Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_02174 H281DRAFT_02174 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_02174 Length = 550 Score = 442 bits (1138), Expect = e-128 Identities = 227/498 (45%), Positives = 337/498 (67%), Gaps = 1/498 (0%) Query: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 L+LE++ I + GV AL +L + AGEVHAL+G+NGAGKST++K++TGA + G + Sbjct: 23 LLLEMQDIGISFGGVPALRGANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSVR 82 Query: 63 FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR 122 F G F TP A++AGIST+YQE+NLVP +VA+N+FLG EPRR GLI ++ + A Sbjct: 83 FEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWRTVQHRAA 142 Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 A+L F L IDV P+ YS A+QQ++A+AR V+ AK++++DE T+SLD +EV++LF + Sbjct: 143 ALLDSFGLHIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFTV 202 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + +L+ G A++F++H LD++Y + DR+TV+R+GQ + + AE+ + +L+ MLGR+L Sbjct: 203 VRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMAEMDKLQLVTTMLGRTLA 262 Query: 243 EQL-VDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 + D +E + R ++ D+ + ++L V G+AVGLAGLLGSGR+E Sbjct: 263 AVVHDDPAAREANLARRGKQAIAARDLGAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETM 322 Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 +FG D ++ GS+ + G + L P DAI+ G+A EDRK +GI+ LS+R+N+ L Sbjct: 323 RLMFGADPLERGSVSIDGATVTLKSPQDAIARGLAYLTEDRKAEGIVPELSVRDNLTLVC 382 Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 + + +QQ I FI L I AD+PI +LSGGNQQKV+LARWLA EP L Sbjct: 383 LRTLTRNGIVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPSL 442 Query: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481 L+LDEPTRGID+GA A++ K++R L D G+++L+++SEL+EL A S++ VV+RD V E Sbjct: 443 LLLDEPTRGIDVGAKADVAKIVRELRDAGLAVLMSASELEELTAVSDRAVVIRDGRTVAE 502 Query: 482 LSGAELTSQHVMQAIAEG 499 L+GAE++ +M AIA G Sbjct: 503 LNGAEMSESAIMDAIAYG 520 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: 663 Number of extensions: 36 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: 550 Length adjustment: 35 Effective length of query: 464 Effective length of database: 515 Effective search space: 238960 Effective search space used: 238960 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