GapMind for catabolism of small carbon sources

 

Aligments for a candidate for epi in Azospirillum brasilense Sp245

Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate AZOBR_RS07250 AZOBR_RS07250 methylmalonyl-CoA epimerase

Query= SwissProt::Q3IZP4
         (134 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS07250 AZOBR_RS07250
           methylmalonyl-CoA epimerase
          Length = 134

 Score =  217 bits (552), Expect = 6e-62
 Identities = 106/133 (79%), Positives = 113/133 (84%)

Query: 1   MIGRLNHVAIAVPDLEAAAAQYRNTLGAEVGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60
           MIG+LNHVAI VPDL AA A YR+TLGA V  P D   HGVTV+F+ LPNTKIELLHP G
Sbjct: 1   MIGKLNHVAIVVPDLTAATALYRDTLGAAVSQPVDLAPHGVTVVFVELPNTKIELLHPFG 60

Query: 61  EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120
           E SPIAGFLEKNP+GGIHHICYEV+DILAARDR+K  GARVLG GEPKIGAH KPVLFLH
Sbjct: 61  EKSPIAGFLEKNPSGGIHHICYEVDDILAARDRMKAQGARVLGDGEPKIGAHDKPVLFLH 120

Query: 121 PKDFNGCLVELEQ 133
           PKDF G LVELEQ
Sbjct: 121 PKDFCGTLVELEQ 133


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: 146
Number of extensions: 6
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 AZOBR_RS07250 AZOBR_RS07250 (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.300.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.6e-52  162.1   0.0    5.1e-52  162.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS07250  AZOBR_RS07250 methylmalonyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS07250  AZOBR_RS07250 methylmalonyl-CoA epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.0   5.1e-52   5.1e-52       1     129 []       4     133 ..       4     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 5.1e-52
                                 TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekk 69 
                                               kl+hvai v+dl +a++lyrd+lGa+vs+  +l+ +gv+vvf+el +tk+ell+p +e+spia+flek+
  lcl|FitnessBrowser__azobra:AZOBR_RS07250   4 KLNHVAIVVPDLTAATALYRDTLGAAVSQPVDLAPHGVTVVFVELPNTKIELLHPFGEKSPIAGFLEKN 72 
                                               79******************************************************************* PP

                                 TIGR03081  70 kgeGlhhialevddieaaletlkekgvrllde.epriGahGkkvaFlhPkdtgGvLielee 129
                                               + +G+hhi++evddi aa + +k +g r+l++ ep+iGah k+v FlhPkd  G L+ele+
  lcl|FitnessBrowser__azobra:AZOBR_RS07250  73 PSGGIHHICYEVDDILAARDRMKAQGARVLGDgEPKIGAHDKPVLFLHPKDFCGTLVELEQ 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 5.69
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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