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.26060.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: 7.95
//
[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