GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Sphingobium czechense LL01

Align BadK (characterized)
to candidate WP_066601421.1 V473_RS05770 2,3-dehydroadipyl-CoA hydratase

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



>NCBI__GCF_001046645.1:WP_066601421.1
          Length = 260

 Score =  177 bits (450), Expect = 1e-49
 Identities = 106/243 (43%), Positives = 144/243 (59%), Gaps = 5/243 (2%)

Query: 16  IITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAWSY 75
           ++ LNRP+  NAL   L+  +  AL A   D  I A+VI G  R FAAGADIA +A+   
Sbjct: 19  LLRLNRPEKRNALATDLLGRIADALDAAAGDPAIRAVVITGADRFFAAGADIAELAS--- 75

Query: 76  SDVYGSNFITRN--WETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPEI 133
            D  G+    R   W  IR   KP++AAV G + G G EL + CD+V+AG SAKF  PE 
Sbjct: 76  RDTGGALADPRPAIWTRIRGFAKPLIAAVEGWSLGAGNELVMCCDLVVAGESAKFGQPET 135

Query: 134 KLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVAL 193
            LG++PGAGGT  LPR +G+++AM M L   PL+A EA + GL++++V+D +       L
Sbjct: 136 NLGIIPGAGGTAILPRLVGRSRAMRMVLLGDPLSAAEALQAGLIAQMVEDGQALSVATEL 195

Query: 194 ATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRAP 253
           AT IAA +  A+   K  +   FE+  +  +L ER+   A F +AD REG  AF EKR P
Sbjct: 196 ATRIAARAPLAMQQGKAMVRATFETHQSAHLLLERQAFSALFGTADKREGTSAFFEKRDP 255

Query: 254 CFS 256
            +S
Sbjct: 256 QWS 258


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: 133
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 24 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