GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Klebsiella michiganensis M5al

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate BWI76_RS07000 BWI76_RS07000 2-hydroxy-3-oxopropionate reductase

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__Koxy:BWI76_RS07000
          Length = 292

 Score =  155 bits (391), Expect = 1e-42
 Identities = 92/270 (34%), Positives = 144/270 (53%), Gaps = 8/270 (2%)

Query: 4   IAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVIS 63
           + F+GLG MG PMA  L KAGH ++V  + P A   L++QGAQ   +A Q  E +E++  
Sbjct: 3   LGFIGLGIMGTPMALRLAKAGHALHVTTIGPVAE-ELLKQGAQHLATAEQVAEQSEIIFI 61

Query: 64  MLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVSG 123
           M+P    V  +  G+ G          ++D S+I+P   ++ A+     G   LDAPVSG
Sbjct: 62  MVPDTPQVADVLFGEHGCAKAALKGKTIVDMSSISPIETKRFAQQVRDLGADYLDAPVSG 121

Query: 124 GVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILMA 183
           G  GAR GTLS +VGG    FAR +P+ + +G+NI   G +G GQ  K+ N +++ + + 
Sbjct: 122 GEIGAREGTLSIMVGGDENVFARVKPLFDILGKNITLVGGNGDGQTCKVANQIIVALNIE 181

Query: 184 GTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVRL 243
             +EAL    K G DPA + + +      +  L ++        +   +  +  GF++ L
Sbjct: 182 AVSEALVFASKAGADPARVRQALMGGFASSRILEVHG-------ERMLNRTFNPGFKISL 234

Query: 244 MNKDLGLALANAQAVQASTPLGALARNLFS 273
             KDL LAL +A+A+  + P  A  + LF+
Sbjct: 235 HQKDLNLALQSAKALALNLPNTATCQELFN 264


Lambda     K      H
   0.317    0.135    0.395 

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: 229
Number of extensions: 10
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: 298
Length of database: 292
Length adjustment: 26
Effective length of query: 272
Effective length of database: 266
Effective search space:    72352
Effective search space used:    72352
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: 48 (23.1 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