GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Escherichia coli BW25113

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 15814 b1695 putative oxidoreductase (VIMSS)

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Keio:15814
          Length = 383

 Score =  169 bits (427), Expect = 2e-46
 Identities = 123/377 (32%), Positives = 182/377 (48%), Gaps = 6/377 (1%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEI-DENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95
           LTEEQ+LL+  +R L             D+N ++P       AD G+    VP E+GG  
Sbjct: 5   LTEEQELLLASIRELITTNFPEEYFRTCDQNGTYPREFMRALADNGISMLGVPEEFGGIP 64

Query: 96  MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAF 155
            D  T  + L E+ K C + A  L+     + S+   GS     K      E      A 
Sbjct: 65  ADYVTQMLALMEVSK-CGAPAF-LITNGQCIHSMRRFGSAEQLRKTAESTLETGDPAYAL 122

Query: 156 AATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYT-DPSKGAKGMS 214
           A TEPGAGSD  +  T   +K  K  INGQK FIT       + V A    P    K  +
Sbjct: 123 ALTEPGAGSDNNSATTTYTRKNGKVYINGQKTFITGAKEYPYMLVLARDPQPKDPKKAFT 182

Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274
            + V+   PG+      K +G       E++ +++EV   ++VGEEG GF  +M    + 
Sbjct: 183 LWWVDSSKPGIKINPLHK-IGWHMLSTCEVYLDNVEVEESDMVGEEGMGFLNVMYNFEME 241

Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334
           R+  A+++ G A+ A E A ++  +R  FGKPI H   IQ  +A MA +++  R +V K 
Sbjct: 242 RLINAARSTGFAECAFEDAARYANQRIAFGKPIGHNQMIQEKLALMAIKIDNMRNMVLKV 301

Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394
               D + +       +AK + + TAM+V  DA+Q+MGG GY  E +V R  R+ +  +I
Sbjct: 302 AWQAD-QHQSLRTSAALAKLYCARTAMEVIDDAIQIMGGLGYTDEARVSRFWRDVRCERI 360

Query: 395 YTGTNQITRMVTGRSLL 411
             GT++I   V GR +L
Sbjct: 361 GGGTDEIMIYVAGRQIL 377


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: 339
Number of extensions: 17
Number of successful extensions: 5
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: 383
Length adjustment: 31
Effective length of query: 383
Effective length of database: 352
Effective search space:   134816
Effective search space used:   134816
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