Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 268 bits (686), Expect = 3e-76 Identities = 164/506 (32%), Positives = 279/506 (55%), Gaps = 23/506 (4%) Query: 20 IVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVE 79 I KR+PGV A D+V V EI +++GENGAGKSTL+KI+ G +KPDAG++ NG R Sbjct: 14 ISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAA 73 Query: 80 FHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKE 139 H+P DA GI+++ Q +L D +TVAENI L RG K S + T K+ Sbjct: 74 IHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLP--RGSKTAAGS----PHAGTNMKQ 127 Query: 140 LLDLI-------GAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 L + I G P+ V L+ +RQ VEI +AL+ +P+++ +DEPTS LT + Sbjct: 128 LAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAV 187 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 + LF + L + G S++++SH+LDE+ + VMR G+ G + ++ ++M Sbjct: 188 QTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLM 247 Query: 253 VGREVEFFPHGIETRPGEIALEVRNLK------WKDKVKNVSFEVRKGEVLGFAGLVGAG 306 +G E ++T PG L VR L + ++ +S ++R GE++G AG+ G G Sbjct: 248 IGGEPPREAR-VQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVSGNG 306 Query: 307 RTETMLLVFGVNQKESGD-IYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKD 365 + E + + G + + + D I ++ + V + + G+ +PE+R +G V M++ Sbjct: 307 QQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMSLAA 366 Query: 366 NIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKW 425 NI+L ++ + +++ + RL +K + + ++LSGGN QK ++ + Sbjct: 367 NILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIVGRE 426 Query: 426 LATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMW 485 + + +LI +PT G+DVGA A+IH + L A G A++++S EL E+ + DR+ V+ Sbjct: 427 IESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRLHVIA 486 Query: 486 EGEITAVLDNREKRVTQEEIMYYASG 511 +G ++ + R+ T+E++ + SG Sbjct: 487 KGRLSPSIPTRD--ATREQVGLWMSG 510 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: 584 Number of extensions: 38 Number of successful extensions: 9 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: 529 Length adjustment: 35 Effective length of query: 485 Effective length of database: 494 Effective search space: 239590 Effective search space used: 239590 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