Align ABC transporter related (characterized, see rationale)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 380 bits (976), Expect = e-110 Identities = 196/497 (39%), Positives = 326/497 (65%), Gaps = 8/497 (1%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 M+ ++ +K++SK +PGV+AL +V L AGEVHAL+GENGAGKSTL+K++ G ++D G+ Sbjct: 1 MTPLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGE 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGL-IHFKKMY 118 IL+ G+P F +P +AQ G+ ++QE+ L+ +LT+AQN+F+G EPR RLGL + K+ Sbjct: 61 ILYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLN 120 Query: 119 ADARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQV 178 A A +L + + +D A +S ++A QQ++ IA+ ++ ++VL++DEPT++L+ E+ Sbjct: 121 AQAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAE 180 Query: 179 LFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238 LF I+ LK +GV I++I+H +D++ QI+DR+TVLR+G+++ + +I M+G Sbjct: 181 LFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVG 240 Query: 239 RSLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRS 298 R+ L D + + E V L + ++ ++ ++ + KG+ +G AGL+G+GR+ Sbjct: 241 RT----LTDAAPSQHIANQGE-VALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRT 295 Query: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358 EV AVFG D ++SG I + G K + P DA++ GI EDRK G+ +S+ NI+ Sbjct: 296 EVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIV 355 Query: 359 LA-LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAI 417 ++ L+ + +L T+ ++ A FI+ L I TP A + + LSGGNQQK+++A+WL Sbjct: 356 MSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLER 415 Query: 418 EPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRY 477 + +L DEPTRGID+GA +EI KL+R+L D+G ++++ SSEL E++ S+++VV+ + Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGR 475 Query: 478 AVRELSGAELTSQHVMQ 494 EL+ A T + +MQ Sbjct: 476 ITGELAAAGATQERIMQ 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: 545 Number of extensions: 34 Number of successful extensions: 8 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: 503 Length adjustment: 34 Effective length of query: 465 Effective length of database: 469 Effective search space: 218085 Effective search space used: 218085 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