GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Methylocystis bryophila S285

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_085772689.1 B1812_RS17255 enoyl-CoA hydratase-related protein

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_002117405.1:WP_085772689.1
          Length = 249

 Score =  107 bits (267), Expect = 2e-28
 Identities = 74/245 (30%), Positives = 118/245 (48%), Gaps = 3/245 (1%)

Query: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAAGA 65
           ++V   G V  + L+RP   NAL   +     AAL E   D+++ A++  G    F AG 
Sbjct: 5   LIVSREGGVLRIVLDRPAKKNALTRDMYLRALAALEEASGDESLRAVLFCGEGGTFTAGN 64

Query: 66  DIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADT 125
           D+    +++   +       R  + V S  KP++AAVAG A+G G  +   CD+++A+ +
Sbjct: 65  DLADFLSFSGEPM--AFPALRFIKAVASFEKPLVAAVAGDAVGIGATMLFHCDLVYASPS 122

Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185
           A+F    I LG+ P  G +   P    +AKA +L +     DA E  R GLV+ ++P   
Sbjct: 123 ARFKAAFIDLGLPPEGGVSLLAPMRFGEAKAAELLMLGEAFDAKEGHRVGLVNAILPEEE 182

Query: 186 LVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMA 245
           L   A  AA  +A  P  A+   +  + R     L E +  E RLF     + + +   A
Sbjct: 183 LQARAFEAATRLAAKPLTALRDTRRLL-RGDRGRLLERIDEEARLFAQALRSPEVQARFA 241

Query: 246 AFVEK 250
           AF++K
Sbjct: 242 AFLKK 246


Lambda     K      H
   0.321    0.134    0.380 

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: 146
Number of extensions: 4
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: 258
Length of database: 249
Length adjustment: 24
Effective length of query: 234
Effective length of database: 225
Effective search space:    52650
Effective search space used:    52650
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 Apr 09 2024. 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