Alignments for a candidate for fadA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Shewanella oneidensis MR-1

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 202206 SO3089 fatty oxidation complex, beta subunit (NCBI ptt file)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__MR1:202206
          Length = 436

 Score =  634 bits (1634), Expect = 0.0
 Identities = 312/426 (73%), Positives = 367/426 (86%)

Query: 11  QGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQM 70
           +G+RIAIV+GLRTPFA+QATAFHGI A+D+GKMVV ELL RSE+  ++IEQLV+GQVVQM
Sbjct: 11  RGERIAIVAGLRTPFAKQATAFHGISALDMGKMVVNELLVRSELDPKLIEQLVYGQVVQM 70

Query: 71  PEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSS 130
           P APNIAREIVLGTGM+V TDAYSV+RACATSFQ+  NVAES+M G I  GIAGGADSSS
Sbjct: 71  PAAPNIAREIVLGTGMDVSTDAYSVTRACATSFQSAVNVAESIMTGNIEIGIAGGADSSS 130

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

Query: 191 MAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSL 250
           MAKTY I+R  QDALAHRSH  A + W+ G L++EVM A +PPYKQ +  DNNIR NS L
Sbjct: 191 MAKTYNISRADQDALAHRSHTLANETWASGHLRDEVMVAHVPPYKQFIERDNNIRENSDL 250

Query: 251 ADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
           A YAKLRPAFD+KHG+VTAANSTPLTDGA+A+ILM+E RAK LG  P+GY++SYAFTAID
Sbjct: 251 ASYAKLRPAFDKKHGSVTAANSTPLTDGASAIILMSEGRAKALGYQPIGYIKSYAFTAID 310

Query: 311 VWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRA 370
           VWQDML+GP+++TPLAL+RAG+ + DLTLI+MHEAFAAQTLAN+Q+  S++FA E LGR 
Sbjct: 311 VWQDMLMGPSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAEEKLGRN 370

Query: 371 HATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAA 430
            A G++D SKFNVLGGS+AYGHPFAATG R+ITQ   EL+RRGGG GL TACAAGGLGAA
Sbjct: 371 RAIGDIDMSKFNVLGGSLAYGHPFAATGTRLITQVCRELKRRGGGTGLATACAAGGLGAA 430

Query: 431 MVLEAE 436
           M++E E
Sbjct: 431 MIVEVE 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: 585
Number of extensions: 11
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 202206 SO3089 (fatty oxidation complex, beta subunit (NCBI ptt file))
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.28293.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.8e-281  917.4   5.5   7.7e-281  917.2   5.5    1.0  1  lcl|FitnessBrowser__MR1:202206  SO3089 fatty oxidation complex, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202206  SO3089 fatty oxidation complex, beta subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  917.2   5.5  7.7e-281  7.7e-281       1     430 []       7     436 .]       7     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 917.2 bits;  conditional E-value: 7.7e-281
                       TIGR02446   1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapniareivlgtg 79 
                                     v++++geriaivaglrtpfa+qatafhgi+a+d+gkmvv+ell+rse+d+klieqlv+gqvvqmp+apniareivlgtg
  lcl|FitnessBrowser__MR1:202206   7 VTNARGERIAIVAGLRTPFAKQATAFHGISALDMGKMVVNELLVRSELDPKLIEQLVYGQVVQMPAAPNIAREIVLGTG 85 
                                     689**************************************************************************** PP

                       TIGR02446  80 mnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdlnkartlgqklkvlsrlg 158
                                     m+v+tdaysvtracatsfqsavnvaesim+g+ieigiaggadsssvlpigvskkla+alvdlnkart+gqkl++++rlg
  lcl|FitnessBrowser__MR1:202206  86 MDVSTDAYSVTRACATSFQSAVNVAESIMTGNIEIGIAGGADSSSVLPIGVSKKLAHALVDLNKARTFGQKLQIFRRLG 164
                                     ******************************************************************************* PP

                       TIGR02446 159 lkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawadgklkeevmtafvepykkfiaednn 237
                                     +kdllpvppavaeystglsmgqtaeqmakty+i+ra+qdalahrshtla+++wa+g+l++evm+a+v+pyk+fi++dnn
  lcl|FitnessBrowser__MR1:202206 165 IKDLLPVPPAVAEYSTGLSMGQTAEQMAKTYNISRADQDALAHRSHTLANETWASGHLRDEVMVAHVPPYKQFIERDNN 243
                                     ******************************************************************************* PP

                       TIGR02446 238 irenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegrakelgleilgyirsyaftaidveqdmllgpsya 316
                                     irens+la+yaklrpafd+k+gsvtaanstpltdga+a+ilmsegrak+lg++++gyi+syaftaidv+qdml+gpsya
  lcl|FitnessBrowser__MR1:202206 244 IRENSDLASYAKLRPAFDKKHGSVTAANSTPLTDGASAIILMSEGRAKALGYQPIGYIKSYAFTAIDVWQDMLMGPSYA 322
                                     ******************************************************************************* PP

                       TIGR02446 317 tplalkraglelsdltlidmheafaaqtlanvkllasekfaeeklgrakaigeidmskfnvlggsiayghpfaatgarl 395
                                     tplalkrag+el+dltli+mheafaaqtlan++++as+kfaeeklgr++aig+idmskfnvlggs+ayghpfaatg+rl
  lcl|FitnessBrowser__MR1:202206 323 TPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAEEKLGRNRAIGDIDMSKFNVLGGSLAYGHPFAATGTRL 401
                                     ******************************************************************************* PP

                       TIGR02446 396 itqtlrelkrrggglglatacaagglgaamileve 430
                                     itq++relkrrggg+glatacaagglgaami+eve
  lcl|FitnessBrowser__MR1:202206 402 ITQVCRELKRRGGGTGLATACAAGGLGAAMIVEVE 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: 00:00:00.02
# Mc/sec: 7.43
//
[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