GapMind for catabolism of small carbon sources

 

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

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase

Query= metacyc::MONOMER-15953
         (257 letters)



>NCBI__GCF_003063475.1:WP_108402835.1
          Length = 268

 Score =  164 bits (415), Expect = 2e-45
 Identities = 105/259 (40%), Positives = 141/259 (54%), Gaps = 6/259 (2%)

Query: 4   TLSVDAPEQGVRLITLQRPEALNALNTQL-LDELAAELALAEQDAETRAVVLTGS-RKAF 61
           TL        V  + L RPE  NALNTQ+ +D L   + L +   + R VVLTG+  K F
Sbjct: 11  TLECTQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAKIF 70

Query: 62  AAGADIKE---MAERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADI 118
             G D+KE   M  +      E     +W  I     P+I A+NG   GGG E+A+  D 
Sbjct: 71  CGGGDLKERNGMTPQAWQYQHEIFERLYWALID-LPLPVIGAINGHAYGGGLEMALCCDF 129

Query: 119 LIAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSE 178
           L A +DARF  PE+ LGIMPG GGTQ L RA+G+  A ++ L+G+   A  A   GLV++
Sbjct: 130 LYASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAWGLVNQ 189

Query: 179 VTLPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTAD 238
           V  P+  +  AL  A+ IA  APL+VR  K+++      +L +  RFE  A+  L  T D
Sbjct: 190 VAAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRLVDTDD 249

Query: 239 RAEGIRAFQEKRRPEFTGR 257
           R EG+ AF +KR P F GR
Sbjct: 250 RREGVAAFNDKRPPVFKGR 268


Lambda     K      H
   0.320    0.134    0.374 

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: 180
Number of extensions: 11
Number of successful extensions: 2
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: 257
Length of database: 268
Length adjustment: 25
Effective length of query: 232
Effective length of database: 243
Effective search space:    56376
Effective search space used:    56376
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 (21.8 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