Align ABC transporter related (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 325 bits (832), Expect = 3e-93 Identities = 190/500 (38%), Positives = 301/500 (60%), Gaps = 6/500 (1%) Query: 2 SLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDM--G 59 S + E++ I+K + GVKAL+ + LRL AGE L GENGAGKSTL+KV++G G Sbjct: 5 SCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDG 64 Query: 60 DILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLG-LIHFKKMY 118 +IL+ G+P + D+++AGI ++QE+ LVP L+VA+N+FLG+E R G + + MY Sbjct: 65 EILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMY 124 Query: 119 ADARAVLTQFKL-DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQ 177 A A A+L + L D++V+ P Y QQL IA+ +A AK+L+LDEPT+SL + E + Sbjct: 125 AKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETE 184 Query: 178 VLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAML 237 VL GI+ LK +GVA ++I+H LD+V ++ D + V+R+G+ I EL LI M+ Sbjct: 185 VLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMV 244 Query: 238 GRSLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-IQSMNLTVPKGQAVGLAGLLGSG 296 GR L+ + V L+ V+ + + ++ + +G+ +G+AGL+G+G Sbjct: 245 GRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAG 304 Query: 297 RSEVCNAVFGLDLVDSG-SIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRE 355 R+E+ +A+FG S + L G+ L + P DAI AG+ + PEDRK GI+ L + + Sbjct: 305 RTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGD 364 Query: 356 NIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWL 415 NI LA ++ R+ + I + ++ T PI +LSGGNQQK +LA+ L Sbjct: 365 NITLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKML 424 Query: 416 AIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475 P +L+LDEPTRG+D+GA AEI +LI L +G+++++ SSE+ E++ +++V+V+ + Sbjct: 425 LARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGE 484 Query: 476 RYAVRELSGAELTSQHVMQA 495 + LT + V+ A Sbjct: 485 GRLRGDFPNQGLTQEQVLAA 504 Score = 94.0 bits (232), Expect = 1e-23 Identities = 70/239 (29%), Positives = 119/239 (49%), Gaps = 19/239 (7%) Query: 15 PGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL-GEPQHFNTP 73 P K ++DVS +L GE+ + G GAG++ LV + GA + LFL G P +P Sbjct: 277 PQRKRVDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSP 336 Query: 74 MDAQKAGISTVYQEVN---LVPNLTVAQNLFL---------GYEPRRLGLIHFKKMYADA 121 DA +AG+ V ++ +VP L V N+ L G+ R+ L+ + A+ Sbjct: 337 ADAIRAGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAER 396 Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 R L P++ S QQ +A+ + KVL+LDEPT +D ++ Sbjct: 397 RVKTASPAL------PIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYR 450 Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240 ++ +L A+GVAIV ++ + +V ++DR+ V+ G+ G++ L Q +++ A + S Sbjct: 451 LIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQEQVLAAAIDTS 509 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: 597 Number of extensions: 32 Number of successful extensions: 10 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: 513 Length adjustment: 34 Effective length of query: 465 Effective length of database: 479 Effective search space: 222735 Effective search space used: 222735 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