GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pseudomonas fluorescens FW300-N2E3

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate AO353_17425 AO353_17425 lactaldehyde reductase

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



>FitnessBrowser__pseudo3_N2E3:AO353_17425
          Length = 382

 Score =  324 bits (831), Expect = 2e-93
 Identities = 172/381 (45%), Positives = 238/381 (62%)

Query: 1   MSFMLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMS 60
           M+    +P +++ G G + + +N + N  + KALIVTD  L K G+   +   L    + 
Sbjct: 1   MTSTFFIPAVNIMGTGCLDEAMNAIRNYGFRKALIVTDAGLAKAGVAGLIAEKLAMQDID 60

Query: 61  YHLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYS 120
             +FD   PNP+   V+ G    Q ++CD +I+ GGGSP D AK + +   N G    Y 
Sbjct: 61  SVIFDGAKPNPSIANVESGLELLQRSQCDCVISLGGGSPHDCAKGIALCATNGGKIADYE 120

Query: 121 GVGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVML 180
           GV +     +PL+AINTTAGTA+EMT   +I D +R VK  I+D N+ P ++V+D ++M 
Sbjct: 121 GVDQSAKPQLPLIAINTTAGTASEMTRFCIITDESRHVKMAIVDRNVTPLLSVNDPALMA 180

Query: 181 EIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEARE 240
            +P  +TAATGMDALTHA+EAYVS  A+P+TDA AL+AI LI+  L  AV DG ++ ARE
Sbjct: 181 AMPKGLTAATGMDALTHAIEAYVSTAANPITDACALKAIELISRNLRLAVHDGSDMIARE 240

Query: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFA 300
            MA+ Q+LAGMAFN+A LG VHA+AHQ G  ++LPHGVCNA+LLP V++FN      R A
Sbjct: 241 NMAYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNAAVCAERLA 300

Query: 301 RIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADP 360
            +AQA+G +T G+S E  +Q AI AIR L++ V IP G   LG   +DI      AL D 
Sbjct: 301 VVAQALGADTLGVSPEEGAQAAIVAIRALARDVEIPGGLRDLGAKLQDIPILAANALKDA 360

Query: 361 CAPCNPRTASRDEVRGLYLEA 381
           C   NPR A + ++  ++  A
Sbjct: 361 CGLTNPRAADQRQIEEIFRSA 381


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: 405
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: 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)

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:

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