GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_01120 H281DRAFT_01120 monosaccharide ABC transporter membrane protein, CUT2 family

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__Burk376:H281DRAFT_01120
          Length = 333

 Score =  189 bits (480), Expect = 8e-53
 Identities = 114/302 (37%), Positives = 174/302 (57%), Gaps = 2/302 (0%)

Query: 8   RETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVA 67
           R   L++   V++VVFS  +  F +  N   I   T+++ I+A+    VI+ + IDLSV 
Sbjct: 34  RPYALYIAFAVLLVVFSFASPWFLSIDNFLNIGRQTALVSIIAIGMTFVIIARQIDLSVG 93

Query: 68  ANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLT 127
           ++LA +GM+ A+  A   D  L+  +   +  GA +G ING +   L IP  +VTLG+L+
Sbjct: 94  SSLALSGMSAALAMAYIGDHWLIGAVA-GIGTGALVGVINGLVTTRLNIPSFLVTLGSLS 152

Query: 128 IYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGR 187
             RG+A +++    V     + I +      + G+PV     ++ VI   +LL Y+ FGR
Sbjct: 153 AARGLALLVTTTKPVIITNDSFIAI-FGEGDIAGVPVPIIWTVLAVIAGILLLHYSVFGR 211

Query: 188 SAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDS 247
             YA GGNPTAA Y+GID      LAF+L+G LAGLA+ +  +R   A  D+  G ELD 
Sbjct: 212 QVYAAGGNPTAARYSGIDIRRVTTLAFILTGVLAGLAALVLSARSHAARPDVVQGLELDV 271

Query: 248 VAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFN 307
           +A+  +GG S+ GG G V GT+LG+L +G + N L ++G+S   Q+ I G +I+ AVAF 
Sbjct: 272 IASVTLGGCSLFGGRGFVLGTLLGSLIIGTLNNGLVLLGVSSSLQLVIKGIIIVAAVAFT 331

Query: 308 AR 309
            +
Sbjct: 332 KK 333


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: 281
Number of extensions: 16
Number of successful extensions: 3
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: 333
Length of database: 333
Length adjustment: 28
Effective length of query: 305
Effective length of database: 305
Effective search space:    93025
Effective search space used:    93025
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. 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