Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 211 bits (537), Expect = 3e-59 Identities = 126/298 (42%), Positives = 183/298 (61%), Gaps = 17/298 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M+ + L +VTK + G + AV+ ++L+I GE ++GPSGCGK+TTLRM+AG E + Sbjct: 1 MSYVRLVNVTKRF-----GGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDL 55 Query: 61 TEGELRLEDRVLNG------VSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDD 114 +GE+ + DR+L+ + + RD MVFQ++A++PH SV N++F L L Sbjct: 56 DDGEIHVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRR-LSAA 114 Query: 115 EIRQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKL 174 EI +R E ++D+ + P LSGG +QRVAL RA+ +P+V L+DEPLS+LD L Sbjct: 115 EIDRRTREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHL 174 Query: 175 RAEMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNL 234 R EMR E++ LQ G + +YVTHDQ+EAM + DR+ V+ +G +QQVGTPLD Y P N Sbjct: 175 REEMRFEIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANS 234 Query: 235 FVAGFIGEPSMNLFDGSLSGD-TFRGDGFDYPLSGAT--RDQLGGASGLTLGIRPEDV 289 FV GFIG N D +L+ + R +G D ++ AT +L A L RP ++ Sbjct: 235 FVFGFIG--LSNFLDVNLTPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEI 290 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: 383 Number of extensions: 15 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: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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