Align ABC transporter related (characterized, see rationale)
to candidate BWI76_RS18245 BWI76_RS18245 L-arabinose transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Koxy:BWI76_RS18245 Length = 504 Score = 348 bits (894), Expect = e-100 Identities = 189/491 (38%), Positives = 304/491 (61%), Gaps = 8/491 (1%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 L I+ +PGVKAL D+S +AG+VHAL+GENGAGKSTL+K+++G G + Sbjct: 8 LSFHGITMTFPGVKALSDISFGCYAGQVHALMGENGAGKSTLLKILSGNYIPTAGSLQIR 67 Query: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124 G+ FN +A AG++ +YQE++L+P +TVA+N++LG P + G+++ + +A Sbjct: 68 GQQMTFNHTTEALNAGVAIIYQELHLIPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 Query: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184 L LDID PL SI Q++ IA+ +A +AK++ DEPT+SL A+E++ LF ++ Sbjct: 128 LKHLGLDIDPETPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIENLFRVIR 187 Query: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEY-LTAELPQPKLIEAMLGRSLQE 243 +L+ +G I++++H +++++ +SD ITV ++G+++ + E+ L++AM+GR L Sbjct: 188 ELRQEGRVIIYVSHRMEEIFALSDAITVFKDGRYVRTFDNMQEVNHDALVQAMVGREL-G 246 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 + Q +E R L LE V G Q ++L+V G+ VGL GL+G+GRSE+ Sbjct: 247 NIYGWQPREYGKER-----LRLEQVKAPGVRQPVSLSVRSGEIVGLFGLVGAGRSELMKG 301 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-ILALQ 362 +FG + G +++ G+ +++ +P AI AG+ LCPEDRK +GII S+R+NI I A + Sbjct: 302 LFGGSRITGGQVYIDGEAIDIRKPAQAIQAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 I ++N + + A I L I TP A++ I LSGGNQQK IL RWL+ E ++ Sbjct: 362 KHILAGCVINNAWEAQNADQHIKSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 +LDEPTRGID+GA EI +I L G++++ ASS+L E++ ++++VV+R+ EL Sbjct: 422 LLDEPTRGIDVGAKHEIYNVIYALAASGVAVVFASSDLPEVLGVADRIVVMREGEIAGEL 481 Query: 483 SGAELTSQHVM 493 Q + Sbjct: 482 LHEHANEQQAL 492 Lambda K H 0.319 0.136 0.377 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: 582 Number of extensions: 24 Number of successful extensions: 7 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: 499 Length of database: 504 Length adjustment: 34 Effective length of query: 465 Effective length of database: 470 Effective search space: 218550 Effective search space used: 218550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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