GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Pedobacter sp. GW460-11-11-14-LB5

Align BadK (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase

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



>FitnessBrowser__Pedo557:CA265_RS20005
          Length = 259

 Score =  145 bits (366), Expect = 8e-40
 Identities = 95/261 (36%), Positives = 137/261 (52%), Gaps = 9/261 (3%)

Query: 1   MSSNPILTETQGRVGIITLNRPDVLNALN-DALMDALGGALLAFDADDGIGAIVIAGNTR 59
           M+   +++E +  +  +T+NR   LNALN D L +       A   D+  G I+     +
Sbjct: 1   MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60

Query: 60  AFAAGADIASMAAWSYSDVYGSNFITRNWE----TIRQIRKPVLAAVAGLAYGGGCELAL 115
           AF AGADI   +   YS   G     R  E     I    KP +AA+ G A GGG ELA+
Sbjct: 61  AFVAGADIKEFS--DYSGKQGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELAM 118

Query: 116 ACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYG 175
           AC I IA  +AK  LPE+ LGL+PG GGTQRL + +GK KA++M  +A  + A +A++ G
Sbjct: 119 ACHIRIASDNAKLGLPEVTLGLIPGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIG 178

Query: 176 LVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235
           LV+ VV    L  +   +   I   +  A+ A  +S+  +  +T   G   E  E    F
Sbjct: 179 LVNVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASINNT--NGYATEIEEFGKCF 236

Query: 236 ASADAREGIQAFLEKRAPCFS 256
            +AD +EG+ AF+EKR   F+
Sbjct: 237 ETADFKEGVTAFVEKRKAIFT 257


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: 126
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: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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