Alignments for a candidate for epi in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for epi in Pedobacter sp. GW460-11-11-14-LB5

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate CA265_RS10815 CA265_RS10815 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>FitnessBrowser__Pedo557:CA265_RS10815
          Length = 135

 Score =  126 bits (317), Expect = 1e-34
 Identities = 60/128 (46%), Positives = 89/128 (69%), Gaps = 1/128 (0%)

Query: 7   RIDHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTEDS 65
           +I+H+GIAVK+L  +I I++ L      + E+V  + V  A  K GEN++ELL+AT  DS
Sbjct: 3   KIEHIGIAVKDLNSSIAIYQKLLNTDCYKTEQVASEFVNTAFFKTGENKVELLQATAPDS 62

Query: 66  PIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSVT 125
            IAKFIEK+GEGIHH+A  V++I +++E L Q+G+ L+ E P+ GA    + F+HPK   
Sbjct: 63  AIAKFIEKKGEGIHHIAFLVDDILAEMERLHQEGFVLLSESPKKGADDKMVCFVHPKDTN 122

Query: 126 GVLLELCE 133
           GVL+E+C+
Sbjct: 123 GVLIEICQ 130


Lambda     K      H
   0.317    0.138    0.389 

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: 87
Number of extensions: 6
Number of successful extensions: 2
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: 136
Length of database: 135
Length adjustment: 15
Effective length of query: 121
Effective length of database: 120
Effective search space:    14520
Effective search space used:    14520
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: 42 (20.8 bits)

Align candidate CA265_RS10815 CA265_RS10815 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

# 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/TIGR03081.hmm
# target sequence database:        /tmp/gapView.31005.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03081  [M=129]
Accession:   TIGR03081
Description: metmalonyl_epim: methylmalonyl-CoA epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    3.4e-45  139.9   0.5    3.8e-45  139.7   0.5    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS10815  CA265_RS10815 methylmalonyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS10815  CA265_RS10815 methylmalonyl-CoA epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.5   3.8e-45   3.8e-45       1     129 []       3     130 ..       3     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 3.8e-45
                                  TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflek 68 
                                                k++h++iavkdl++ +++y+++l ++  ++e+++ + v+++f++ ge+k+ell++++ ds+iakf+ek
  lcl|FitnessBrowser__Pedo557:CA265_RS10815   3 KIEHIGIAVKDLNSSIAIYQKLLNTDCYKTEQVASEFVNTAFFKTGENKVELLQATAPDSAIAKFIEK 70 
                                                79****************************************************************** PP

                                  TIGR03081  69 kkgeGlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                                k geG+hhia+ vddi a +e l+++g  ll+e+p+ Ga  k v F+hPkdt+GvLie+++
  lcl|FitnessBrowser__Pedo557:CA265_RS10815  71 K-GEGIHHIAFLVDDILAEMERLHQEGFVLLSESPKKGADDKMVCFVHPKDTNGVLIEICQ 130
                                                *.*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (135 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 5.87
//
[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