GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Rhizorhabdus wittichii RW1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  145 bits (367), Expect = 9e-40
 Identities = 84/220 (38%), Positives = 125/220 (56%), Gaps = 11/220 (5%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG-------ELRLEDRV 71
           G   A+  +SLD+  GE +V+ GPSG GKST +R + GLET  EG       E+R + RV
Sbjct: 12  GGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRV 71

Query: 72  LNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISD 131
           L  + A+   + MVFQ + L+PH ++  N +    +  GL  D       E  + + I+D
Sbjct: 72  LQRIRAR---VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIAD 128

Query: 132 LLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGV 191
             D+ P QLSGGQQQR A+ RA+   PE+ L DEP S LDA++  E+   ++ L  E G+
Sbjct: 129 QADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GI 187

Query: 192 TTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRP 231
           T + VTH+   A  + DR+  +D G++ + G+P D +  P
Sbjct: 188 TMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227


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: 229
Number of extensions: 17
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: 383
Length of database: 241
Length adjustment: 27
Effective length of query: 356
Effective length of database: 214
Effective search space:    76184
Effective search space used:    76184
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: 48 (23.1 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