GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate H281DRAFT_00785 H281DRAFT_00785 2-hydroxy-3-oxopropionate reductase

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__Burk376:H281DRAFT_00785
          Length = 302

 Score =  158 bits (399), Expect = 2e-43
 Identities = 101/276 (36%), Positives = 147/276 (53%), Gaps = 9/276 (3%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60
           M  I F+GLG MG  MA NLLK GH + V    P  V   + +       +    + A++
Sbjct: 1   MAKIGFIGLGIMGAHMARNLLKGGHTLFVNGAYP--VPEDLGKSTNVVSDSTAVAQAADI 58

Query: 61  VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120
           VI M+P    V ++   DDG+ A +    L+ID S+I+P   +  A+   A G+  LDAP
Sbjct: 59  VIIMVPDTPDVANVLFADDGVAAGLTAGKLVIDMSSISPLDTQAFAKKINALGVDYLDAP 118

Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180
           VSGG  GAR  TL+ +VGGP + FA+A+P+ E MG+NI   GD+GAGQ  K+ N +++ +
Sbjct: 119 VSGGEVGAREATLTIMVGGPEKAFAQAKPLFELMGKNISLIGDNGAGQTCKVANQIIVAL 178

Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240
            +   AEAL    ++G DP     V K   GG  +  +      V  +      +  GF+
Sbjct: 179 NIEAVAEALLFASRSGADP---ERVRKALMGGFASSRILE----VHGERMTKRTFNPGFR 231

Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHA 276
           + L  KDL LAL  A+ +  + P  A A+ LFS+ A
Sbjct: 232 IELHQKDLNLALDGARKLGIALPHTASAQQLFSVCA 267


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: 242
Number of extensions: 12
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: 302
Length adjustment: 27
Effective length of query: 271
Effective length of database: 275
Effective search space:    74525
Effective search space used:    74525
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