GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS07000 BWI76_RS07000
           2-hydroxy-3-oxopropionate reductase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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