GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PV4:5209191 Shew_1669 butyryl-CoA dehydrogenase
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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