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 [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate 6937205 Sama_1375 Acetyl-CoA C-acetyltransferase (RefSeq)

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



>FitnessBrowser__SB2B:6937205
          Length = 392

 Score =  664 bits (1712), Expect = 0.0
 Identities = 341/388 (87%), Positives = 360/388 (92%)

Query: 9   EIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLG 68
           +IVIVAAKRT MG FQGSLS + S  LAATA+KALL DT +   +VDE+LMGCVLPAGLG
Sbjct: 5   DIVIVAAKRTAMGGFQGSLSEVPSPKLAATAVKALLDDTGLDGARVDELLMGCVLPAGLG 64

Query: 69  QAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAP 128
           QAPARQA LGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAP
Sbjct: 65  QAPARQAALGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAP 124

Query: 129 YLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFALSS 188
           YLLDKAR G+RMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTAD++G+TRE MDAFALSS
Sbjct: 125 YLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADDYGLTRESMDAFALSS 184

Query: 189 LEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTITA 248
           LEKANAAINSGAF+ EIVPVTVS R+GDV +  DEQPGNARPEKIPTLRPAFAKDGTITA
Sbjct: 185 LEKANAAINSGAFEAEIVPVTVSSRKGDVEVKVDEQPGNARPEKIPTLRPAFAKDGTITA 244

Query: 249 ANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNV 308
           ANSSSISDGAAALML +R  A+ LGL VLATIKGHTTHAQEPA+FTTAPVGAM KLLSNV
Sbjct: 245 ANSSSISDGAAALMLMSRDQADALGLKVLATIKGHTTHAQEPAMFTTAPVGAMTKLLSNV 304

Query: 309 GWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTLIH 368
           GWSKDEVDLFEINEAFAMVTMLA+SEL LD  +VNVNGGACALGHPIGCSGAR+LVTLIH
Sbjct: 305 GWSKDEVDLFEINEAFAMVTMLAISELKLDAARVNVNGGACALGHPIGCSGARVLVTLIH 364

Query: 369 ALKARGLKRGVASLCIGGGEATAMAIEV 396
           ALKARGLKRGVASLCIGGGEATAMAIEV
Sbjct: 365 ALKARGLKRGVASLCIGGGEATAMAIEV 392


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: 609
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: 392
Length adjustment: 31
Effective length of query: 365
Effective length of database: 361
Effective search space:   131765
Effective search space used:   131765
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 6937205 Sama_1375 (Acetyl-CoA C-acetyltransferase (RefSeq))
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.11769.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.6e-130  418.9   8.7   1.1e-129  418.7   8.7    1.0  1  lcl|FitnessBrowser__SB2B:6937205  Sama_1375 Acetyl-CoA C-acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937205  Sama_1375 Acetyl-CoA C-acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.7   8.7  1.1e-129  1.1e-129       1     385 []       8     391 ..       8     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 418.7 bits;  conditional E-value: 1.1e-129
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 
                                       iv+a Rt++g ++gsl+e+++ +L+a+++k+ll+ +gld +++de+ +G+vl+ag ++++aR+aal aglp sv a+
  lcl|FitnessBrowser__SB2B:6937205   8 IVAAKRTAMGGFQGSLSEVPSPKLAATAVKALLDDTGLDGARVDELLMGCVLPAGLGQAPARQAALGAGLPLSVGAT 84 
                                       8*********99***************************************************************** PP

                         TIGR01930  78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsm 151
                                       tvn+vC+Sg+++v+la + ikaG a+vv+aGG+EsmS++p+ll+++  r ++++g+ k+ d++  d+   ++t+ +m
  lcl|FitnessBrowser__SB2B:6937205  85 TVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPYLLDKA--RGGMRMGHGKVLDHMFLDGledAYTGGAM 159
                                       ********************************************98..89***********9999999*999***** PP

                         TIGR01930 152 getAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpa 226
                                       g+ A+++a++yg++Re++D++al+S +ka++Ai++g f++eivpv+v  +  ++ v+ De++  n   ek+ +L+pa
  lcl|FitnessBrowser__SB2B:6937205 160 GTFAQKTADDYGLTRESMDAFALSSLEKANAAINSGAFEAEIVPVTVSSRkgDVEVKVDEQPG-NARPEKIPTLRPA 235
                                       ***********************************************9999888888898876.99*********** PP

                         TIGR01930 227 fkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisd 303
                                       f++ +g t+tA+Nss+++DGAaal+lms++ a++lgl++la+i ++++ + +p+ ++++pv A++k+L+  g+s ++
  lcl|FitnessBrowser__SB2B:6937205 236 FAK-DG-TITAANSSSISDGAAALMLMSRDQADALGLKVLATIKGHTTHAQEPAMFTTAPVGAMTKLLSNVGWSKDE 310
                                       *95.9*.6********************************************************************* PP

                         TIGR01930 304 idlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380
                                       +dl+EinEAFA ++++++ el+ ld ++vNvnGGA AlGHP+G+sGar+++tl+++Lk rg k+G+a+lC+ggG ++
  lcl|FitnessBrowser__SB2B:6937205 311 VDLFEINEAFAMVTMLAISELK-LDAARVNVNGGACALGHPIGCSGARVLVTLIHALKARGLKRGVASLCIGGGEAT 386
                                       **********************.88**************************************************** PP

                         TIGR01930 381 Avile 385
                                       A+ +e
  lcl|FitnessBrowser__SB2B:6937205 387 AMAIE 391
                                       **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.39
//
[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