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.29761.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.00
//
[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