Align ABC transporter related (characterized, see rationale)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS01820 Length = 544 Score = 444 bits (1142), Expect = e-129 Identities = 227/499 (45%), Positives = 339/499 (67%), Gaps = 1/499 (0%) Query: 2 SLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61 S +LE++ I + GV AL +L + AGEVHAL+G+NGAGKST++K++TGA + G + Sbjct: 16 SPLLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSV 75 Query: 62 LFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADA 121 F G F TP A++AGIST+YQE+NLVP +VA+N+FLG EPRR GLI + + A Sbjct: 76 RFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWHAVQQRA 135 Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 A+L F L IDV P+ YS A+QQ++A+AR V+ AK++++DE T+SLD +EV++LF Sbjct: 136 AALLESFGLQIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFT 195 Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241 ++ +L+ G A++F++H LD++Y + DR+TV+R+GQ + + A++ + +L+ MLGR+L Sbjct: 196 VVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTTMLGRTL 255 Query: 242 QEQLVDKQE-KERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEV 300 + D E +E + R +++ +S + ++L V G+AVGLAGLLGSGR+E Sbjct: 256 AAVVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLGSGRTET 315 Query: 301 CNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA 360 +FG D ++ GS+ + G+ + L P DAIS G+A EDRK +GI+ LS+R+N+ L Sbjct: 316 MRLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVRDNLTLV 375 Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420 + + +QQ I FI L I AD+PI +LSGGNQQKV+LARWLA EP Sbjct: 376 CLRTLAKNGVVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPS 435 Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR 480 LL+LDEPTRGID+GA AE+ K++R L D G+++L+++SEL+EL A +++ VV+RD V Sbjct: 436 LLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIRDGRTVA 495 Query: 481 ELSGAELTSQHVMQAIAEG 499 EL+GA+++ +M AIA G Sbjct: 496 ELNGADMSETAIMDAIAYG 514 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: 659 Number of extensions: 35 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: 544 Length adjustment: 35 Effective length of query: 464 Effective length of database: 509 Effective search space: 236176 Effective search space used: 236176 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