GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Methanococcus aeolicus Nankai-3

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  132 bits (331), Expect = 1e-35
 Identities = 79/232 (34%), Positives = 137/232 (59%), Gaps = 6/232 (2%)

Query: 8   IKMKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67
           I+ K L++  ++ K +  G+     + GI+++IKEGE + ++G SGCGKSTL   +  L 
Sbjct: 12  IEKKELIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLD 71

Query: 68  RPDGGKIFFEGKDITNLNDKEMKPYRKKMQ-IIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
            P+ G ++ +GK  T  ++ +   +R+K+   IFQ    +L   +T    +E PL++ + 
Sbjct: 72  VPNKGMVYIKGKKTTMFSENDRAVFRRKISGFIFQQ--FNLINTLTALENVELPLVLDE- 128

Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186
             K  R K+ ++LL ++ +G    N +P++ SGGQQQR+ IARAL+ NPK I  DEP   
Sbjct: 129 KNKNYRIKKAKKLLKIINLGHRE-NYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGN 187

Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEY 238
           LD     +++D+L+E+ +K GI+ + + H     ++ S ++  M  G+IVE+
Sbjct: 188 LDSKNSREVMDILKELNEKEGITVIMVTHEPEFAKYAS-RIINMKDGEIVEH 238


Lambda     K      H
   0.321    0.142    0.417 

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: 190
Number of extensions: 11
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: 328
Length of database: 238
Length adjustment: 26
Effective length of query: 302
Effective length of database: 212
Effective search space:    64024
Effective search space used:    64024
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 (21.8 bits)
S2: 47 (22.7 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