GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Limnohabitans curvus MWH-C5

Align BadK (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase

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



>NCBI__GCF_003063475.1:WP_108402835.1
          Length = 268

 Score =  145 bits (366), Expect = 8e-40
 Identities = 89/258 (34%), Positives = 136/258 (52%), Gaps = 11/258 (4%)

Query: 8   TETQGRVGIITLNRPDVLNALNDAL-MDALGGALLAFDADDGIGAIVIAG-NTRAFAAGA 65
           T+    V  + LNRP+V NALN  + +D L   +   D    +  +V+ G   + F  G 
Sbjct: 15  TQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAKIFCGGG 74

Query: 66  DIASM-----AAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120
           D+         AW Y          R +  +  +  PV+ A+ G AYGGG E+AL CD +
Sbjct: 75  DLKERNGMTPQAWQYQH----EIFERLYWALIDLPLPVIGAINGHAYGGGLEMALCCDFL 130

Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180
            A + A+FALPE+ LG++PG GGTQ LPRA+G+ +A ++ L+ RP +AE+A  +GLV++V
Sbjct: 131 YASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAWGLVNQV 190

Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240
              D +    +  A  IAA +  ++  +K+S+    +  L     FE    +    + D 
Sbjct: 191 AAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRLVDTDDR 250

Query: 241 REGIQAFLEKRAPCFSHR 258
           REG+ AF +KR P F  R
Sbjct: 251 REGVAAFNDKRPPVFKGR 268


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: 141
Number of extensions: 4
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: 268
Length adjustment: 25
Effective length of query: 233
Effective length of database: 243
Effective search space:    56619
Effective search space used:    56619
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 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