Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 371 bits (953), Expect = e-107 Identities = 206/494 (41%), Positives = 300/494 (60%), Gaps = 9/494 (1%) Query: 7 LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66 L+ GI K+F AL + PG++HALMGENGAGKSTL+K+L G + P G++ + Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75 Query: 67 GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126 + + S +G+ +I+QEL + P ++VA N+F+G L GLI+ +R + A Sbjct: 76 EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLG-HLPASFGLINRGVLRQQALA 134 Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186 L+ L + GRLS+ ++Q VEIA+AL + ++ DEPT++LS RE ++L ++ Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELV-RDEIDSERIVQMMVGRSLS 245 RLRDEG ++Y+SHRM EV+ + + VTV +DG FV + +++V MVGR + Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTELARL 304 + Y + R P A L +V L G +R P SF+ GE+LG GLVGAGRTEL R+ Sbjct: 255 DIYDY-RSRPRGAVAL----KVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRM 309 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 L G + G + L GR + + PR A+ AGI PEDRK +G+ +VA N ++ Sbjct: 310 LSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARG 369 Query: 365 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423 H+ G L+R A I+ L VK + + LSGGNQQK +L RWL + KVL Sbjct: 370 AHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVL 429 Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483 +LDEPTRG+DI AK+EIYQ++H LA+ G+AV+V+SS+L EV+GI DR+LV+ EG + GEL Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489 Query: 484 AGAAITQENIMRLA 497 + N+++LA Sbjct: 490 TREQANESNLLQLA 503 Score = 87.0 bits (214), Expect = 1e-21 Identities = 61/217 (28%), Positives = 110/217 (50%), Gaps = 6/217 (2%) Query: 32 GEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQEL- 90 GEI L G GAG++ L ++LSG+ G + L GR + L P + AAGI L ++ Sbjct: 290 GEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRK 349 Query: 91 --AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGF-GASDLAGRLS 145 + P SVA N+ + + + G L+ + D ++ L A+ LS Sbjct: 350 KEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLS 409 Query: 146 IAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAE 205 QQ+ + R L +++++DEPT + +++ ++ L G+A+I +S + E Sbjct: 410 GGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLME 469 Query: 206 VYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 V ++DR+ VL +G+ GEL R++ + ++Q+ + R Sbjct: 470 VMGISDRILVLCEGAMRGELTREQANESNLLQLALPR 506 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: 652 Number of extensions: 28 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 486 Effective length of database: 479 Effective search space: 232794 Effective search space used: 232794 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 Apr 09 2024. 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