Align ABC transporter related (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 349 bits (895), Expect = e-100 Identities = 193/503 (38%), Positives = 314/503 (62%), Gaps = 14/503 (2%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 M +L+LK I K +PGVKAL +L ++ G V AL+GENGAGKST++KV+TG ++D G Sbjct: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYE-PRRLGLIHFKKMYA 119 +L+LG+ F P +Q+AGI ++QE+NL+P LT+A+N+FLG E R G I +K MYA Sbjct: 61 LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 +A +L + L + D SI QQ++ IA+ ++ +KV+++DEPT +L E + L Sbjct: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 F ++ +LK++G IV+I+H + ++++I D +TV R+GQFI E A L + LIE M+GR Sbjct: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240 Query: 240 SLQEQL--VDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGR 297 L++Q +DK + + L ++++ G + ++ T+ KG+ +G++GL+G+GR Sbjct: 241 KLEDQYPHLDKAPGD--------IRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGR 291 Query: 298 SEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI 357 +E+ ++G SG + L G ++ P D ++ GI EDRK DG++ +S++EN+ Sbjct: 292 TELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENM 351 Query: 358 IL-ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416 L AL+ L + +Q+ FI + TP ++ I LSGGNQQKV +AR L Sbjct: 352 SLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLM 411 Query: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDR 476 P +L+LDEPTRG+D+GA EI +LI +G+S+++ SSE+ E++ S++++V+ + Sbjct: 412 TRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEG 471 Query: 477 YAVRELSGAELTSQHVMQAIAEG 499 + E + E +Q V+ A A G Sbjct: 472 HLSGEFT-REQATQEVLMAAAVG 493 Score = 102 bits (255), Expect = 2e-26 Identities = 73/236 (30%), Positives = 121/236 (51%), Gaps = 18/236 (7%) Query: 15 PGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPM 74 PGV DVS L GE+ + G GAG++ L+KV+ GA + G + G +P Sbjct: 266 PGVN---DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 Query: 75 DAQKAGISTVYQEVN---LVPNLTVAQNLFLG---YEPRRLGLIHFKKMYADARAVLTQF 128 D GI + ++ LV ++V +N+ L Y R G + +AD + ++ F Sbjct: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLK----HADEQQAVSDF 378 Query: 129 KLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 +V P + +I + QQ +AIARG+ KVL+LDEPT +D + ++ ++ Sbjct: 379 IRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLI 438 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 NQ KA G++I+ ++ + +V +SDRI V+ G GE+ + Q L+ A +G+ Sbjct: 439 NQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 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: 582 Number of extensions: 32 Number of successful extensions: 8 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: 501 Length adjustment: 34 Effective length of query: 465 Effective length of database: 467 Effective search space: 217155 Effective search space used: 217155 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