Align ABC transporter related (characterized, see rationale)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Koxy:BWI76_RS00275 Length = 501 Score = 357 bits (915), Expect = e-103 Identities = 197/501 (39%), Positives = 317/501 (63%), Gaps = 10/501 (1%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 M +L+LK I K +PGVKAL SL ++ G V AL+GENGAGKST++KV+TG ++D G Sbjct: 1 MEALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGS 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYE-PRRLGLIHFKKMYA 119 +L+LG+ FN P +Q+AGI ++QE+NL+P LT+A+N+FLG E R G I +K MYA Sbjct: 61 LLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 +A +L + L + + D SI QQ++ IA+ ++ +KV+++DEPT +L E + L Sbjct: 121 EADKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 F ++ +LK++G IV+I+H + ++++I D +TV R+GQFI E A L + LIE M+GR Sbjct: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGR 240 Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299 L++Q R AV L ++++ G +++++ + +G+ +G+AGL+G+GR+E Sbjct: 241 KLEDQY------PRLDKAPGAVRLKVDNLCGSG-VENISFILRQGEILGVAGLMGAGRTE 293 Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359 + ++G SGS+ L G+++ P D ++ GI EDRK DG++ +S++EN+ L Sbjct: 294 LMKVLYGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSL 353 Query: 360 -ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418 AL+ L + +Q+ FI + TP ++ I LSGGNQQKV +AR L Sbjct: 354 TALRYFSRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTR 413 Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 P +L+LDEPTRG+D+GA EI +LI EG+S+++ SSE+ E++ S++++V+ + + Sbjct: 414 PKVLILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHL 473 Query: 479 VRELSGAELTSQHVMQAIAEG 499 E + E +Q V+ A A G Sbjct: 474 GGEFT-REQATQEVLMAAAVG 493 Score = 101 bits (252), Expect = 5e-26 Identities = 69/231 (29%), Positives = 120/231 (51%), Gaps = 15/231 (6%) Query: 20 LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKA 79 +E++S L GE+ + G GAG++ L+KV+ GA + G + G +P D Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327 Query: 80 GISTVYQEVN---LVPNLTVAQNLFLG---YEPRRLGLIHFKKMYADARAVLTQFKLDID 133 GI + ++ LV ++V +N+ L Y R G + K D + ++ F + Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGGGSLKHK----DEQQAVSDFIRLFN 383 Query: 134 VSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKA 188 V P + +I + QQ +AIARG+ KVL+LDEPT +D + ++ ++NQ KA Sbjct: 384 VKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443 Query: 189 KGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 +G++I+ ++ + +V +SDRI V+ G GE+ + Q L+ A +G+ Sbjct: 444 EGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 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: 603 Number of extensions: 33 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