GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Klebsiella michiganensis M5al

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>FitnessBrowser__Koxy:BWI76_RS13115
          Length = 255

 Score =  211 bits (537), Expect = 1e-59
 Identities = 121/253 (47%), Positives = 157/253 (62%), Gaps = 2/253 (0%)

Query: 6   LLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGA 65
           L +    RV  +TLNRPQA NALN  L+ ++   L     DP +G  V++G+ + FAAGA
Sbjct: 4   LFIARHARVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGA 63

Query: 66  DIKEMAELTYPQIYLDDFFADA-DRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADN 124
           D+ EMAE   P   LDD       RI    KPLIA+V GYALG GCELAL+CD+I A DN
Sbjct: 64  DLNEMAENDLPAT-LDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDN 122

Query: 125 ARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAES 184
           ARFG PE+ LG++PG GGTQRL R+VGKA A  M L+G  +DA +A RAGLV+ V+P   
Sbjct: 123 ARFGLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPAL 182

Query: 185 LLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMA 244
             E  L  A  +A  S  A    K+S+  + E +L  G++ ER++F  + AT D++EG+ 
Sbjct: 183 TDEYALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGID 242

Query: 245 AFSEKRKPEFTNR 257
           AF  KR  EF  R
Sbjct: 243 AFLHKRTAEFKGR 255


Lambda     K      H
   0.321    0.135    0.375 

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: 144
Number of extensions: 6
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: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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