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_008411161.1 DESHY_RS05820 ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TZ92 (517 letters) >NCBI__GCF_000315365.1:WP_008411161.1 Length = 280 Score = 109 bits (272), Expect = 1e-28 Identities = 83/254 (32%), Positives = 127/254 (50%), Gaps = 8/254 (3%) Query: 27 ITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQFNGQDFRPGSRTQAEELGVR 86 ++L + GE L G NGAGK+T +++ L PT G + NGQ + ++G Sbjct: 20 LSLHIKPGEFFGLLGPNGAGKTTTLRLLTALTPPTAGQITVNGQPVSRNNTAAKRQIG-- 77 Query: 87 MVMQELNLLPTLTVAENLFLDNLPSHCGWISRKQLRKAAIEAMAQVGLDAIDPDTLVGSL 146 +V Q +NL P LTV ENL L L + +SR+++ + +A L A + L G+L Sbjct: 78 LVPQHINLEPELTVEENLRLHGLLYN---MSRQEINRRIDRLLAFSDL-AAERKALAGNL 133 Query: 147 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISHRLE 206 G ++ V IAR L+ +L+LDEPTA L +++ I L ARG+ I+ +H LE Sbjct: 134 SGGMKRKVMIARALMHQPALLLLDEPTAGLDVFSRRRVWDLIKSLNARGMTILLTTHYLE 193 Query: 207 ELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTLMVGRELGEHIDLGPRTIGGPALT-VK 265 E + RI +L+ G+L+ + +Q+ ++V G DL G AL Sbjct: 194 EAEHLCSRIGLLKKGRLIMTGSVEELR-QQVGPVVVEVFAGHQTDLYFFRDQGSALDFAA 252 Query: 266 GLTRSDKVRDVSFE 279 GLT +R S E Sbjct: 253 GLTNEFTIRQASLE 266 Score = 84.0 bits (206), Expect = 6e-21 Identities = 68/232 (29%), Positives = 111/232 (47%), Gaps = 15/232 (6%) Query: 273 VRDVSFEVRAGEIYGISGLIGAGRTELLRLIFGADLADSGTVALGSPAQVVSIRSPVDAV 332 V +S ++ GE +G+ G GAG+T LRL+ +G + + Q VS + A Sbjct: 17 VDHLSLHIKPGEFFGLLGPNGAGKTTTLRLLTALTPPTAGQITVNG--QPVSRNNT--AA 72 Query: 333 GHGIALITEDRKGEGLLLTQSISANIALGNMPEISGGGVVNSRDETALAKRQIDAMRIRS 392 I L+ + E L ++ N+ L + +N R + LA + A R Sbjct: 73 KRQIGLVPQHINLEPEL---TVEENLRLHGLLYNMSRQEINRRIDRLLAFSDLAAER--- 126 Query: 393 SSPAQLVSELSGGNQQKVVIGRWLERDCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGK 452 L LSGG ++KV+I R L +++L DEPT G+DV ++ ++ L+ L +G Sbjct: 127 ---KALAGNLSGGMKRKVMIARALMHQPALLLLDEPTAGLDVFSRRRVWDLIKSLNARGM 183 Query: 453 ALVVVSSDLRELMLICDRIGVLSAGRLIETFERDSWTQD--ELLAAAFAGYQ 502 +++ + L E +C RIG+L GRLI T + Q ++ FAG+Q Sbjct: 184 TILLTTHYLEEAEHLCSRIGLLKKGRLIMTGSVEELRQQVGPVVVEVFAGHQ 235 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: 318 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 280 Length adjustment: 30 Effective length of query: 487 Effective length of database: 250 Effective search space: 121750 Effective search space used: 121750 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: 50 (23.9 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