Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 340 bits (871), Expect = 9e-98 Identities = 189/477 (39%), Positives = 289/477 (60%), Gaps = 6/477 (1%) Query: 18 KGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGER 77 + I KR+ GV A+D+VDF V E V L GENG+GKSTLIKI++GV AG + + G+ Sbjct: 13 RAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQE 72 Query: 78 VEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRS 137 +P + G+ VI Q+ +L N++VAENI + + ++R R + + Sbjct: 73 HVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQ-LSTRQRLFKFRAVRDI----A 127 Query: 138 KELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFE 197 + LD IG + DA V L AQ+Q+V IC+AL + ++I MDEPT++LT +E RL Sbjct: 128 RAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQG 187 Query: 198 IIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257 II MLK G++V+FVSH+L EV+ +S+++VV+R+GK++ E EFD ++ M GR+V Sbjct: 188 IIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDV 247 Query: 258 EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGV 317 P + ++V+ L ++SF++R GEVLG GL+G GRT +FG+ Sbjct: 248 PEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGL 307 Query: 318 NQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISR 377 ++G I V+G V + +P+ A IG +PEDR +GL L ++ N+ + L + Sbjct: 308 VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTS 367 Query: 378 WGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDE 437 G LD + + D+++RL +K P + ++LSGGNQQ+V LA+WL+ +LI + Sbjct: 368 GGF-LDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNG 426 Query: 438 PTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLD 494 P+ G+DVG+KA+IH +IRELA +G VI+IS +LPE+L R++VM EG I L+ Sbjct: 427 PSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALE 483 Lambda K H 0.319 0.138 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: 565 Number of extensions: 25 Number of successful extensions: 6 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: 520 Length of database: 498 Length adjustment: 34 Effective length of query: 486 Effective length of database: 464 Effective search space: 225504 Effective search space used: 225504 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 (21.7 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