Alignments for a candidate for fucO in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucO in Klebsiella michiganensis M5al

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate BWI76_RS00645 BWI76_RS00645 lactaldehyde reductase

Query= metacyc::STM4044-MONOMER
         (382 letters)



>FitnessBrowser__Koxy:BWI76_RS00645
          Length = 382

 Score =  690 bits (1780), Expect = 0.0
 Identities = 344/382 (90%), Positives = 364/382 (95%)

Query: 1   MSFMLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMS 60
           MSFMLALPKISLHGAGAI DMV LVA K+WGKALIVTDGQLVKLGLLDSLF+A+DE QM+
Sbjct: 1   MSFMLALPKISLHGAGAIGDMVKLVAGKRWGKALIVTDGQLVKLGLLDSLFAAMDEQQMA 60

Query: 61  YHLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYS 120
           YHLFDEVFPNPTE LVQKG+AAY  A CDY+IAFGGGSPIDTAKAVKILTANPGPSTAYS
Sbjct: 61  YHLFDEVFPNPTEALVQKGYAAYCEAGCDYLIAFGGGSPIDTAKAVKILTANPGPSTAYS 120

Query: 121 GVGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVML 180
           GVGKV N GVPLVAINTTAGTAAEMTSNAVIID+ R+VKEVIIDPNIIPDIAVDDASVML
Sbjct: 121 GVGKVTNPGVPLVAINTTAGTAAEMTSNAVIIDAERQVKEVIIDPNIIPDIAVDDASVML 180

Query: 181 EIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEARE 240
           +IP ++TAATGMDALTHA+EA+VSVGAHPLTDANA EAIRLINLWLPKAVDDGHNLEARE
Sbjct: 181 DIPPAITAATGMDALTHAIEAFVSVGAHPLTDANAQEAIRLINLWLPKAVDDGHNLEARE 240

Query: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFA 300
           QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPI+ENFNRPNAV+RFA
Sbjct: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIIENFNRPNAVSRFA 300

Query: 301 RIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADP 360
           R+AQAMGV+TRGMSDEAAS EAINAIR LSKRVGIP+GFS+LGV+K DIEGWLDKALADP
Sbjct: 301 RVAQAMGVDTRGMSDEAASMEAINAIRALSKRVGIPQGFSQLGVSKADIEGWLDKALADP 360

Query: 361 CAPCNPRTASRDEVRGLYLEAL 382
           CAPCNPR ASRDEVR LYLEAL
Sbjct: 361 CAPCNPRAASRDEVRELYLEAL 382


Lambda     K      H
   0.317    0.133    0.384 

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: 660
Number of extensions: 12
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS00645 BWI76_RS00645 (lactaldehyde reductase)
to HMM TIGR02638 (fucO: lactaldehyde reductase (EC 1.1.1.77))

# 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/TIGR02638.hmm
# target sequence database:        /tmp/gapView.4789.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02638  [M=379]
Accession:   TIGR02638
Description: lactal_redase: lactaldehyde reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.1e-180  585.4   1.4   2.4e-180  585.2   1.4    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00645  BWI76_RS00645 lactaldehyde reduc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00645  BWI76_RS00645 lactaldehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.2   1.4  2.4e-180  2.4e-180       1     379 []       2     378 ..       2     378 .. 1.00

  Alignments for each domain:
  == domain 1  score: 585.2 bits;  conditional E-value: 2.4e-180
                               TIGR02638   1 snrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPt 71 
                                             s++l+l+++s++GaGai d+vk v+ + + kal+vtd +l+klg++d++++++de+++ay+lfdev+pnPt
  lcl|FitnessBrowser__Koxy:BWI76_RS00645   2 SFMLALPKISLHGAGAIGDMVKLVAGKRWGKALIVTDGQLVKLGLLDSLFAAMDEQQMAYHLFDEVFPNPT 72 
                                             589******************************************************************** PP

                               TIGR02638  72 vevvkeGlaafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGt 142
                                              ++v++G aa+ e+g+dylia+GGGspidtaka++i+++nP++++++s  Gv+++ +++vp++ai+ttaGt
  lcl|FitnessBrowser__Koxy:BWI76_RS00645  73 EALVQKGYAAYCEAGCDYLIAFGGGSPIDTAKAVKILTANPGPSTAYS--GVGKVTNPGVPLVAINTTAGT 141
                                             **********************************************99..********************* PP

                               TIGR02638 143 aaevtinyvitdeekkrklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltd 213
                                             aae+t+n+vi+d e+++k vi+dp+ iP++av+da++ml++P+++taatG+dalthaie++++ ga+ ltd
  lcl|FitnessBrowser__Koxy:BWI76_RS00645 142 AAEMTSNAVIIDAERQVKEVIIDPNIIPDIAVDDASVMLDIPPAITAATGMDALTHAIEAFVSVGAHPLTD 212
                                             *********************************************************************** PP

                               TIGR02638 214 alelkaieliaralksavedgkdkeareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanail 284
                                             a++ +ai+li+ +l++av+dg++ eare++a+gqy+aGmaf+++GlGlvh+lah++ga+++lPhGv+nail
  lcl|FitnessBrowser__Koxy:BWI76_RS00645 213 ANAQEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAIL 283
                                             *********************************************************************** PP

                               TIGR02638 285 lPivmefnaekagekyreiakamgvkteelseeeareaaveavktlskrvgiPeklselgvkeediealae 355
                                             lPi+++fn+++a+++++++a+amgv t+++s+e a+ +a++a+++lskrvgiP+++s+lgv+++die +++
  lcl|FitnessBrowser__Koxy:BWI76_RS00645 284 LPIIENFNRPNAVSRFARVAQAMGVDTRGMSDEAASMEAINAIRALSKRVGIPQGFSQLGVSKADIEGWLD 354
                                             *********************************************************************** PP

                               TIGR02638 356 aaladvCtggnPreataeeieely 379
                                             +alad+C+++nPr a+++e++ely
  lcl|FitnessBrowser__Koxy:BWI76_RS00645 355 KALADPCAPCNPRAASRDEVRELY 378
                                             ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (379 nodes)
Target sequences:                          1  (382 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.95
//
[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