GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Methanococcus aeolicus Nankai-3

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::Q9WXN4
         (268 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  113 bits (282), Expect = 4e-30
 Identities = 73/229 (31%), Positives = 125/229 (54%), Gaps = 12/229 (5%)

Query: 7   KNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGE 66
           KN+ KI+  G   + +   ++ ++ ++KE E V+++G SG GK+T   ++  L  P  G 
Sbjct: 21  KNIWKIYGGG---EAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGM 77

Query: 67  IYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNK 126
           +Y +GK      ++  ++  FRRK+       F   N    +E      +   +NK    
Sbjct: 78  VYIKGKKTTMFSENDRAV--FRRKISGFIFQQFNLINTLTALENVELPLVLDEKNKNYRI 135

Query: 127 KEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMID 186
           K+A +L+K     + +  ++    YP+Q+SGGQ+QR+ IAR     P +I ADEPT  +D
Sbjct: 136 KKAKKLLKI----INLGHRE--NYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLD 189

Query: 187 ASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVE 235
           + +   ++ +L+EL E++G ++I +TH+   A Y S  I  MK+GEIVE
Sbjct: 190 SKNSREVMDILKELNEKEGITVIMVTHEPEFAKYAS-RIINMKDGEIVE 237


Lambda     K      H
   0.319    0.139    0.397 

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: 177
Number of extensions: 9
Number of successful extensions: 2
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: 268
Length of database: 238
Length adjustment: 24
Effective length of query: 244
Effective length of database: 214
Effective search space:    52216
Effective search space used:    52216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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