Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 369 bits (948), Expect = e-106 Identities = 197/492 (40%), Positives = 320/492 (65%), Gaps = 4/492 (0%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD-ILF 63 LE++ IS+ +PGVKAL+ V+L + AGEV AL GENGAGKSTL+K++TG + D G IL Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGLIHFKKMYADAR 122 G+ A+ G++ +YQE+ +V NLTV +N+FL EPR RLGLI +MY +AR Sbjct: 70 EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129 Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 VL +DID + +S+ S+ QQ+I IA+ + +K +++DEPTASL E VL GI Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + +L+ + +A+V+I+H L+++++++DR+TVLR+G+ +G A++ + L+ M+ R L Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVARELS 249 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDV-SVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 E + Q E LSL+ V + I+ ++ T+ +G+ +G+AGL+GSGR+E+ Sbjct: 250 ELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRTEIM 309 Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 +FG+ +GS+ + G+ +++ P DAI +GI EDRK G+I +++REN L Sbjct: 310 EMIFGMRAC-TGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSLTH 368 Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 R ++++ + R++E + F+ L I TP ++ + LSGGNQQK+++A+W+A P + Sbjct: 369 LERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARSPKV 428 Query: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481 L++DEPTRGID+GA AE+ LI L EG+ ++V SS+L E++A S++++ +R+ E Sbjct: 429 LIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRISGE 488 Query: 482 LSGAELTSQHVM 493 LS A+ + + VM Sbjct: 489 LSRAQASQEKVM 500 Score = 73.9 bits (180), Expect = 1e-17 Identities = 53/225 (23%), Positives = 117/225 (52%), Gaps = 10/225 (4%) Query: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVD-SGSIHLAGQKLNLSQPVDAI 331 ++ +NL + G+ + LAG G+G+S + + G+ D G+I + GQ++ L+ A Sbjct: 24 ALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILVEGQEVALADSHHAR 83 Query: 332 SAGIALCPEDRKIDGIIGPLSIRENIILALQ--ARIGWWRYLSNTRQQEIAQFFIDKLQI 389 + G+ + ++ ++G L++ ENI LA + R+G + R A+ + + + Sbjct: 84 TLGVNIIYQEL---AVVGNLTVGENIFLAREPRTRLG---LIDRPRMYREAREVLATIDM 137 Query: 390 ATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDE 449 A + + +LS G QQ + +A+ L +++DEPT + + ++ +++ L + Sbjct: 138 DIDPATR-VSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGIVKRLRER 196 Query: 450 GMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494 ++++ S L+E+ +++V VLRD V A++T + +++ Sbjct: 197 NIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVR 241 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: 574 Number of extensions: 25 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 505 Length adjustment: 34 Effective length of query: 465 Effective length of database: 471 Effective search space: 219015 Effective search space used: 219015 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