GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Shewanella oneidensis MR-1

Align BadK (characterized)
to candidate 200845 SO1680 enoyl-CoA hydratase/isomerase family protein (NCBI ptt file)

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__MR1:200845
          Length = 257

 Score =  125 bits (314), Expect = 9e-34
 Identities = 88/260 (33%), Positives = 129/260 (49%), Gaps = 13/260 (5%)

Query: 6   ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAG 64
           ++   +G   I+T+N P   N      + AL   +L  +A+  I A+V+ G   + F+AG
Sbjct: 4   LVERIEGHTAILTMNNPPA-NTWTAQSLQALKAKVLELNANKDIYALVLTGEGNKFFSAG 62

Query: 65  ADIASMA------AWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACD 118
           AD+   +      A S +  +G  F     ET+ Q R   +AA+ G A GGG E+ALACD
Sbjct: 63  ADLKLFSDGDKGNAASMAKHFGEAF-----ETLSQFRGVSIAAINGYAMGGGLEVALACD 117

Query: 119 IVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVS 178
           I IA   A  ALPE  +GLLP AGGTQ L   +G+  A  M L    +NA +A    LV 
Sbjct: 118 IRIAETQAVMALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERVNAAQALNLRLVE 177

Query: 179 RVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASA 238
            VV+     +  +ALA  +A  S  ++ A K  +    +   ++ +  E       F + 
Sbjct: 178 EVVETGEALNAAIALAAKVANQSPSSVTACKTLIQAGRQMPRSQALPIEHELFVGLFDTE 237

Query: 239 DAREGIQAFLEKRAPCFSHR 258
           D  EG+ AFLEKR   + +R
Sbjct: 238 DQAEGVNAFLEKRKADWKNR 257


Lambda     K      H
   0.321    0.135    0.389 

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: 107
Number of extensions: 5
Number of successful extensions: 1
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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