GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Dyadobacter tibetensis Y620-1

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_000566685.1:WP_025764976.1
          Length = 387

 Score =  234 bits (596), Expect = 4e-66
 Identities = 137/384 (35%), Positives = 206/384 (53%), Gaps = 3/384 (0%)

Query: 29  QRRDTMNELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVP 88
           Q  ++     E  +L+ E VR+ A++ I P  +E DE+  FP        +LGL+  LVP
Sbjct: 5   QHTESGEHREENCRLIQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVP 64

Query: 89  VEYGGTGMDITTFAMVLEEIGKVCASTALMLLAQADGMLS-IILDGSPALKEKYLPRFGE 147
            +YGG G+    +   +  + KV  S  L + A      + I++ G+   K KYLP+   
Sbjct: 65  EQYGGAGLGYQEYITAIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLAS 124

Query: 148 KSTLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPS 207
              +  A+  TEP  GSD   MKT AV+ G+ +++NG K FITNG    +  V   T   
Sbjct: 125 GEWI-GAWGLTEPNTGSDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEP 183

Query: 208 KGAKGMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYL 267
               G + F+VE GT G   G  E K+GMR     EL FED  +     +G+ G+GF   
Sbjct: 184 GDKHGATAFIVEHGTHGFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQS 243

Query: 268 MGALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAA 327
           +  L   R+  A+  VG A GA E A+ +++ER QFGK I+    I F +ADM T+++A+
Sbjct: 244 LKILDGGRISIAALGVGTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQAS 303

Query: 328 RLLVRKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMR 387
            LL  +A    D   K   L G +AK  +S+TA++V T+AVQ+ GG G+ ++Y  E+  R
Sbjct: 304 TLLTFQAGKEKDLGQKVS-LSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYR 362

Query: 388 EAKLTQIYTGTNQITRMVTGRSLL 411
           ++KL  I  GT++I +MV  + +L
Sbjct: 363 DSKLCTIGEGTSEIQKMVISKEIL 386


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: 336
Number of extensions: 17
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: 387
Length adjustment: 31
Effective length of query: 383
Effective length of database: 356
Effective search space:   136348
Effective search space used:   136348
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