GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Synechococcus elongatus PCC 7942

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__SynE:Synpcc7942_0947
          Length = 355

 Score =  246 bits (628), Expect = 7e-70
 Identities = 152/365 (41%), Positives = 208/365 (56%), Gaps = 17/365 (4%)

Query: 4   LTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEG 63
           L L  + K Y+      +V V  +SL +  GEFL L+GPSGCGKSTTLR++AGL+  T G
Sbjct: 6   LELRQLRKAYSPS----VVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSG 61

Query: 64  ELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEET 123
            + L DR +  +   DRD+AMVFQSYALYPH +VR N++ GL+        EI QR+++ 
Sbjct: 62  SIWLGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRR-TSAAEIEQRLQQV 120

Query: 124 TDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 183
              L +  LLDR+P QLSGGQ+QRVALGRA+VR P VFL+DEPLSNLDA LR ++R +++
Sbjct: 121 AHNLELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMK 180

Query: 184 RLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEP 243
            L  +     VYVTHDQTEA+++  R+A+L+ G LQQ+ +P   Y  P N FVAGFIG P
Sbjct: 181 ALFSQQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSP 240

Query: 244 SMNLFDGSL-SGDTFRGD-GFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTF 301
            MNL    + SG  + G      P   A R Q      +  G+RPE + +      +R  
Sbjct: 241 RMNLLPLPIHSGQAWLGSRALPIPSHLAARSQ------VLWGLRPEHLKLATPEV-ERAI 293

Query: 302 DAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGE 361
             ++ + E  G +  + +      E        + Q          V+F  ++ H F   
Sbjct: 294 PVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQ---PIPTDLQVTFEPESQHWFCPS 350

Query: 362 TGDAL 366
           TGD L
Sbjct: 351 TGDRL 355


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: 390
Number of extensions: 21
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: 355
Length adjustment: 30
Effective length of query: 353
Effective length of database: 325
Effective search space:   114725
Effective search space used:   114725
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.

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