GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucA in Escherichia coli BW25113

Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate 16884 b2800 L-fuculose phosphate aldolase (NCBI)

Query= BRENDA::P0AB87
         (215 letters)



>lcl|FitnessBrowser__Keio:16884 b2800 L-fuculose phosphate aldolase
           (NCBI)
          Length = 215

 Score =  433 bits (1114), Expect = e-126
 Identities = 215/215 (100%), Positives = 215/215 (100%)

Query: 1   MERNKLARQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDG 60
           MERNKLARQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDG
Sbjct: 1   MERNKLARQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDG 60

Query: 61  NGKHEEGKLPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGG 120
           NGKHEEGKLPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGG
Sbjct: 61  NGKHEEGKLPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGG 120

Query: 121 NSIPCAPYATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQL 180
           NSIPCAPYATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQL
Sbjct: 121 NSIPCAPYATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQL 180

Query: 181 YLTTLAITDPVPVLSDEEIAVVLEKFKTYGLRIEE 215
           YLTTLAITDPVPVLSDEEIAVVLEKFKTYGLRIEE
Sbjct: 181 YLTTLAITDPVPVLSDEEIAVVLEKFKTYGLRIEE 215


Lambda     K      H
   0.319    0.134    0.394 

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: 279
Number of extensions: 7
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: 215
Length of database: 215
Length adjustment: 22
Effective length of query: 193
Effective length of database: 193
Effective search space:    37249
Effective search space used:    37249
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 (21.8 bits)
S2: 45 (21.9 bits)

Align candidate 16884 b2800 (L-fuculose phosphate aldolase (NCBI))
to HMM TIGR01086 (fucA: L-fuculose phosphate aldolase (EC 4.1.2.17))

# 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/TIGR01086.hmm
# target sequence database:        /tmp/gapView.21503.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01086  [M=214]
Accession:   TIGR01086
Description: fucA: L-fuculose phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-138  444.7   0.2     3e-138  444.6   0.2    1.0  1  lcl|FitnessBrowser__Keio:16884  b2800 L-fuculose phosphate aldol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16884  b2800 L-fuculose phosphate aldolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.6   0.2    3e-138    3e-138       1     214 []       2     215 .]       2     215 .] 1.00

  Alignments for each domain:
  == domain 1  score: 444.6 bits;  conditional E-value: 3e-138
                       TIGR01086   1 nraelsqkiidtclemtrlglnqgtagnvsvrykdgmlitptgipyeklteehivyvdgngkfeegklpssewrfhlav 79 
                                     +r++l+++iidtclemtrlglnqgtagnvsvry+dgmlitptgipyeklte+hiv++dgngk+eegklpssewrfh+a+
  lcl|FitnessBrowser__Keio:16884   2 ERNKLARQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFIDGNGKHEEGKLPSSEWRFHMAA 80 
                                     79***************************************************************************** PP

                       TIGR01086  80 yqsrpdanavvhnhaihcaavsilnksipaihymvaasgadeipcvpyatfgsrklaeyvaegikeskaillqhhglia 158
                                     yqsrpdanavvhnha+hc+avsiln+sipaihym+aa+g+++ipc+pyatfg+r+l+e+va+++k++ka+llqhhglia
  lcl|FitnessBrowser__Keio:16884  81 YQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAGGNSIPCAPYATFGTRELSEHVALALKNRKATLLQHHGLIA 159
                                     ******************************************************************************* PP

                       TIGR01086 159 cevnlekalwlahevevladlylktlaitdevpvlseeelavvlekfktyglriee 214
                                     cevnlekalwlahevevla+lyl+tlaitd+vpvls+ee+avvlekfktyglriee
  lcl|FitnessBrowser__Keio:16884 160 CEVNLEKALWLAHEVEVLAQLYLTTLAITDPVPVLSDEEIAVVLEKFKTYGLRIEE 215
                                     ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (214 nodes)
Target sequences:                          1  (215 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: 7.44
//
[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 preprint 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