Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate H281DRAFT_05226 H281DRAFT_05226 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A1N7TZ92 (517 letters) >FitnessBrowser__Burk376:H281DRAFT_05226 Length = 531 Score = 715 bits (1846), Expect = 0.0 Identities = 376/510 (73%), Positives = 429/510 (84%), Gaps = 8/510 (1%) Query: 8 AVLSVSGIGKTYAQPVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQF 67 A+LSVSGIGKTYA+PVL+D++L+L GEVLALTGENGAGKSTLSKIIGGLV PT G M+ Sbjct: 11 AILSVSGIGKTYAEPVLADVSLSLRAGEVLALTGENGAGKSTLSKIIGGLVDPTAGTMRL 70 Query: 68 NGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPS----HCGWISRKQLRK 123 GQ + P SRT+AE LGVRMVMQELNLLPTL+VAENLFL+ LP GWI R++LR+ Sbjct: 71 AGQPYAPASRTEAEALGVRMVMQELNLLPTLSVAENLFLNRLPRAGAFSFGWIDRRKLRE 130 Query: 124 AAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183 A AMAQVGLDAI PDTLVG LGIGHQQMVEIARNLI DC VLILDEPTAMLTAREV++ Sbjct: 131 DARHAMAQVGLDAIHPDTLVGELGIGHQQMVEIARNLIDDCRVLILDEPTAMLTAREVDL 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 VRDVSFEVRAGEI+G+SGLIGAGRTEL+RLI Sbjct: 251 RELGEQIDLGVRNIGAPLLKVDRLTRGKVVRDVSFEVRAGEIFGVSGLIGAGRTELMRLI 310 Query: 304 FGADLADSGTVAL----GSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANIA 359 +GAD DSG VAL G+P V I SP DAV GIALITEDRKGEGLLL Q I+AN++ Sbjct: 311 YGADQKDSGAVALAATPGAPPTPVRIDSPSDAVRAGIALITEDRKGEGLLLPQPIAANVS 370 Query: 360 LGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERD 419 LGN+ ++ G+V+++ E ALAK+QIDAMRIRSS P Q+V ELSGGNQQKVVIGRWL RD Sbjct: 371 LGNIGSVARHGIVDAKRENALAKKQIDAMRIRSSGPGQIVGELSGGNQQKVVIGRWLARD 430 Query: 420 CSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL 479 C V+LFDEPTRGIDVGAKFDIY L+G L R+G+ALVVVSSDLRELMLICDRIGV+SAG L Sbjct: 431 CRVLLFDEPTRGIDVGAKFDIYGLMGALAREGRALVVVSSDLRELMLICDRIGVMSAGSL 490 Query: 480 IETFERDSWTQDELLAAAFAGYQKRDALLN 509 FERD+W+QD LLAAAFAGY+ R+ALL+ Sbjct: 491 TGVFERDTWSQDALLAAAFAGYRSREALLH 520 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: 928 Number of extensions: 37 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: 531 Length adjustment: 35 Effective length of query: 482 Effective length of database: 496 Effective search space: 239072 Effective search space used: 239072 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