GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Ruegeria conchae TW15

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_000192475.1:WP_010441027.1
          Length = 385

 Score =  192 bits (488), Expect = 1e-53
 Identities = 130/384 (33%), Positives = 198/384 (51%), Gaps = 21/384 (5%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLF---ADLGLLSPLVPVEYGG 93
           +T+E ++  EM        + P   +  E+    V  RD +      GL++  +  EYGG
Sbjct: 11  VTDEHRMFAEMAGRFMDDALVPNTEKWAEDG---VVDRDFWLQAGQTGLMAGSIAEEYGG 67

Query: 94  TGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-----GSPALKEKYLPRFGEK 148
            G  +   ++ L E       TA        G+ SI+       GS   K K+LP+    
Sbjct: 68  VGGGMGFDSVTLYE------QTARGDAGWGYGIQSIVTHYITTYGSEDQKHKWLPKLAS- 120

Query: 149 STLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSK 208
             ++ A A TEPG GSD+ A+KT A K G+ Y + G K FITNG  AD++ V A TD S 
Sbjct: 121 GEMIGALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL 180

Query: 209 GAKGMSTFVVE-RGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVG-EEGKGFAY 266
           GAKG+S   VE  GT G   G N +K+GM+G   +ELFFED++VP  NL+G EEG+GF  
Sbjct: 181 GAKGVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQ 240

Query: 267 LMGALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEA 326
           LM  L   R+     A+G    A+   +++ +ER+ FG+ +      +F +A+  T+ E 
Sbjct: 241 LMKQLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEV 300

Query: 327 ARLLVRKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMM 386
            R  V      L+A  +       M K + S+   ++  + +Q+ GG G+M EY + R+ 
Sbjct: 301 LRSFVNDCIGKLEA-GELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLY 359

Query: 387 REAKLTQIYTGTNQITRMVTGRSL 410
            +A++  IY GTN++ + +  RSL
Sbjct: 360 ADARVQMIYGGTNEVMKELIARSL 383


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: 332
Number of extensions: 19
Number of successful extensions: 4
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: 385
Length adjustment: 31
Effective length of query: 383
Effective length of database: 354
Effective search space:   135582
Effective search space used:   135582
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