Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 181 bits (460), Expect = 2e-50 Identities = 102/313 (32%), Positives = 183/313 (58%), Gaps = 12/313 (3%) Query: 31 QQITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDL 90 Q++ ++ +++ ++ F+ S +F ++N++ + S + G+++ + + + DL Sbjct: 35 QKLLAFASLLLMILFFSFAS---PNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDL 91 Query: 91 SVGSTVAFAGVLCAMVLNATGNTF-IAIVAAVAAGGVIGFVNGAVIAYLRINALITTLAT 149 SVG+ + F V+ +VL G + I AA+ G + G+++G VIA L++ I TL Sbjct: 92 SVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGM 151 Query: 150 MEIVRGLGFIVSHGQAVGVS-SDTFIALGGLSFFG-----VSLPIWVTLLCFIVFG--VM 201 M +++GL ++S + + + ++ F A+ S G + +P V +L + G ++ Sbjct: 152 MMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASII 211 Query: 202 LNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNA 261 LN+TV+GR T A+G N EA RL+G+ V+ +V ++ GA+ +AG+I+ASR+ S QP Sbjct: 212 LNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPAL 271 Query: 262 AQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAI 321 QG+EL+ I+A V+GG SL GG TI G +IG IM + N + +M++ +Q +V G I Sbjct: 272 GQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVI 331 Query: 322 LLAAVLLDQLKNR 334 ++ AV LD L+ R Sbjct: 332 IILAVYLDILRRR 344 Lambda K H 0.326 0.139 0.396 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: 290 Number of extensions: 20 Number of successful extensions: 3 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: 338 Length of database: 347 Length adjustment: 29 Effective length of query: 309 Effective length of database: 318 Effective search space: 98262 Effective search space used: 98262 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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