglatacaagglgaamileve 430
                                       hpfaatgarlitq+++elkrrggg+gl+tacaagglgaamileve
  lcl|FitnessBrowser__SB2B:6938035 392 HPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAAMILEVE 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: 00:00:00.00
# Mc/sec: 22.22
//
[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