Alignments for a candidate for fucO in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucO in Bacteroides thetaiotaomicron VPI-5482

Align Lactaldehyde reductase (characterized, see rationale)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)

Query= uniprot:Q8A199
         (384 letters)



>FitnessBrowser__Btheta:353293
          Length = 384

 Score =  755 bits (1950), Expect = 0.0
 Identities = 384/384 (100%), Positives = 384/384 (100%)

Query: 1   MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY 60
           MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY
Sbjct: 1   MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPY 60

Query: 61  ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL 120
           ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL
Sbjct: 61  ELYSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSL 120

Query: 121 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM 180
           EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM
Sbjct: 121 EGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELM 180

Query: 181 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR 240
           YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR
Sbjct: 181 YSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAR 240

Query: 241 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK 300
           EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK
Sbjct: 241 EAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPK 300

Query: 301 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN 360
           YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN
Sbjct: 301 YIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFN 360

Query: 361 DVCTGGNPRPTSVAEIEVLYRKAF 384
           DVCTGGNPRPTSVAEIEVLYRKAF
Sbjct: 361 DVCTGGNPRPTSVAEIEVLYRKAF 384


Lambda     K      H
   0.317    0.133    0.379 

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: 678
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: 384
Length of database: 384
Length adjustment: 30
Effective length of query: 354
Effective length of database: 354
Effective search space:   125316
Effective search space used:   125316
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 353293 BT3767 (lactaldehyde reductase (NCBI ptt file))
to HMM TIGR02638 (fucO: lactaldehyde reductase (EC 1.1.1.77))

# 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/TIGR02638.hmm
# target sequence database:        /tmp/gapView.1796.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02638  [M=379]
Accession:   TIGR02638
Description: lactal_redase: lactaldehyde reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.4e-200  651.9  11.0   1.5e-200  651.7  11.0    1.0  1  lcl|FitnessBrowser__Btheta:353293  BT3767 lactaldehyde reductase (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353293  BT3767 lactaldehyde reductase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.7  11.0  1.5e-200  1.5e-200       1     379 []       1     380 [.       1     380 [. 0.99

  Alignments for each domain:
  == domain 1  score: 651.7 bits;  conditional E-value: 1.5e-200
                          TIGR02638   1 snrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPtvevvk 76 
                                        +nr+ilne+syfGaG++++i+ e +rrgfkka++vtdkdlik+gv++++++++d+++++yel+++v++nPt+++v+
  lcl|FitnessBrowser__Btheta:353293   1 MNRIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSDVKANPTIANVQ 76 
                                        69************************************************************************** PP

                          TIGR02638  77 eGlaafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGtaaevtinyvi 152
                                        +G+aa+k+sgad+++a+GGGs+idtak+igi+vnnP+fadv+sleGvadtk+kavp++a+pttaGtaaevtinyvi
  lcl|FitnessBrowser__Btheta:353293  77 NGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVADTKHKAVPTFALPTTAGTAAEVTINYVI 152
                                        **************************************************************************** PP

                          TIGR02638 153 tdeekkrklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltdalelkaieliaralk 228
                                        +de++++k+v+vdp+diPava+vd+elm+s+Pk ltaatG+dalthaie+yit+gaw+++d++elkaie+ia++lk
  lcl|FitnessBrowser__Btheta:353293 153 IDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLK 228
                                        **************************************************************************** PP

                          TIGR02638 229 savedgkdkeareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanaillPivmefnae.kagekyrei 303
                                        +av++gkd+ are+++++qy+aGm+fsnvGlG+vh++ahplga+yd+PhGvana+llP+vme+nae  a+ ky++i
  lcl|FitnessBrowser__Btheta:353293 229 AAVDNGKDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAEsPAAPKYIHI 304
                                        *****************************************************************967999***** PP

                          TIGR02638 304 akamgvkteelseeeareaaveavktlskrvgiPeklselgvkeediealaeaaladvCtggnPreataeeieely 379
                                        akamgv+t++++e+e ++aa+eavk+ls ++giP+kl+e++vkeedi+ala aa++dvCtggnPr+++++eie ly
  lcl|FitnessBrowser__Btheta:353293 305 AKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPRPTSVAEIEVLY 380
                                        *************************************************************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (379 nodes)
Target sequences:                          1  (384 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: 12.26
//
[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