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 [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate 200842 SO1677 acetyl-CoA acetyltransferase (NCBI ptt file)

Query= reanno::MR1:200842
         (396 letters)



>FitnessBrowser__MR1:200842
          Length = 396

 Score =  762 bits (1968), Expect = 0.0
 Identities = 396/396 (100%), Positives = 396/396 (100%)

Query: 1   MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG 60
           MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG
Sbjct: 1   MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG 60

Query: 61  CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG 120
           CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG
Sbjct: 61  CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG 120

Query: 121 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ 180
           MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ
Sbjct: 121 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ 180

Query: 181 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF 240
           MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF
Sbjct: 181 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF 240

Query: 241 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA 300
           AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA
Sbjct: 241 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA 300

Query: 301 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA 360
           MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA
Sbjct: 301 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA 360

Query: 361 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396
           RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV
Sbjct: 361 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396


Lambda     K      H
   0.316    0.131    0.364 

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: 682
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 200842 SO1677 (acetyl-CoA acetyltransferase (NCBI ptt file))
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.23338.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.8e-132  425.4   9.2   1.1e-131  425.2   9.2    1.0  1  lcl|FitnessBrowser__MR1:200842  SO1677 acetyl-CoA acetyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200842  SO1677 acetyl-CoA acetyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.2   9.2  1.1e-131  1.1e-131       1     385 []      12     395 ..      12     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 425.2 bits;  conditional E-value: 1.1e-131
                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpaltv 79 
                                     iv+a Rtp+g+++gsl+ +++ +L+a++ik+ll+ +++ p+k+dev +G+vl+ag ++++aR+a+l aglp sv a+tv
  lcl|FitnessBrowser__MR1:200842  12 IVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQAPARQATLGAGLPLSVGATTV 90 
                                     8****************************************************************************** PP

                       TIGR01930  80 nrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmgetA 155
                                     n+vC+Sg+++v+la + ikaG a+vv+aGG+EsmS++p+ll+++  r+++++g+ k+ d++  d+   ++t+ +mg+ A
  lcl|FitnessBrowser__MR1:200842  91 NKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPYLLDKA--RAGIRMGHGKVLDHMFLDGledAYTGGAMGTFA 167
                                     ******************************************98..89***********9999999*999********* PP

                       TIGR01930 156 enlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkg 232
                                     +++a+++gi+Re++D++al+S +ka++Ai++g fk eivpv+v ++  ++++++De++  n   ek+ +L+paf++ +g
  lcl|FitnessBrowser__MR1:200842 168 QKTADEFGITREQMDAFALSSLEKANAAINSGAFKTEIVPVTVSDRrgDVTIDTDEQPG-NARPEKIPTLRPAFAK-DG 244
                                     ********************************************99*999999999886.99************95.9* PP

                       TIGR01930 233 stvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinE 311
                                      t+tA+Nss+++DGAaal+l++++ a++lglt+la+i ++++ + +p+ ++++pv A+ k+L+  g+s +++dl+EinE
  lcl|FitnessBrowser__MR1:200842 245 -TITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNVGWSKDEVDLFEINE 322
                                     .6***************************************************************************** PP

                       TIGR01930 312 AFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                     AFA ++++++ elg ld  kvNvnGGA AlGHP+G+sGar+++tl+++Lk rg k+G+a+lC+ggG ++A+ +e
  lcl|FitnessBrowser__MR1:200842 323 AFAMVTMLAVSELG-LDMTKVNVNGGACALGHPIGCSGARLLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395
                                     **************.88******************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (396 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: 12.29
//
[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