GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Dinoroseobacter shibae DFL-12

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Dino:3607424
          Length = 382

 Score =  234 bits (597), Expect = 3e-66
 Identities = 148/381 (38%), Positives = 211/381 (55%), Gaps = 12/381 (3%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           +T+E ++L EM RN    E AP      +             +LGLL P VP  YGG G 
Sbjct: 7   MTDEHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGG 66

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLS--IILDGSPALKEKYLPRFGEKSTLMTA 154
           D    A +L EI +   S          G+++  I+  GS   K+K+LP+      ++ A
Sbjct: 67  DFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKM-VSGEMVGA 125

Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214
            A TEPGAGSDL  +KTRAVK G+ Y ++G K FITNG  A+++ V A TDPS GAKG+S
Sbjct: 126 LAMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVS 185

Query: 215 TFVVE-RGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLV-GEEGKGFAYLMGALS 272
             V+E  G  G   G N  K+GM     SELFF+++ +P ENL+ GE GKGF  +M  L 
Sbjct: 186 LVVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLP 245

Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVR 332
             R+  A+ AVG  +GA+ER + + +ER+ FG PI      +F +A+  T+   AR  + 
Sbjct: 246 QERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLN 305

Query: 333 KATTLLDAKDKRGPLI---GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREA 389
           +      A+   G L      MAK + +DT  +V  + VQ+ GG GYM EY + +M  +A
Sbjct: 306 ECM----AEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDA 361

Query: 390 KLTQIYTGTNQITRMVTGRSL 410
           ++ +IY GTN+I + + GR+L
Sbjct: 362 RVQRIYGGTNEIMKELIGRAL 382


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: 384
Number of extensions: 20
Number of successful extensions: 6
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: 382
Length adjustment: 31
Effective length of query: 383
Effective length of database: 351
Effective search space:   134433
Effective search space used:   134433
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