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_RS20685 BPHYT_RS20685 ribose ABC transporter ATPase
Query= uniprot:A0A1N7TZ92 (517 letters) >FitnessBrowser__BFirm:BPHYT_RS20685 Length = 537 Score = 714 bits (1843), Expect = 0.0 Identities = 375/520 (72%), Positives = 435/520 (83%), Gaps = 7/520 (1%) Query: 1 MSSSAPNAVLSVSGIGKTYAQPVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTP 60 ++ +AP VL V GIGKTYA+PVL+D++L L+ GEVLALTGENGAGKSTLSKIIGGLVTP Sbjct: 8 LADAAP--VLRVHGIGKTYAEPVLADVSLDLHAGEVLALTGENGAGKSTLSKIIGGLVTP 65 Query: 61 TTGHMQFNGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSH--CGWISR 118 TTG M G + P SR AE LGVRMVMQELNLLPTL+VAENLFL+ LP GWI R Sbjct: 66 TTGSMTLAGAAYTPASRKDAEALGVRMVMQELNLLPTLSVAENLFLNRLPQRGIFGWIDR 125 Query: 119 KQLRKAAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTA 178 +LR+ A AMAQVGLDAIDPDTLVG+LGIGHQQMVEIARNLIGDC VLILDEPTAMLTA Sbjct: 126 AKLREDARHAMAQVGLDAIDPDTLVGTLGIGHQQMVEIARNLIGDCRVLILDEPTAMLTA 185 Query: 179 REVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLV 238 REV++LFEQ+ RL+ARGVA++YISHRLEEL R+A+R AVLRDG+LV V+ MAN +++LV Sbjct: 186 REVDLLFEQVERLKARGVALVYISHRLEELKRIARRAAVLRDGRLVHVDEMANLTTDRLV 245 Query: 239 TLMVGRELGEHIDLGPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTE 298 TLMVGR++G+ IDLG R IG V G+TR VRDVSFEV+AGEI+GISGLIGAGRTE Sbjct: 246 TLMVGRDIGDRIDLGERRIGEMTFKVSGMTREPVVRDVSFEVKAGEIFGISGLIGAGRTE 305 Query: 299 LLRLIFGADLADSGTVAL---GSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSIS 355 L+RLI+GAD AD+GTV++ G + V+I SP DAV HGIALITEDRKGEGLLLTQ I+ Sbjct: 306 LMRLIYGADRADAGTVSIVREGGALEPVTIASPSDAVKHGIALITEDRKGEGLLLTQPIA 365 Query: 356 ANIALGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRW 415 ANI+LG++ +S GVV+ R E +LA+RQIDAMRIRSS PAQ VSELSGGNQQKVVIGRW Sbjct: 366 ANISLGHLRSVSSKGVVDGRREASLARRQIDAMRIRSSGPAQPVSELSGGNQQKVVIGRW 425 Query: 416 LERDCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLS 475 L RDC+V+LFDEPTRGIDVGAKFDIYAL+G L R+G+ALVVVSSDLRELM ICDRI V+S Sbjct: 426 LARDCTVLLFDEPTRGIDVGAKFDIYALMGALAREGRALVVVSSDLRELMAICDRIAVMS 485 Query: 476 AGRLIETFERDSWTQDELLAAAFAGYQKRDALLNDAVLRD 515 AGR+ FER +WTQD LLAAAFAGY KRD +L++ + D Sbjct: 486 AGRMTGLFERGNWTQDALLAAAFAGYAKRDDMLHEPIEPD 525 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: 915 Number of extensions: 41 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: 537 Length adjustment: 35 Effective length of query: 482 Effective length of database: 502 Effective search space: 241964 Effective search space used: 241964 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