Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 331 bits (848), Expect = 4e-95 Identities = 175/473 (36%), Positives = 286/473 (60%), Gaps = 6/473 (1%) Query: 5 LLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSIL 64 L+L+ + ++K Y GV AL D L L AG VHAL G NGAGKST + ++ G +D G IL Sbjct: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 Query: 65 LNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRT 124 G P FN P +A AGI+ + QE+ +P +TVA+N++LG EPRR G ++ K + Sbjct: 63 FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLG-LIHFKKMYADA 121 Query: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 R +L + D+D ++P+ S+A QL+ IA+ + +V+++DEPT+++ E Q LF Sbjct: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 + +L A+G IV+++H L ++ QI+D ++ R+G F+ A++ + L+ ++G+ L Sbjct: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241 Query: 245 TR--IDHKVGREC---AANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFL 299 +D + A L ++++S G ++L + +G+ +G+ GL+GSGRSE Sbjct: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 Query: 300 NCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSA 359 N ++GL + DSGS+ L G+ + + P I+AG++L EDRK G++ SI NI L+ Sbjct: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 Query: 360 YKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVC 419 R+ W ++ ++ ++A+ + +LQI T + P+ +SGGNQQKV+LA+ L+ EP+ Sbjct: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 Query: 420 LLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFK 472 L+ DEPTRGID GA EI L+ G + +V SSE EL+ S+++ V + Sbjct: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLR 474 Score = 75.1 bits (183), Expect = 5e-18 Identities = 57/224 (25%), Positives = 108/224 (48%), Gaps = 5/224 (2%) Query: 21 ALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALA 80 +++ L++ G L G G+G+S + + G+ D+GSI L G + ++P +A++ Sbjct: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332 Query: 81 AGIAMITQELEP---IPYMTVAENIWLGREPRRAGC-IVDNKALNRRTRELLDSLEFDV- 135 AGIA+ ++ + I +++ ENI L + R + N + +D L+ Sbjct: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATP 392 Query: 136 DATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAG 195 DA P+ +LS Q V +A+ + + ++++DEPT I + K IR L +G Sbjct: 393 DADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS 452 Query: 196 IVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGI 239 ++ S L EL ++ + RD V A++ H+++ I Sbjct: 453 LLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQAI 496 Lambda K H 0.319 0.135 0.381 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: 533 Number of extensions: 20 Number of successful extensions: 6 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: 495 Length of database: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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