GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Alkalihalobacterium alkalinitrilicum DSM 22532

Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  148 bits (374), Expect = 2e-40
 Identities = 90/287 (31%), Positives = 154/287 (53%), Gaps = 4/287 (1%)

Query: 19  MIVVFSTRA-ADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFTGMAI 77
           +I++FS  + + FA+  N   I    S L+I+AL    V+  K  DLS+ A  +  G+  
Sbjct: 28  IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87

Query: 78  AMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAFVLS 137
           A++ A+    P++  +L+ +++G  +G  NG +V   ++   V TL   T+  G+ F L+
Sbjct: 88  ALLAAS--GTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLT 145

Query: 138 GGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATGGNPT 197
           GGA V    +   F  + ++ +  LP LS +  ++VI+ + ++  T  GR  YA GGN  
Sbjct: 146 GGATV-FENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEK 204

Query: 198 AAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAACVIGGIS 257
           A+  +GI+    K +AF L G LA     L  SR   A+    +GF L++ AA  +G   
Sbjct: 205 ASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTI 264

Query: 258 IAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAV 304
           +  GV ++ GT+ GA  +G++ N L ++ +  F Q  I+G +II+A+
Sbjct: 265 VKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIAL 311


Lambda     K      H
   0.328    0.141    0.413 

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: 290
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 333
Length of database: 321
Length adjustment: 28
Effective length of query: 305
Effective length of database: 293
Effective search space:    89365
Effective search space used:    89365
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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