GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Pedobacter sp. GW460-11-11-14-LB5

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Pedo557:CA265_RS15880
          Length = 330

 Score =  146 bits (369), Expect = 7e-40
 Identities = 81/245 (33%), Positives = 144/245 (58%), Gaps = 16/245 (6%)

Query: 4   LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63
           +++ ++TK Y  E  G I   + +S +I  G+ + ++G SG GKST L+ + GL    EG
Sbjct: 6   ISVKNLTKQYQAEQAGGI---KNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEG 62

Query: 64  ELRLEDRVLNGVSAQ----DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQR 119
           E+  ED+ + G   Q     + + MV Q ++L  +  V  N++      + L + +++ +
Sbjct: 63  EIFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIA------SQLSNTDLKTK 116

Query: 120 VEETTDM---LGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176
            E+T  +   L I  L ++K  +LSGG+QQRVA+ +A+V D +V L+DEP S +DA L+ 
Sbjct: 117 AEKTLQIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKN 176

Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236
           ++R +++R+  E GVT + V+HD  + + + D++ +L +GEL Q G P + Y  P +++ 
Sbjct: 177 QLRADIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYT 236

Query: 237 AGFIG 241
           A  +G
Sbjct: 237 AQILG 241


Lambda     K      H
   0.316    0.136    0.384 

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: 275
Number of extensions: 19
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: 383
Length of database: 330
Length adjustment: 29
Effective length of query: 354
Effective length of database: 301
Effective search space:   106554
Effective search space used:   106554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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