GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Klebsiella michiganensis M5al

Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= reanno::Pedo557:CA265_RS09125
         (258 letters)



>FitnessBrowser__Koxy:BWI76_RS20065
          Length = 285

 Score = 86.7 bits (213), Expect = 5e-22
 Identities = 61/185 (32%), Positives = 96/185 (51%), Gaps = 7/185 (3%)

Query: 10  AERIATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGD-AFSAGADLAY 68
           A+ IA ITINRP+ +NA  P  + E+  A   A  DD + V++L   GD AF AG D   
Sbjct: 31  ADGIAKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKAFCAGGDQKV 90

Query: 69  LQQLQYNTFEENVADSNHLKKL--FTTIYYLPKVVIAQVEGHAIAGGCGLATICDIVFAT 126
             +  Y  ++++ +  +HL  L     I   PK V+A V G++I GG  L  +CD+  A 
Sbjct: 91  --RGDYGGYQDD-SGVHHLNVLDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMCDLTIAA 147

Query: 127 PESNFGYTEVKIG-FVPAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYNLINFVTNS 185
             + FG T  K+G F     + ++   V +  A+EI    + + A++AL   L+N V   
Sbjct: 148 ENAIFGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPL 207

Query: 186 SDIHQ 190
           +D+ +
Sbjct: 208 ADLEK 212


Lambda     K      H
   0.318    0.133    0.367 

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: 118
Number of extensions: 6
Number of successful extensions: 3
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: 285
Length adjustment: 25
Effective length of query: 233
Effective length of database: 260
Effective search space:    60580
Effective search space used:    60580
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