GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  160 bits (405), Expect = 4e-44
 Identities = 99/287 (34%), Positives = 166/287 (57%), Gaps = 7/287 (2%)

Query: 42  LCIGFSVLT-ENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVA 100
           + I FS+L+  +FA + N   I +Q S  +++A G T V+     DLS+G++ S+  V++
Sbjct: 28  IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87

Query: 101 MLVSLM--PQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVG 158
            L++    P +  L VP  ++ G + G  NGA+V   K+  F+ TL   T + G+   + 
Sbjct: 88  ALLAASGTPIIFCLLVP--IIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLT 145

Query: 159 NDSTIY-NPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEA 217
             +T++ N   GF F+G  ++  +P L +I F +V + W+++ +T LG ++YA+GGN +A
Sbjct: 146 GGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKA 205

Query: 218 ARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTS 277
           + +SGI +       +A+ G+LA   G + ++RL +A+    G  + L+A AAV LG T 
Sbjct: 206 SEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTG-GDGFFLNAYAAVFLGMTI 264

Query: 278 FVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAV 324
              G  +I+GTL GA II +++NGL +L V    Q II G +II A+
Sbjct: 265 VKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIAL 311


Lambda     K      H
   0.325    0.141    0.409 

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: 372
Number of extensions: 22
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: 337
Length of database: 321
Length adjustment: 28
Effective length of query: 309
Effective length of database: 293
Effective search space:    90537
Effective search space used:    90537
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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