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.
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:
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