GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Acidovorax caeni R-24608

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_001298675.1:WP_054255950.1
          Length = 376

 Score =  254 bits (648), Expect = 4e-72
 Identities = 142/377 (37%), Positives = 220/377 (58%), Gaps = 7/377 (1%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           LT++Q ++ + VR+    +I P A   D+ H FP       A LG     VP +YGG G+
Sbjct: 3   LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAF 155
           D  T A+VLEEI      T+  +      + +I++  GS A K+++L     +  ++ AF
Sbjct: 63  DYVTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGSEAQKQQWLAPLA-RGEMLGAF 121

Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMST 215
             TEP  GSD  A++T A ++GD YVING K FIT+G    +  V A TD + G KGMS 
Sbjct: 122 CLTEPHVGSDASALRTTATREGDDYVINGVKQFITSGKNGHVAIVIAVTDKAAGKKGMSA 181

Query: 216 FVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINR 275
           F+V    PG      E+K+G      +++ F++  +PA NL+G EG+G+   + AL   R
Sbjct: 182 FLVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIALSALEGGR 241

Query: 276 VFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKAT 335
           +  A+Q+VG+A+ A E A+Q+++ERE FG+PI +   + F +AD AT++EAAR L+  A 
Sbjct: 242 IGIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAARQLIWHAA 301

Query: 336 TLLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393
           +L DA     P +    MAK FAS+ A +V + A+Q +GG G + ++ VER  R+ ++ Q
Sbjct: 302 SLRDAGQ---PCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRDVRVCQ 358

Query: 394 IYTGTNQITRMVTGRSL 410
           IY GT+ + +++  R+L
Sbjct: 359 IYEGTSDVQKIIIQRAL 375


Lambda     K      H
   0.318    0.133    0.375 

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: 330
Number of extensions: 15
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: 414
Length of database: 376
Length adjustment: 31
Effective length of query: 383
Effective length of database: 345
Effective search space:   132135
Effective search space used:   132135
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 24 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