Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 434 bits (1115), Expect = e-126 Identities = 228/491 (46%), Positives = 322/491 (65%), Gaps = 2/491 (0%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 +L+L+GI K FPGV+AL G +L + PG V AL+GENGAGKST+MKVL GI+ D G ++ Sbjct: 7 VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 + +GP ++ GI IHQEL+L +L++AENI+LG RFG +DW + A+ + Sbjct: 67 AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126 Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 +L KL + F + VGDLSI +QQMVEIA+ L+ ++K +I DEPT +LTD E LF V Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186 Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243 I +L+ QG GI YISHRM+EIF+I D ++V RDGQ+ A E+++ +MM+GRKL+ Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246 Query: 244 DQYPHLDKAPGDIRLKVDNL-CGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302 G++ L+V L CG DV+F +R+GE++G GL+GAGRTE+ + L+G Sbjct: 247 LSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLR 306 Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362 TSG + LDG EV SP D + GI + EDRK GLVLGM+ ++NM+L + +A Sbjct: 307 NPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDL-KA 365 Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422 G + E + +++TP +Q +G LSGGNQQK+ I + L RP VLI+DEP Sbjct: 366 GPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEP 425 Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482 TRG+DVG+K EI+ L+ A G ++I++SSEMPEVL ++DRI+ M+ G + FT E+ Sbjct: 426 TRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEV 485 Query: 483 TQEVLMAAAVG 493 T+E L+AA G Sbjct: 486 TEENLIAAISG 496 Score = 98.6 bits (244), Expect = 5e-25 Identities = 73/234 (31%), Positives = 110/234 (47%), Gaps = 13/234 (5%) Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV + VS T+ GE+ + G GAG++ LMKVL G G + + VV P Sbjct: 18 PGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVMSGPL 77 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTAL--RYFSRAGGSLKHADEQQAVSDFIR 380 D A GIV+I ++ L +SV EN+ L L + F + A + Sbjct: 78 DAKAKGIVFIHQELS---LADELSVAENIYLGELPRKRFGLVDWAELEAKTNAILEKLKV 134 Query: 381 LFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440 FN KT +G LS NQQ V IAR L K +I DEPT + K ++++I+ Sbjct: 135 GFNAKT-----RVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEVISD 189 Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 + G+ I +S M E+ ++DRI V+ +G G + +E + +G+ Sbjct: 190 LQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGR 243 Score = 84.7 bits (208), Expect = 7e-21 Identities = 60/219 (27%), Positives = 106/219 (48%), Gaps = 5/219 (2%) Query: 30 GRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPKSSQEAGIGIIHQELN 89 G V+ G GAG++ + + L G+ +G++ G E T P + E GI ++ ++ Sbjct: 282 GEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRK 341 Query: 90 ---LIPQLTIAENIFLGREFVNRFGK-IDWKTMYAEADKLLAKLNLRFKSDK-LVGDLSI 144 L+ + +N+ L + + G + A D+ KL++R K LVG+LS Sbjct: 342 GQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSG 401 Query: 145 GDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKEI 204 G+QQ + I K LS V+I+DEPT + + ++R+L +QG ++ IS M E+ Sbjct: 402 GNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEV 461 Query: 205 FEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243 + D + G+ + +TE++LI + G E Sbjct: 462 LHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTE 500 Lambda K H 0.318 0.137 0.380 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: 674 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 501 Length of database: 503 Length adjustment: 34 Effective length of query: 467 Effective length of database: 469 Effective search space: 219023 Effective search space used: 219023 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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