GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Shewanella sp. ANA-3

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 7025069 Shewana3_2232 lactoylglutathione lyase (RefSeq)

Query= BRENDA::P0AC81
         (135 letters)



>FitnessBrowser__ANA3:7025069
          Length = 136

 Score =  192 bits (488), Expect = 2e-54
 Identities = 96/134 (71%), Positives = 110/134 (82%), Gaps = 1/134 (0%)

Query: 2   RLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPE-TEEAVIELTYN 60
           +LLHTMLRVG+L+RSI FYT+VLGMKLLRTSENPEYKYSLAFVG+G E T +AVIELTYN
Sbjct: 3   QLLHTMLRVGNLERSIAFYTQVLGMKLLRTSENPEYKYSLAFVGFGEESTGQAVIELTYN 62

Query: 61  WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK 120
           WG +KY+LGTA+GHIA+  ++    CE I   GG VTR  GPV GGTT IAFVEDPDGYK
Sbjct: 63  WGTEKYDLGTAFGHIAIGDEDIYARCEAIAAAGGKVTRAPGPVAGGTTEIAFVEDPDGYK 122

Query: 121 IELIEEKDAGRGLG 134
           IE I+ K A +GLG
Sbjct: 123 IEFIQMKSATQGLG 136


Lambda     K      H
   0.315    0.137    0.397 

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: 121
Number of extensions: 2
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: 135
Length of database: 136
Length adjustment: 15
Effective length of query: 120
Effective length of database: 121
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: 42 (22.0 bits)
S2: 42 (20.8 bits)

Align candidate 7025069 Shewana3_2232 (lactoylglutathione lyase (RefSeq))
to HMM TIGR00068 (gloA: lactoylglutathione lyase (EC 4.4.1.5))

# 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/TIGR00068.hmm
# target sequence database:        /tmp/gapView.5957.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00068  [M=150]
Accession:   TIGR00068
Description: glyox_I: lactoylglutathione lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.1e-66  209.0   0.0    1.2e-66  208.9   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7025069  Shewana3_2232 lactoylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025069  Shewana3_2232 lactoylglutathione lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.0   1.2e-66   1.2e-66      17     148 ..       3     135 ..       1     136 [] 0.96

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 1.2e-66
                         TIGR00068  17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedess.aavieLtynwgtekydlGngfGhiai 92 
                                       +llhtmlrvg+l++s+ fyt+vlGmkllr++++pe+k+slaf+g+++es+ +avieLtynwgtekydlG++fGhiai
  lcl|FitnessBrowser__ANA3:7025069   3 QLLHTMLRVGNLERSIAFYTQVLGMKLLRTSENPEYKYSLAFVGFGEESTgQAVIELTYNWGTEKYDLGTAFGHIAI 79 
                                       79*******************************************99976369************************ PP

                         TIGR00068  93 avddvykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkktkeal 148
                                       + +d+y+ ce++ a+Ggkv+r pgpv ggt++iafv+DPDGykie+++ k+++++l
  lcl|FitnessBrowser__ANA3:7025069  80 GDEDIYARCEAIAAAGGKVTRAPGPVAGGTTEIAFVEDPDGYKIEFIQMKSATQGL 135
                                       **************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (150 nodes)
Target sequences:                          1  (136 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: 4.48
//
[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