GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Klebsiella michiganensis M5al

Align BadK (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__Koxy:BWI76_RS20065
          Length = 285

 Score =  102 bits (253), Expect = 1e-26
 Identities = 84/245 (34%), Positives = 116/245 (47%), Gaps = 7/245 (2%)

Query: 17  ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAGADIASMAAWS- 74
           IT+NRP V NA     +  +  AL     DD IG IV+ G   +AF AG D      +  
Sbjct: 37  ITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKAFCAGGDQKVRGDYGG 96

Query: 75  YSDVYGSNFITRNWETIRQIR---KPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131
           Y D  G + +    +  RQIR   KPVLA VAG + GGG  L + CD+ IA  +A F   
Sbjct: 97  YQDDSGVHHLNV-LDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMCDLTIAAENAIFGQT 155

Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191
             K+G   G  G   + R +G+ KA ++    R  +A++A   GLV+ VV    L  ETV
Sbjct: 156 GPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPLADLEKETV 215

Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251
                +   S  AL  LK +LN   +       L     +   + + + +EG  AF +KR
Sbjct: 216 RWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNATM-LFYMTEEGQEGRNAFNQKR 274

Query: 252 APCFS 256
            P FS
Sbjct: 275 QPDFS 279


Lambda     K      H
   0.321    0.135    0.389 

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: 119
Number of extensions: 7
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 ( 7.4 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