Alignments for a candidate for rhaA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaA in Klebsiella michiganensis M5al

Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate BWI76_RS00675 BWI76_RS00675 L-rhamnose isomerase

Query= reanno::Koxy:BWI76_RS00675
         (419 letters)



>FitnessBrowser__Koxy:BWI76_RS00675
          Length = 419

 Score =  859 bits (2220), Expect = 0.0
 Identities = 419/419 (100%), Positives = 419/419 (100%)

Query: 1   MTTQLEQAWEIAKQRYASVGVDVEEALRQLDRLPVSMHCWQGDDVVGFENPEGSLTGGIQ 60
           MTTQLEQAWEIAKQRYASVGVDVEEALRQLDRLPVSMHCWQGDDVVGFENPEGSLTGGIQ
Sbjct: 1   MTTQLEQAWEIAKQRYASVGVDVEEALRQLDRLPVSMHCWQGDDVVGFENPEGSLTGGIQ 60

Query: 61  ATGNYPGKARNASELRADLEQAMSLIPGPKRLNLHALYLESDTPVSRNEIKPEHFKNWVE 120
           ATGNYPGKARNASELRADLEQAMSLIPGPKRLNLHALYLESDTPVSRNEIKPEHFKNWVE
Sbjct: 61  ATGNYPGKARNASELRADLEQAMSLIPGPKRLNLHALYLESDTPVSRNEIKPEHFKNWVE 120

Query: 121 WAKTNKLGLDFNPSCFSHPLSADGFTLSHANDEIRQFWIDHCKASRRISAYFGEQLGTPS 180
           WAKTNKLGLDFNPSCFSHPLSADGFTLSHANDEIRQFWIDHCKASRRISAYFGEQLGTPS
Sbjct: 121 WAKTNKLGLDFNPSCFSHPLSADGFTLSHANDEIRQFWIDHCKASRRISAYFGEQLGTPS 180

Query: 181 VMNIWIPDGMKDITVDRFAPRQRLLNALDEVISEKLDPAHHIDAVESKLFGIGAESYTVG 240
           VMNIWIPDGMKDITVDRFAPRQRLLNALDEVISEKLDPAHHIDAVESKLFGIGAESYTVG
Sbjct: 181 VMNIWIPDGMKDITVDRFAPRQRLLNALDEVISEKLDPAHHIDAVESKLFGIGAESYTVG 240

Query: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYIPRLLLHVSRPVRWDSDHVVL 300
           SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYIPRLLLHVSRPVRWDSDHVVL
Sbjct: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYIPRLLLHVSRPVRWDSDHVVL 300

Query: 301 LDDETQAIASEIIRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAQL 360
           LDDETQAIASEIIRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAQL
Sbjct: 301 LDDETQAIASEIIRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAQL 360

Query: 361 RQLEVDGDYTARLALLEEQKCLPWHAIWEMYCQRHDTPAGSQWLDNVRAYENAVLSQRG 419
           RQLEVDGDYTARLALLEEQKCLPWHAIWEMYCQRHDTPAGSQWLDNVRAYENAVLSQRG
Sbjct: 361 RQLEVDGDYTARLALLEEQKCLPWHAIWEMYCQRHDTPAGSQWLDNVRAYENAVLSQRG 419


Lambda     K      H
   0.320    0.135    0.417 

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: 813
Number of extensions: 21
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 BWI76_RS00675 BWI76_RS00675 (L-rhamnose isomerase)
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.32069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.9e-248  809.0   0.0   5.5e-248  808.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00675  BWI76_RS00675 L-rhamnose isomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00675  BWI76_RS00675 L-rhamnose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.8   0.0  5.5e-248  5.5e-248       1     414 []       5     418 ..       5     418 .. 1.00

  Alignments for each domain:
  == domain 1  score: 808.8 bits;  conditional E-value: 5.5e-248
                               TIGR01748   1 iekayevakqryeavgidveealrqledvkislhcwqgddvegfenpegeltggiqatgnypgkartaeel 71 
                                             +e+a+e+akqry++vg+dveealrql+++++s+hcwqgddv gfenpeg+ltggiqatgnypgkar+a+el
  lcl|FitnessBrowser__Koxy:BWI76_RS00675   5 LEQAWEIAKQRYASVGVDVEEALRQLDRLPVSMHCWQGDDVVGFENPEGSLTGGIQATGNYPGKARNASEL 75 
                                             689******************************************************************** PP

                               TIGR01748  72 rrdlekalslipgkkrlnlhaiyvetdekverdeikpkhfknwvewakeqglgldfnptlfshelaadglt 142
                                             r+dle+a+slipg+krlnlha+y+e+d++v+r+eikp+hfknwvewak ++lgldfnp++fsh+l+adg+t
  lcl|FitnessBrowser__Koxy:BWI76_RS00675  76 RADLEQAMSLIPGPKRLNLHALYLESDTPVSRNEIKPEHFKNWVEWAKTNKLGLDFNPSCFSHPLSADGFT 146
                                             *********************************************************************** PP

                               TIGR01748 143 lshadkeirefwiehckasrriseyfgkelgtpsvtniwipdglkdipvdrltprkrllealdevlsekld 213
                                             lsha++eir+fwi+hckasrris+yfg++lgtpsv+niwipdg+kdi+vdr++pr+rll+aldev+sekld
  lcl|FitnessBrowser__Koxy:BWI76_RS00675 147 LSHANDEIRQFWIDHCKASRRISAYFGEQLGTPSVMNIWIPDGMKDITVDRFAPRQRLLNALDEVISEKLD 217
                                             *********************************************************************** PP

                               TIGR01748 214 ekytldavesklfglgaesytvgshefylgyaltrdklllldaghfhptevisnkisslllyskklllhvs 284
                                             +++++davesklfg+gaesytvgs+efy+gya++r+++l+ldaghfhptevis+kis+++ly ++lllhvs
  lcl|FitnessBrowser__Koxy:BWI76_RS00675 218 PAHHIDAVESKLFGIGAESYTVGSNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYIPRLLLHVS 288
                                             *********************************************************************** PP

                               TIGR01748 285 rpvrwdsdhvvvlddelreiaseivrndllekvaigldffdasinriaawvigtrnmkkallkalleptad 355
                                             rpvrwdsdhvv+ldde+++iasei+r+dl+++v+igldffdasinriaawvigtrnmkkall+allepta+
  lcl|FitnessBrowser__Koxy:BWI76_RS00675 289 RPVRWDSDHVVLLDDETQAIASEIIRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAQ 359
                                             *********************************************************************** PP

                               TIGR01748 356 lkkleeegdyterlalleelkslpfgavwesycerkgvpvgeewlkevkayekevllkr 414
                                             l++le +gdyt+rlallee+k lp+ a+we+yc+r+++p+g++wl++v+aye+ vl++r
  lcl|FitnessBrowser__Koxy:BWI76_RS00675 360 LRQLEVDGDYTARLALLEEQKCLPWHAIWEMYCQRHDTPAGSQWLDNVRAYENAVLSQR 418
                                             ********************************************************997 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: 8.44
//
[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:

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