GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Cupriavidus basilensis 4G11

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate RR42_RS00895 RR42_RS00895 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Cup4G11:RR42_RS00895
          Length = 376

 Score =  255 bits (652), Expect = 1e-72
 Identities = 144/374 (38%), Positives = 211/374 (56%), Gaps = 1/374 (0%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           LT EQ++  D VR  A +EIAP A   D    FP+      A LG     +P  YGG  +
Sbjct: 3   LTPEQEMIRDAVRQFAQQEIAPHAAAWDRDKTFPQAVHRELAALGAYGVAVPEQYGGAGL 62

Query: 64  GVLTLALILEELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYLRRFAGESTLLTALA 123
             L+LALILEE+      T+ ++      +  ++   + E +++          +L A  
Sbjct: 63  DYLSLALILEEIAAGDGGTSTVISVNNCPVCSMLMAFASEAQKQQWLVPLARGEMLGAFC 122

Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183
            TEP  GSD  A++T AVR GD YV+NG K FIT+G  ADV +V A TD   G +GISAF
Sbjct: 123 LTEPHVGSDAAALRTSAVRDGDDYVLNGVKQFITSGKNADVAIVLAVTDKAAGKRGISAF 182

Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243
           +V   TPG +  R E K+G   S  +++ FE+  VPA N++G EG G+   +  L   R+
Sbjct: 183 LVPTATPGYIVARLEEKLGQHSSDTAQILFEDCRVPAANMLGEEGAGYKMALSGLEGGRI 242

Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303
             A+Q++G+A+ A D A+ + ++R  FG+P+     VQF +ADMAT +E +R +   AA 
Sbjct: 243 GIASQSIGMARAAFDAALAYAKERESFGQPLFAHQAVQFRLADMATKIEVARQMVWHAAS 302

Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363
           L D G +  +   +M K  AS+ A  V + A+QV GG GY+ +  VER+ RD ++ QIY 
Sbjct: 303 LKDAG-RPCLKEAAMGKLYASEMAEEVCSAAIQVFGGYGYVSDFPVERIYRDVRVCQIYE 361

Query: 364 GTNQITRMVTGRAL 377
           GT+ I +++  RAL
Sbjct: 362 GTSDIQKILIARAL 375


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: 309
Number of extensions: 8
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: 376
Length adjustment: 30
Effective length of query: 350
Effective length of database: 346
Effective search space:   121100
Effective search space used:   121100
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