GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Pseudomonas fluorescens GW456-L13

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate PfGW456L13_2591 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2591
          Length = 387

 Score =  249 bits (637), Expect = 7e-71
 Identities = 154/379 (40%), Positives = 219/379 (57%), Gaps = 21/379 (5%)

Query: 11  TLDMVRD----VATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66
           T+DM+RD       +EIAPRA ++D  +LFP      F  +GLL   +P  YGG  +G L
Sbjct: 13  TIDMLRDQVQSFVAKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITVPEEYGGAGLGYL 72

Query: 67  TLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTALAA 124
              + +EE+ R  AS AL   A ++  +  I+  G+ E K +YL +  +GE   + ALA 
Sbjct: 73  AHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNHEQKSKYLPKLISGEH--IGALAM 130

Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184
           +EP AGSD+++MK RA ++GDKYV+NG K +ITNG  A+  V+YA TD EKG  GI+AF+
Sbjct: 131 SEPNAGSDVVSMKLRADKRGDKYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFI 190

Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244
           VE+   G        K+GMRGS   ELFF+++EVP ENI+G    G   LM  L   RV 
Sbjct: 191 VERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVLMSGLDYERVV 250

Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304
            +    GI Q  +D+ V +  DR QFG+ I     +Q  VADM T + ASR      A+ 
Sbjct: 251 LSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQA 310

Query: 305 LDDGDKK------AVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKL 358
            + G+         +LY       +++ A ++  DA+Q+LGG+GY+ E    R++RDAKL
Sbjct: 311 CERGETTRKDAAGVILY-------SAERATQMALDAIQILGGNGYINEFPAGRLLRDAKL 363

Query: 359 TQIYTGTNQITRMVTGRAL 377
            +I  GT++I RM+ GR L
Sbjct: 364 YEIGAGTSEIRRMLIGREL 382


Lambda     K      H
   0.319    0.134    0.371 

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: 338
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 380
Length of database: 387
Length adjustment: 30
Effective length of query: 350
Effective length of database: 357
Effective search space:   124950
Effective search space used:   124950
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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