Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 309 bits (791), Expect = 1e-88 Identities = 181/384 (47%), Positives = 239/384 (62%), Gaps = 19/384 (4%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + +D++ K + G + I L+I DGEF+ +GPSGCGKST LR +AGLE + Sbjct: 1 MATIRIDNLRKSF-----GSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENL 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 G +RL DR + + + RDIAMVFQ+YALYPH +VR N+SFGL + G+ +EI +RV Sbjct: 56 DGGSIRLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALN-GMKRNEIDRRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 ++L I++LLDRKP QLSGGQ+QRVA+GRAIVR+P++FL+DEPLSNLDA LR MR Sbjct: 115 NNAAEILRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRV 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 EL L LGVT +YVTHDQ EAMT+ DRV VLD G + Q GTPL+ ++RP NLFVAGFI Sbjct: 175 ELAALHERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFI 234 Query: 241 GEPSMNLFDGSLSGD-----TFRGDGFDYPLSGATR--DQLGGASGLTLGIRPEDVTVGE 293 G P MN ++ T G G P++ TR + L +TLGIRP+ + + Sbjct: 235 GSPRMNFLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTS 294 Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353 V +VE G E+ VH+R V+G G TA G V + D+ + P + Sbjct: 295 PEEAH--LAGTVRLVERLGTESHVHIR-VEG--GGDLTAVVRGTHPVASRDQVHLRLPPE 349 Query: 354 AIHLFDGETGDALKNRELPSNRAI 377 HLFD E G A+ R P +A+ Sbjct: 350 HCHLFDAE-GTAIARRLDPETKAL 372 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: 472 Number of extensions: 27 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: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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: 50 (23.9 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