GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Pseudomonas fluorescens FW300-N2E2

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate Pf6N2E2_449 Lactoylglutathione lyase (EC 4.4.1.5)

Query= BRENDA::Q88GF8
         (175 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449
          Length = 173

 Score =  296 bits (759), Expect = 1e-85
 Identities = 142/173 (82%), Positives = 150/173 (86%)

Query: 1   MSLHDLQTLPGVTAQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAA 60
           MSLH+L T PGVTAQPDAATA+FVFNHTMLRVKDI KSLDFYTRVLGF LV+KRDFPEA 
Sbjct: 1   MSLHELNTFPGVTAQPDAATAKFVFNHTMLRVKDITKSLDFYTRVLGFSLVEKRDFPEAE 60

Query: 61  FSLYFLALVDPAQIPADDTARHQWMKSIPGVLELTHNHGTENDADFAYHNGNTDPRGFGH 120
           FSLYFLALVD  QIPAD  AR +WMKSIPG+LELTHNHGTE+D  FAYHNGNTDPRGFGH
Sbjct: 61  FSLYFLALVDKNQIPADAAARTEWMKSIPGILELTHNHGTESDPAFAYHNGNTDPRGFGH 120

Query: 121 ICISVPDVRAACARFEELEVPFQKRLQDGRMNHLAFVKDPDGYWVEVIQPTEL 173
           ICISVPDV AAC RFE L   FQKRL DGRM  LAF+KDPDGYWVE+IQP  L
Sbjct: 121 ICISVPDVAAACERFEALGCDFQKRLNDGRMKSLAFIKDPDGYWVEIIQPAPL 173


Lambda     K      H
   0.323    0.139    0.431 

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: 224
Number of extensions: 2
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: 175
Length of database: 173
Length adjustment: 19
Effective length of query: 156
Effective length of database: 154
Effective search space:    24024
Effective search space used:    24024
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 (21.9 bits)
S2: 44 (21.6 bits)

Align candidate Pf6N2E2_449 (Lactoylglutathione lyase (EC 4.4.1.5))
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.31549.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    6.6e-54  167.6   0.0    7.7e-54  167.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449  Lactoylglutathione lyase (EC 4.4


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449  Lactoylglutathione lyase (EC 4.4.1.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   7.7e-54   7.7e-54       7     141 ..      14     170 ..       7     173 .] 0.97

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 7.7e-54
                                     TIGR00068   7 avedeatkkylllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessa.... 67 
                                                   a+ d at k+++ htmlrv+d+ ksldfyt+vlG +l+ k+dfpe +fsl+fl+  d+++     
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449  14 AQPDAATAKFVFNHTMLRVKDITKSLDFYTRVLGFSLVEKRDFPEAEFSLYFLALVDKNQIpada 78 
                                                   677999******************************************************9**** PP

                                     TIGR00068  68 ...........avieLtynwgtek.....ydlGn....gfGhiaiavddvykacervkakGgkvv 112
                                                               ++eLt+n+gte+     y++Gn    gfGhi i+v+dv++acer++a+G ++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449  79 aartewmksipGILELTHNHGTESdpafaYHNGNtdprGFGHICISVPDVAAACERFEALGCDFQ 143
                                                   **********99***************************************************** PP

                                     TIGR00068 113 repgpvkggtkviafvkDPDGykiellek 141
                                                   ++    +g++k +af+kDPDGy++e+++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_449 144 KRL--NDGRMKSLAFIKDPDGYWVEIIQP 170
                                                   **9..**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (150 nodes)
Target sequences:                          1  (173 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 4.79
//
[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