Alignments for a candidate for rhaA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaA in Escherichia coli BW25113

Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate 1937180 b3903 L-rhamnose isomerase (NCBI)

Query= BRENDA::P32170
         (419 letters)



>FitnessBrowser__Keio:1937180
          Length = 419

 Score =  852 bits (2201), Expect = 0.0
 Identities = 419/419 (100%), Positives = 419/419 (100%)

Query: 1   MTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQ 60
           MTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQ
Sbjct: 1   MTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQ 60

Query: 61  ATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVE 120
           ATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVE
Sbjct: 61  ATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVE 120

Query: 121 WAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPS 180
           WAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPS
Sbjct: 121 WAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPS 180

Query: 181 VMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240
           VMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG
Sbjct: 181 VMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240

Query: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVL 300
           SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVL
Sbjct: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVL 300

Query: 301 LDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAEL 360
           LDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAEL
Sbjct: 301 LDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAEL 360

Query: 361 RKLEAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRRG 419
           RKLEAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRRG
Sbjct: 361 RKLEAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRRG 419


Lambda     K      H
   0.319    0.134    0.410 

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: 774
Number of extensions: 19
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: 419
Length of database: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
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: 50 (23.9 bits)

Align candidate 1937180 b3903 (L-rhamnose isomerase (NCBI))
to HMM TIGR01748 (rhaA: L-rhamnose isomerase (EC 5.3.1.14))

# 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/TIGR01748.hmm
# target sequence database:        /tmp/gapView.32316.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01748  [M=414]
Accession:   TIGR01748
Description: rhaA: L-rhamnose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.1e-254  829.4   0.0   3.4e-254  829.2   0.0    1.0  1  lcl|FitnessBrowser__Keio:1937180  b3903 L-rhamnose isomerase (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:1937180  b3903 L-rhamnose isomerase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  829.2   0.0  3.4e-254  3.4e-254       1     414 []       5     418 ..       5     418 .. 1.00

  Alignments for each domain:
  == domain 1  score: 829.2 bits;  conditional E-value: 3.4e-254
                         TIGR01748   1 iekayevakqryeavgidveealrqledvkislhcwqgddvegfenpegeltggiqatgnypgkartaeelrrdlek 77 
                                       +e+a+e+akqr++avgidveealrql+++++s+hcwqgddv+gfenpeg+ltggiqatgnypgkar+a+elr+dle+
  lcl|FitnessBrowser__Keio:1937180   5 LEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQATGNYPGKARNASELRADLEQ 81 
                                       689************************************************************************** PP

                         TIGR01748  78 alslipgkkrlnlhaiyvetdekverdeikpkhfknwvewakeqglgldfnptlfshelaadgltlshadkeirefw 154
                                       a++lipg+krlnlhaiy+e+d++v+rd+ikp+hfknwvewak+++lgldfnp++fsh+l+adg+tlshad++ir+fw
  lcl|FitnessBrowser__Keio:1937180  82 AMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVEWAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFW 158
                                       ***************************************************************************** PP

                         TIGR01748 155 iehckasrriseyfgkelgtpsvtniwipdglkdipvdrltprkrllealdevlsekldekytldavesklfglgae 231
                                       i+hckasrr+s+yfg++lgtpsv+niwipdg+kdi+vdrl+pr+rll+aldev+sekl++++++davesklfg+gae
  lcl|FitnessBrowser__Keio:1937180 159 IDHCKASRRVSAYFGEQLGTPSVMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAE 235
                                       ***************************************************************************** PP

                         TIGR01748 232 sytvgshefylgyaltrdklllldaghfhptevisnkisslllyskklllhvsrpvrwdsdhvvvlddelreiasei 308
                                       sytvgs+efy+gya++r+++l+ldaghfhptevis+kis+++ly+++lllhvsrpvrwdsdhvv+ldde+++iasei
  lcl|FitnessBrowser__Keio:1937180 236 SYTVGSNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVLLDDETQAIASEI 312
                                       ***************************************************************************** PP

                         TIGR01748 309 vrndllekvaigldffdasinriaawvigtrnmkkallkalleptadlkkleeegdyterlalleelkslpfgavwe 385
                                       vr+dl+++v+igldffdasinriaawvigtrnmkkall+allepta+l+kle++gdyt+rlallee+kslp++avwe
  lcl|FitnessBrowser__Keio:1937180 313 VRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAELRKLEAAGDYTARLALLEEQKSLPWQAVWE 389
                                       ***************************************************************************** PP

                         TIGR01748 386 sycerkgvpvgeewlkevkayekevllkr 414
                                       +yc+r+++p+g+ewl++v+ayeke+l++r
  lcl|FitnessBrowser__Keio:1937180 390 MYCQRHDTPAGSEWLESVRAYEKEILSRR 418
                                       ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (414 nodes)
Target sequences:                          1  (419 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.05
//
[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