GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Shewanella loihica PV-4

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 5209191 Shew_1669 butyryl-CoA dehydrogenase (RefSeq)

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__PV4:5209191
          Length = 385

 Score =  258 bits (660), Expect = 2e-73
 Identities = 145/375 (38%), Positives = 208/375 (55%), Gaps = 2/375 (0%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L E+Q+   E+    A  E+AP A + DE H FP        +LG  S   P   GG G+
Sbjct: 5   LNEDQRQFAELATQFAQEELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGL 64

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156
                +++ E++   C +T  ML         +   GS  L++++       + L  ++ 
Sbjct: 65  SRLDSSIIFEQLAMGCTATTAMLTIHNMATWMVTSFGSQTLRDEWSEALTTGNKL-ASYC 123

Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216
            TE GAGSD  ++KT+AV++GD+YVI+G K FI+     ++L V   T  + G KG+S  
Sbjct: 124 LTEAGAGSDAASLKTKAVREGDEYVISGAKMFISGAGSTELLVVMCRTGDA-GPKGISAI 182

Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276
            +     G+ YG  E KMG    P  E+ F+ + VP  NL+GEEG+GF + M  L   R+
Sbjct: 183 AIPADAAGISYGKAEDKMGWNAQPTREITFDKVRVPVTNLLGEEGQGFTFAMKGLDGGRI 242

Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336
             A+ +VG AQ ALERA Q+  ER+QFGKPIA    +QF +ADMATE+ AAR +VR A  
Sbjct: 243 NIATCSVGTAQAALERAQQYMNERQQFGKPIAAFQALQFKLADMATELVAARQMVRLAAF 302

Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396
            LD+ D        MAK FA+D    V   A+Q+ GG GY++EY +ER  R+ ++ QI  
Sbjct: 303 KLDSGDPEATAYCAMAKRFATDVGFNVCDSALQLHGGYGYIREYPLERHFRDVRVHQILE 362

Query: 397 GTNQITRMVTGRSLL 411
           GTN+I R++  R LL
Sbjct: 363 GTNEIMRLIIARRLL 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: 337
Number of extensions: 9
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: 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 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