GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Pseudomonas fluorescens FW300-N2E3

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate AO353_25670 AO353_25670 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25670
          Length = 383

 Score =  251 bits (642), Expect = 2e-71
 Identities = 149/375 (39%), Positives = 217/375 (57%), Gaps = 3/375 (0%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           LTEEQ +  DM RD A  EIAP A   ++     +       +LGLL  ++P  +GGT +
Sbjct: 6   LTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYV 65

Query: 64  GVLTLALILEELGRVCAST-ALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTAL 122
             +  AL +EE+     +T AL+ I  + G  P+++ G+ E K+ +L   A    +    
Sbjct: 66  DYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAI-GCF 124

Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182
             TEP AGS+   ++TRA  +  ++VING K F++NG  A + +V+A TDP+ G KG+SA
Sbjct: 125 CLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSA 184

Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242
           F+V   TPG +  R+E KMG+R S    +   N  +P  N++G  G G A  +  L   R
Sbjct: 185 FLVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGR 244

Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302
           +  AAQA+GIA+ A + A+ + +DRVQF KPI     V  M+ADM T + A+RLL   AA
Sbjct: 245 IGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILHAA 304

Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362
            L   G K  +   S AK  AS+ A +V + A+Q+ GG GY+++  VER  RDA++TQIY
Sbjct: 305 RLRSAG-KPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIY 363

Query: 363 TGTNQITRMVTGRAL 377
            G+++I RMV  R L
Sbjct: 364 EGSSEIQRMVIAREL 378


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: 347
Number of extensions: 13
Number of successful extensions: 3
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: 380
Length of database: 383
Length adjustment: 30
Effective length of query: 350
Effective length of database: 353
Effective search space:   123550
Effective search space used:   123550
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.

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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