GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Phaeobacter inhibens BS107

Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate GFF2418 PGA1_c24490 methylmalonyl-CoA epimerase

Query= SwissProt::Q3IZP4
         (134 letters)



>FitnessBrowser__Phaeo:GFF2418
          Length = 134

 Score =  258 bits (658), Expect = 3e-74
 Identities = 124/134 (92%), Positives = 130/134 (97%)

Query: 1   MIGRLNHVAIAVPDLEAAAAQYRNTLGAEVGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60
           MIGRLNHVAIAVPDL+AA+AQYRNTLGA+VGAPQDEPDHGVTV+FI LPNTKIELL+PLG
Sbjct: 1   MIGRLNHVAIAVPDLDAASAQYRNTLGAKVGAPQDEPDHGVTVVFIELPNTKIELLYPLG 60

Query: 61  EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120
           E SPIAGFLEKNPAGGIHHICYEV+DILAARDRLK  GARVLGSGEPKIGAHGKPVLFLH
Sbjct: 61  EASPIAGFLEKNPAGGIHHICYEVDDILAARDRLKAEGARVLGSGEPKIGAHGKPVLFLH 120

Query: 121 PKDFNGCLVELEQV 134
           PKDFNGCLVELEQV
Sbjct: 121 PKDFNGCLVELEQV 134


Lambda     K      H
   0.319    0.141    0.421 

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: 178
Number of extensions: 8
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: 134
Length of database: 134
Length adjustment: 15
Effective length of query: 119
Effective length of database: 119
Effective search space:    14161
Effective search space used:    14161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 42 (20.8 bits)

Align candidate GFF2418 PGA1_c24490 (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.20475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.5e-55  171.8   0.0      5e-55  171.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2418  PGA1_c24490 methylmalonyl-CoA ep


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2418  PGA1_c24490 methylmalonyl-CoA epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.0     5e-55     5e-55       1     129 []       4     133 ..       4     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 5e-55
                          TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeGlhh 76 
                                        +l+hvaiav+dl++a++ yr++lGakv   ++ p++gv+vvf+el +tk+ell pl+e spia+flek++++G+hh
  lcl|FitnessBrowser__Phaeo:GFF2418   4 RLNHVAIAVPDLDAASAQYRNTLGAKVGAPQDEPDHGVTVVFIELPNTKIELLYPLGEASPIAGFLEKNPAGGIHH 79 
                                        79************************************************************************** PP

                          TIGR03081  77 ialevddieaaletlkekgvrllde.epriGahGkkvaFlhPkdtgGvLielee 129
                                        i++evddi aa + lk +g r+l++ ep+iGahGk+v FlhPkd +G L+ele+
  lcl|FitnessBrowser__Phaeo:GFF2418  80 ICYEVDDILAARDRLKAEGARVLGSgEPKIGAHGKPVLFLHPKDFNGCLVELEQ 133
                                        ***********************988**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (134 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 3.47
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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