GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Echvi_1073 Echvi_1073 Acyl-CoA dehydrogenases

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Cola:Echvi_1073
          Length = 599

 Score =  184 bits (466), Expect = 8e-51
 Identities = 123/392 (31%), Positives = 195/392 (49%), Gaps = 26/392 (6%)

Query: 36  ELTEEQKLLMEMVRNLAVREIAPRAIEID--ENHSFPVHARDLFADLGLLSPLVPVEYGG 93
           E TEEQ+++ +  ++    EI P++ EID  +N            +LGLL   VP EY G
Sbjct: 28  EFTEEQRMMAQACQDFIDTEILPKSEEIDSMKNPDLVPAILKKAGELGLLGISVPEEYQG 87

Query: 94  TGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMT 153
            GM   T  ++ + IG   + +         G L I+  G+   K+KYLP+         
Sbjct: 88  LGMSFNTSMLIADIIGAAGSFSTTYGAHTGIGTLPILYYGTEEQKKKYLPKLAT-GEWAA 146

Query: 154 AFAATEPGAGSDLLAMKTRAV--KKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAK 211
            +  TEP AGSD  + KT+A   + G  Y++NGQK +I+NG  AD+  V+A     K   
Sbjct: 147 CYCLTEPDAGSDANSGKTKATLTEDGKHYLLNGQKMWISNGGFADLFIVFAKIGEDKN-- 204

Query: 212 GMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGAL 271
            ++ F+VE+   G+     EKKMG++G    ++FF D +VP EN++ +   GF   +  L
Sbjct: 205 -LTAFIVEKDFGGITMNEEEKKMGIKGSSTRQVFFNDCKVPVENMLSDRQNGFKIAVNIL 263

Query: 272 SINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAAR-LL 330
           +I RV   +  +G  +  ++ A+Q++ ER+QFG  I     I+  +A+MA +   +  L 
Sbjct: 264 NIGRVKLGAGVLGGCRQVIKNALQYSSERKQFGVSINTFGAIKSKLAEMAVKTYVSESLC 323

Query: 331 VRKATTLLDAKD---------KRGPLIG--------GMAKTFASDTAMKVTTDAVQVMGG 373
            R    + D  D          +  L G         +AK   S+    V    VQ+ GG
Sbjct: 324 YRLGQNIEDRIDALMASGMEANQAKLKGVEQFAMECAIAKIHGSEVLDYVVDQGVQIYGG 383

Query: 374 SGYMQEYQVERMMREAKLTQIYTGTNQITRMV 405
            GY  +  +ER  R+A++++IY GTN+I RM+
Sbjct: 384 MGYSADAPMERAYRDARISRIYEGTNEINRML 415


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: 564
Number of extensions: 31
Number of successful extensions: 7
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: 599
Length adjustment: 34
Effective length of query: 380
Effective length of database: 565
Effective search space:   214700
Effective search space used:   214700
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: 52 (24.6 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