Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 286 bits (732), Expect = 1e-81 Identities = 178/491 (36%), Positives = 271/491 (55%), Gaps = 24/491 (4%) Query: 3 QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 62 Q P LQ+R I K + LA + L+I PGEIHAL+GENGAGKSTLMK++ GV D GE Sbjct: 10 QIPRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGE 69 Query: 63 ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANV--FMGSELRTRLGLIDHAAM 120 ++ G+ V +R+P +R GI +++Q ++ +SVA N+ MG+ T + Sbjct: 70 MIWQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGT------PKQL 123 Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 + V ++ G L LSI E+Q+VEI R L+ R++I+DEPT+ L+ +E + Sbjct: 124 EPKIREVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEAD 183 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 +LF +RRL EG +I++ISH++ EV AL TVLR G G V + ++ Q+MV Sbjct: 184 ELFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMV 243 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALA-------GGKIRPASFDVRAGEVLGFAGL 293 G + + ++ ADA + V L+ G ++ FDVR+GE++G AG+ Sbjct: 244 GEAAELITDYPKVMGADA-----FLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGV 298 Query: 294 VGAGRTELARLLFGAD--PR-SGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFL 350 G G+ EL LL G + PR I G+PV +P A + G+A+VP +R G G Sbjct: 299 AGNGQDELLALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVP 358 Query: 351 QMAVAANATMNVASRH-TRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQK 409 ++++A NA + + GLV+ + +A I+R VK P LSGGN QK Sbjct: 359 ELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQK 418 Query: 410 VLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICD 469 +L R + PK+L+ PT GVD+ A + I++ + L G A++VIS +L E+ ICD Sbjct: 419 FILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICD 478 Query: 470 RVLVMREGMIT 480 R+ + G ++ Sbjct: 479 RLGALCGGQLS 489 Score = 81.3 bits (199), Expect = 8e-20 Identities = 59/215 (27%), Positives = 103/215 (47%), Gaps = 9/215 (4%) Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPE 341 + GE+ G GAG++ L ++++G G+++ +G+ V + P A GI V + Sbjct: 36 IAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQGQRVTMRNPAQARGLGIGMVFQ 95 Query: 342 DRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGK 401 LF ++VA N + + + + L R QR + + PE V Sbjct: 96 HFS---LFETLSVAQNIALAMGA-----AAGTPKQLEPKIREVSQRYGMAL-EPERLVHS 146 Query: 402 LSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSEL 461 LS G +Q+V + R L ++LILDEPT + E++ + RLA++G +++ IS +L Sbjct: 147 LSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFISHKL 206 Query: 462 PEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496 EV +C V+R G + G A + + +L Sbjct: 207 GEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQL 241 Lambda K H 0.320 0.135 0.378 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: 733 Number of extensions: 50 Number of successful extensions: 9 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: 521 Length of database: 521 Length adjustment: 35 Effective length of query: 486 Effective length of database: 486 Effective search space: 236196 Effective search space used: 236196 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 (21.8 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