Alignments for a candidate for fucA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucA in Klebsiella michiganensis M5al

Align L-fuculose phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate BWI76_RS22915 BWI76_RS22915 fuculose phosphate aldolase

Query= reanno::Koxy:BWI76_RS22915
         (215 letters)



>FitnessBrowser__Koxy:BWI76_RS22915
          Length = 215

 Score =  434 bits (1117), Expect = e-127
 Identities = 215/215 (100%), Positives = 215/215 (100%)

Query: 1   MERNRLARQIIDTCLEMTRLGLNQGTAGNVSVRYQGGMLITPTGIPYEKLTEAHIVYIDA 60
           MERNRLARQIIDTCLEMTRLGLNQGTAGNVSVRYQGGMLITPTGIPYEKLTEAHIVYIDA
Sbjct: 1   MERNRLARQIIDTCLEMTRLGLNQGTAGNVSVRYQGGMLITPTGIPYEKLTEAHIVYIDA 60

Query: 61  EGQHEQGKLPSSEWRFHLAAYQTRPDAHAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGG 120
           EGQHEQGKLPSSEWRFHLAAYQTRPDAHAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGG
Sbjct: 61  EGQHEQGKLPSSEWRFHLAAYQTRPDAHAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGG 120

Query: 121 NSIPCAPYATFGTRELSEHVAVALKNRKATLLQHHGLIACEENLEKALWLAHEVEVLAQL 180
           NSIPCAPYATFGTRELSEHVAVALKNRKATLLQHHGLIACEENLEKALWLAHEVEVLAQL
Sbjct: 121 NSIPCAPYATFGTRELSEHVAVALKNRKATLLQHHGLIACEENLEKALWLAHEVEVLAQL 180

Query: 181 YLSTLAIIDPVPVLDDEAIAVVLEKFKTYGLRIEE 215
           YLSTLAIIDPVPVLDDEAIAVVLEKFKTYGLRIEE
Sbjct: 181 YLSTLAIIDPVPVLDDEAIAVVLEKFKTYGLRIEE 215


Lambda     K      H
   0.320    0.135    0.402 

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: 267
Number of extensions: 3
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 BWI76_RS22915 BWI76_RS22915 (fuculose phosphate aldolase)
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.7567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     3e-132  425.0   0.2   3.3e-132  424.8   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22915  BWI76_RS22915 fuculose phosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22915  BWI76_RS22915 fuculose phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.8   0.2  3.3e-132  3.3e-132       1     214 []       2     215 .]       2     215 .] 1.00

  Alignments for each domain:
  == domain 1  score: 424.8 bits;  conditional E-value: 3.3e-132
                               TIGR01086   1 nraelsqkiidtclemtrlglnqgtagnvsvrykdgmlitptgipyeklteehivyvdgngkfeegklpss 71 
                                             +r++l+++iidtclemtrlglnqgtagnvsvry+ gmlitptgipyeklte hivy+d +g++e+gklpss
  lcl|FitnessBrowser__Koxy:BWI76_RS22915   2 ERNRLARQIIDTCLEMTRLGLNQGTAGNVSVRYQGGMLITPTGIPYEKLTEAHIVYIDAEGQHEQGKLPSS 72 
                                             69********************************************************************* PP

                               TIGR01086  72 ewrfhlavyqsrpdanavvhnhaihcaavsilnksipaihymvaasgadeipcvpyatfgsrklaeyvaeg 142
                                             ewrfhla+yq+rpda avvhnha+hc+avsiln++ipaihym+aa+g+++ipc+pyatfg+r+l+e+va +
  lcl|FitnessBrowser__Koxy:BWI76_RS22915  73 EWRFHLAAYQTRPDAHAVVHNHAVHCTAVSILNRPIPAIHYMIAAAGGNSIPCAPYATFGTRELSEHVAVA 143
                                             *********************************************************************** PP

                               TIGR01086 143 ikeskaillqhhgliacevnlekalwlahevevladlylktlaitdevpvlseeelavvlekfktyglrie 213
                                             +k++ka+llqhhgliace+nlekalwlahevevla+lyl tlai d+vpvl++e +avvlekfktyglrie
  lcl|FitnessBrowser__Koxy:BWI76_RS22915 144 LKNRKATLLQHHGLIACEENLEKALWLAHEVEVLAQLYLSTLAIIDPVPVLDDEAIAVVLEKFKTYGLRIE 214
                                             **********************************************************************9 PP

                               TIGR01086 214 e 214
                                             e
  lcl|FitnessBrowser__Koxy:BWI76_RS22915 215 E 215
                                             7 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: 6.82
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources