GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Kocuria turfanensis HO-9042

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_062734336.1 AYX06_RS03005 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_001580365.1:WP_062734336.1
          Length = 279

 Score =  179 bits (454), Expect = 6e-50
 Identities = 87/203 (42%), Positives = 125/203 (61%), Gaps = 1/203 (0%)

Query: 71  GKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130
           GK +C GLNY DHA E    IP  P +F K+ +A++GP D + +P  S+K DWE EL  V
Sbjct: 62  GKILCAGLNYYDHAEEVGQEIPEHPTIFAKYATALIGPTDPIAMPEESEKIDWEAELTAV 121

Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDE 190
           IG    +   + A + +AGY ++ND+S R++Q  R   W +GK  D   P+GP +VT DE
Sbjct: 122 IGSPLRHATPEQARAAIAGYTIMNDISVRDWQ-GRTSEWFQGKNFDRTTPVGPVVVTPDE 180

Query: 191 VADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMG 250
           V     L +   VDG  +Q+  T  MIF    +V YLSRF++L+PGD+++ GTP GVG+ 
Sbjct: 181 VDPEAGLAIRCSVDGVLHQDSGTDRMIFSAVALVEYLSRFLTLEPGDLVACGTPAGVGLA 240

Query: 251 VKPEAVYLRAGQTMRLGIDGLGE 273
            KP  ++LR GQ +   I+G+G+
Sbjct: 241 KKPRRIWLRDGQEVVTEIEGIGQ 263


Lambda     K      H
   0.316    0.138    0.419 

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: 241
Number of extensions: 6
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 281
Length of database: 279
Length adjustment: 26
Effective length of query: 255
Effective length of database: 253
Effective search space:    64515
Effective search space used:    64515
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: 42 (22.0 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