Align ABC transporter related (characterized, see rationale)
to candidate BPHYT_RS23875 BPHYT_RS23875 sugar ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS23875 Length = 549 Score = 461 bits (1186), Expect = e-134 Identities = 243/504 (48%), Positives = 335/504 (66%), Gaps = 10/504 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 IL +SK +PGVKAL+ V RLF GE+H L+G+NGAGKSTL+ V+TG + D G I Sbjct: 42 ILATAGVSKTFPGVKALQRVDFRLFPGEIHTLMGQNGAGKSTLINVLTGVLAPDEGTIRL 101 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 GE F +P +A+ AG+ T+YQEVNL PNL+VA+N+F G +PRR G I + + A+A Sbjct: 102 GGELVAFASPQEAEGAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIKRRAQA 161 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 L + + +DV+ L Y IAVQQ++AIAR +++ A+VL+LDEPT+SLD EV LF IL Sbjct: 162 ALARLDVTLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDGEVSQLFKIL 221 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG----- 238 LK G+AI+F+THF++Q Y ISDRITV+RNG+ GEYL +LP +L+ M+G Sbjct: 222 RHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARDLPADQLVSKMVGHERMS 281 Query: 239 ---RSLQEQLVDKQEKERTVTRAEAV--LLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLL 293 R + E A+AV + L V +G++Q ++L V GQ +GLAGLL Sbjct: 282 ARLREAAHEGHQGHEAHAGPQAAQAVQPFVELRGVGRRGTMQPIDLDVQPGQILGLAGLL 341 Query: 294 GSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSI 353 GSGR+E +FG D DSG+I + G+ + L P DA+ GI C EDRK +GI+ LSI Sbjct: 342 GSGRTETARLLFGADRADSGTILVEGRPVRLRSPRDAVRHGIGYCAEDRKKEGIVAELSI 401 Query: 354 RENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILAR 413 R+NI+LALQAR GWWR +S R +E+A +I++L I DA++PI LSGGNQQK +LAR Sbjct: 402 RDNILLALQARRGWWRKISRQRARELADLWIERLGIKAADAEQPIGLLSGGNQQKALLAR 461 Query: 414 WLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 WLA +P LL+LDEPTRGID+ A +I+ + LC G+S+L SSE+ E++ S++V VL Sbjct: 462 WLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCASGLSILFISSEISEVLRVSHRVAVL 521 Query: 474 RDRYAVRELSGAELTSQHVMQAIA 497 RDR + E++G ++ + IA Sbjct: 522 RDRRKIAEVAGKASNEDNIYRLIA 545 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: 695 Number of extensions: 31 Number of successful extensions: 6 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: 549 Length adjustment: 35 Effective length of query: 464 Effective length of database: 514 Effective search space: 238496 Effective search space used: 238496 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