Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__psRCH2:GFF857 Length = 371 Score = 285 bits (728), Expect = 2e-81 Identities = 168/373 (45%), Positives = 225/373 (60%), Gaps = 22/373 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA +TL D+ K Y G I I LDI+DGEF+V VGPSGCGKST LR++AGLE + Sbjct: 1 MASVTLRDICKSYD---GTPIT--RHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G+L ++++ +N + +DR + MVFQSYALYPH +V NM+FGL+ ++ + EI++RV Sbjct: 56 TSGDLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLAS-VDKREIKRRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E ++L + LL+RKP LSGGQ+QRVA+GR +VR+P+VFL DEPLSNLDA LR +MR Sbjct: 115 EAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRI 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ RL + T +YVTHDQ EAMT+ D++ VL+ GE+ QVG PL YH P N FVAGF+ Sbjct: 175 EIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFL 234 Query: 241 GEPSMNLFDG---SLSGDTF-----RGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVG 292 G P MN + S S +T G P+ G+ + LTLGIRPE + Sbjct: 235 GSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSA---VSPGDPLTLGIRPEHFVMP 291 Query: 293 ERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPE 352 + TF ++ V E G N ++L + T G RV G+ Sbjct: 292 D--EADFTFHGQITVAERLGQYNLLYLTLERLQD--VITLCVDGNLRVTEGETFAAGLKA 347 Query: 353 DAIHLFDGETGDA 365 D HLF E G+A Sbjct: 348 DKCHLF-RENGEA 359 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: 463 Number of extensions: 30 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: 371 Length adjustment: 30 Effective length of query: 353 Effective length of database: 341 Effective search space: 120373 Effective search space used: 120373 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