GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate WP_279338484.1 HTA01S_RS01495 NAD(P)-dependent oxidoreductase

Query= SwissProt::P28811
         (298 letters)



>NCBI__GCF_001592305.1:WP_279338484.1
          Length = 301

 Score =  151 bits (381), Expect = 2e-41
 Identities = 102/286 (35%), Positives = 148/286 (51%), Gaps = 12/286 (4%)

Query: 3   DIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVI 62
           +IA LG+G MG P+A  L  AG++V+ ++  P     L   GAQ  D+  Q    A++VI
Sbjct: 14  NIAVLGIGMMGWPIARRLCVAGYQVSAWNRSPDKAERLRPFGAQVCDTPAQAVAQADLVI 73

Query: 63  SMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVS 122
           ++L  G+ VE + L   G    +    L++D S+I P  AR  A   AA G+  LDAPVS
Sbjct: 74  TLLEDGKVVEDV-LFRQGTTEGLRPGALVVDMSSIQPRQARDHAARLAAIGVHHLDAPVS 132

Query: 123 GGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILM 182
           GG  GA   TL+ + GG    F RARPV E++GR   H G HG+GQ+AK+ N M++GI +
Sbjct: 133 GGTVGAEQATLAIMAGGKPADFERARPVFEHLGRPT-HVGPHGSGQLAKLANQMIVGITI 191

Query: 183 AGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVR 242
              AEAL L  K G D A + + +      +  L ++        Q      +A    + 
Sbjct: 192 GAVAEALLLCEKGGADMAKVRQAITGGFADSRILQVHG-------QRMVERDFAKRGAIS 244

Query: 243 LMNKDLGLALANAQAVQASTPLGALARNLFSL---HAQADAEHEGL 285
           +  KD+  A+A A+ +    P+ AL   LF+    H  AD +H  L
Sbjct: 245 VQLKDMRNAMATAREIGFEAPITALFEQLFAQAADHGLADLDHSAL 290


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: 269
Number of extensions: 14
Number of successful extensions: 4
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: 301
Length adjustment: 27
Effective length of query: 271
Effective length of database: 274
Effective search space:    74254
Effective search space used:    74254
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 Apr 09 2024. 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