Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 438 bits (1126), Expect = e-127 Identities = 232/493 (47%), Positives = 331/493 (67%), Gaps = 4/493 (0%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 +LQLKG+ K FPGV AL G L++ G V A+ GENGAGKST+MK+++G Y D G + + Sbjct: 22 ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 GK F +Q AGI IIHQELNL+P L++AENI+L RE R +D++T+ A A Sbjct: 82 EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLARE-PKRGPFVDYRTLNANAQ 140 Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 + L ++ L LVG LSI QQMVEIAK LS +++V+IMDEPT +LT++ET LFR+ Sbjct: 141 RCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 200 Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243 IREL++ G I+YISHR+ E+ EI D VTV RDG+ IA + AS T + ++ MVGR L+ Sbjct: 201 IRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALD 260 Query: 244 DQYPHLDKAPGD-IRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGA 301 D YP + P + + ++V +L +SF LRKGEILG +GLMGAGRTE+ + ++GA Sbjct: 261 DAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFGA 320 Query: 302 LPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSR 361 SG + L V RSP++ + +GI Y+SEDRK+DGL L M V N++L+ +R S Sbjct: 321 ERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAIS- 379 Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421 + G L+ ++E ++R ++TP+++Q LSGGNQQK+ I++ L ++L DE Sbjct: 380 SRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDE 439 Query: 422 PTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQ 481 PTRG+DVGAK IY+L+++ ADG+ ++L+SSE+PE+LGM+DRI V HEG ++ Q Sbjct: 440 PTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETRQ 499 Query: 482 ATQEVLMAAAVGK 494 +QE ++ A G+ Sbjct: 500 TSQEEILHYASGR 512 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: 637 Number of extensions: 24 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 515 Length adjustment: 34 Effective length of query: 467 Effective length of database: 481 Effective search space: 224627 Effective search space used: 224627 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