Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate WP_037149946.1 RHSP_RS05960 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TZ92 (517 letters) >NCBI__GCF_000359745.1:WP_037149946.1 Length = 511 Score = 401 bits (1031), Expect = e-116 Identities = 223/505 (44%), Positives = 321/505 (63%), Gaps = 5/505 (0%) Query: 1 MSSSAPNAVLSVSGIGKTYAQPV-LSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVT 59 +S + + +L + GIGK + V L ++++ + RG+ L GENGAGKSTL ++GG+ Sbjct: 6 VSGTDDDFILKLDGIGKRFPGVVALRNVSMQIGRGKGHILLGENGAGKSTLINLLGGVFR 65 Query: 60 PTTGHMQFNGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSHCGWISRK 119 P GH+ F+GQ + P S +A + G+R++ QEL+ L LTVAENL ++LP G ++ K Sbjct: 66 PDDGHILFDGQRYDPSSPLEAFKAGIRVIHQELHPLSNLTVAENLLFEHLPRRYGLVNYK 125 Query: 120 QLRKAAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAR 179 ++ A E +A+VGLD + P TL L + Q++EIA+ L + +L+LDEPTA LT++ Sbjct: 126 EMNSRAAELLAEVGLD-VAPTTLASRLSVAQLQLLEIAKALCYESKLLVLDEPTATLTSK 184 Query: 180 EVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVT 239 EV+ LFE + RL+ARGV +YISHRLEE+ V + VLRDG+ V P+A Q+V Sbjct: 185 EVDRLFEILRRLKARGVTTLYISHRLEEIFEVGDDVTVLRDGQHVITRPLAGLAIPQIVE 244 Query: 240 LMVGRELGEHIDL-GPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTE 298 LMVGR L +H G + G AL V GL + ++SF V GEI GI+GL+G+GRTE Sbjct: 245 LMVGRTLSDHGAFRGDSVVSGEALGVSGLKVTRNSPELSFSVAKGEIVGIAGLVGSGRTE 304 Query: 299 LLRLIFGADLADSGTVALGSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANI 358 +R IFGAD +G + + V I SP DAV G+ L TEDRK +GL+L S + N Sbjct: 305 AVRAIFGADTKAAGEIRIDGKR--VEIDSPKDAVAAGLCLATEDRKMQGLMLDMSCAENT 362 Query: 359 ALGNMPEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLER 418 + ++ ++S G+++ E A+R + +RI++ S Q+V SGGNQQKVVI +WL R Sbjct: 363 TITDLGKVSRNGLISRNAEDDHAQRLVRELRIKTPSIHQIVRTFSGGNQQKVVIAKWLFR 422 Query: 419 DCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGR 478 V++FDEPTRGIDVGAK +IY LL + +GK ++VVSSDL EL+ IC RI VLS G+ Sbjct: 423 GPKVLIFDEPTRGIDVGAKAEIYDLLWKFAAEGKGVLVVSSDLPELIGICHRIIVLSDGK 482 Query: 479 LIETFERDSWTQDELLAAAFAGYQK 503 + RD + + +L+ A+ Y + Sbjct: 483 IAGEIARDQFEESRILSLAYKEYSR 507 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: 706 Number of extensions: 34 Number of successful extensions: 8 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: 511 Length adjustment: 35 Effective length of query: 482 Effective length of database: 476 Effective search space: 229432 Effective search space used: 229432 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 24 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