GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Dyella japonica UNC79MFTsu3.2

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2193
         (272 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0930
          Length = 264

 Score =  199 bits (505), Expect = 7e-56
 Identities = 120/264 (45%), Positives = 158/264 (59%), Gaps = 3/264 (1%)

Query: 4   FNTLELHSDPRGVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGKHF 63
           + +L+L +D  GV T+ ++R   +NAF+  +I EL  AL     D N+R +++ G G  F
Sbjct: 2   YTSLQL-ADRAGVRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAGASF 60

Query: 64  SAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLISAC 123
           SAGADL WM+  A+     N +D+  LA LM  L  L  PT+A V GAA+GG +GLI+ C
Sbjct: 61  SAGADLNWMRGMAKASEAENREDSLRLAALMRTLQFLPKPTVARVNGAAYGGGVGLIACC 120

Query: 124 DMAIGADEAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGLLS 183
           D+AIG D A+F L+EV++GL PAVISP+V+ AIG R +RR  LT E FD   A+ IGLL 
Sbjct: 121 DIAIGVDSAKFGLTEVKLGLVPAVISPYVIAAIGLRQSRRLFLTGELFDASTAQRIGLLH 180

Query: 184 ESYPAEVLDQQVEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENA--IARIR 241
           +   AE LD  +   +       P A   +K L   V       A R   ENA  IAR+R
Sbjct: 181 QCVRAEELDDALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAERIDRENAELIARLR 240

Query: 242 VSPEGQEGLRAFLQKRAPNWQAES 265
           VS EGQEGL AFL KRA  W A++
Sbjct: 241 VSAEGQEGLGAFLDKRAAAWTAQA 264


Lambda     K      H
   0.318    0.133    0.382 

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: 190
Number of extensions: 5
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: 272
Length of database: 264
Length adjustment: 25
Effective length of query: 247
Effective length of database: 239
Effective search space:    59033
Effective search space used:    59033
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: 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