Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate BPHYT_RS11215 BPHYT_RS11215 ribose ABC transporter ATPase
Query= uniprot:A0A1N7TZ92 (517 letters) >FitnessBrowser__BFirm:BPHYT_RS11215 Length = 532 Score = 713 bits (1841), Expect = 0.0 Identities = 377/512 (73%), Positives = 430/512 (83%), Gaps = 8/512 (1%) Query: 8 AVLSVSGIGKTYAQPVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQF 67 AVLSVSGIGKTYA+PVL+DI+L+L GEVLALTGENGAGKSTLSKIIGGLV PT G MQ Sbjct: 11 AVLSVSGIGKTYAEPVLADISLSLRAGEVLALTGENGAGKSTLSKIIGGLVEPTAGTMQL 70 Query: 68 NGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPS----HCGWISRKQLRK 123 G + P SRTQAE LGVRMVMQELNLLPTL+VAENLFL+ LP GWI R++LR+ Sbjct: 71 GGVPYAPASRTQAEALGVRMVMQELNLLPTLSVAENLFLNRLPRAGAFSFGWIDRRKLRE 130 Query: 124 AAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183 A +AMAQVGLDAIDPDTLVG LGIGHQQMVEIARNLI DC VLILDEPTAMLTAREV++ Sbjct: 131 DARQAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIDDCRVLILDEPTAMLTAREVDL 190 Query: 184 LFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTLMVG 243 LFEQI RL+ARGVA++YISHRLEELARVA++IAVLRDG+LV V+ MAN S+++VT MVG Sbjct: 191 LFEQIDRLKARGVALVYISHRLEELARVAEQIAVLRDGRLVHVDAMANLTSDEIVTWMVG 250 Query: 244 RELGEHIDLGPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTELLRLI 303 RELGE IDLG R IG P L V LTR VR+VSFEVRAGEI+GISGLIGAGRTEL+RLI Sbjct: 251 RELGERIDLGVRNIGAPLLKVDRLTRGKVVREVSFEVRAGEIFGISGLIGAGRTELMRLI 310 Query: 304 FGADLADSGTVAL----GSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANIA 359 +GAD DSGTV+L G+P V I SP DAV GIALITEDRKGEGLLL Q I+AN++ Sbjct: 311 YGADPKDSGTVSLAATPGAPPTPVQIASPSDAVRAGIALITEDRKGEGLLLPQPIAANVS 370 Query: 360 LGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERD 419 LGN+ ++ G+V+++ E ALA+ QI AMRIR+S P Q+V ELSGGNQQKVVIGRWL RD Sbjct: 371 LGNIGSVARHGIVDAKRENALAQTQIAAMRIRTSGPGQIVGELSGGNQQKVVIGRWLARD 430 Query: 420 CSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL 479 C V+LFDEPTRGIDVGAKFDIY L+G L R+G+ALVVVSSDLRELMLICDRIGV+SAG + Sbjct: 431 CRVLLFDEPTRGIDVGAKFDIYGLMGALAREGRALVVVSSDLRELMLICDRIGVMSAGSM 490 Query: 480 IETFERDSWTQDELLAAAFAGYQKRDALLNDA 511 FERD+W+QD LLAAAFAGY+ R+ALL+ A Sbjct: 491 TGVFERDNWSQDALLAAAFAGYRSREALLHAA 522 Lambda K H 0.319 0.136 0.382 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: 913 Number of extensions: 38 Number of successful extensions: 7 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: 517 Length of database: 532 Length adjustment: 35 Effective length of query: 482 Effective length of database: 497 Effective search space: 239554 Effective search space used: 239554 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