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_07245 AO353_07245 alcohol dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_07245
          Length = 382

 Score =  251 bits (640), Expect = 3e-71
 Identities = 148/371 (39%), Positives = 214/371 (57%), Gaps = 3/371 (0%)

Query: 12  LHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNP 71
           L GAGAI  +   +        LIVTD  LVK G ++   + L     +Y +FD V P+P
Sbjct: 13  LTGAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVELALAQLGGR--TYEIFDRVLPDP 70

Query: 72  TEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVP 131
              +V+     Y+    D +I  GGGS ID AK+V       G      G+ +V   G P
Sbjct: 71  EIAIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALEDLFGIDQVPRKGPP 130

Query: 132 LVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATG 191
           L+AI TTAGT +E+T+ A++ D   ++K+ II   ++PD+A+    + L  P SVTAA+G
Sbjct: 131 LIAIPTTAGTGSEVTNVAILSDRVAQLKKGIISDYLLPDVALVSPQMTLTCPRSVTAASG 190

Query: 192 MDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGM 251
           +DAL HAVE+Y+S+ A P+TDA A+ AI+LI   LPKA  +  NL+ARE MA    +AGM
Sbjct: 191 VDALVHAVESYLSLNASPITDALAIGAIKLIIKALPKAYTNPSNLQAREDMATASLMAGM 250

Query: 252 AFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETR 311
           AF +AG+G VHALA+  G   N+ HGV NA+LLP V  +N+   + R   IA+A+GV+T 
Sbjct: 251 AFGNAGVGAVHALAYPLGGRFNVTHGVSNALLLPYVMAWNKMACIERMQDIAEALGVKTA 310

Query: 312 GMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGW-LDKALADPCAPCNPRTAS 370
            +S E A+ +A+ A+  L   V IP+G   LG+ ++ I    ++ A  +     NPR  S
Sbjct: 311 QLSAEEAADKAVEAMARLCAAVEIPQGLHSLGIPEDAIPAMAVEAAGIERLMRNNPRKLS 370

Query: 371 RDEVRGLYLEA 381
             ++  +Y  A
Sbjct: 371 TADIEKIYRAA 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: 414
Number of extensions: 15
Number of successful extensions: 2
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