Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20250 Length = 514 Score = 390 bits (1001), Expect = e-113 Identities = 209/494 (42%), Positives = 313/494 (63%), Gaps = 9/494 (1%) Query: 7 LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66 L+ GI KSF AL+++ PG++HALMGENGAGKSTL+K+L G + P G++ + Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 Query: 67 GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126 + +A + S A+G+ +I+QEL + P ++VA N+F+G L R GL++ +R + Sbjct: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLG-HLPARFGLVNRGVLRQQALT 134 Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186 +L+ L + GRLS+ ++Q VEIA+AL + ++ DEPT++LS RE ++L ++ Sbjct: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR-DEIDSERIVQMMVGRSLS 245 RLRDEG ++Y+SHRM EV+ + + VTV +DG +V E+ +++V MVGR + Sbjct: 195 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIR-PASFDVRAGEVLGFAGLVGAGRTELARL 304 + Y ++ D A +QV++L G +R P SF V GE+LG GLVGAGRTEL RL Sbjct: 255 DIYDYRPRERGDVA-----LQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRL 309 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 L G + +S G ++L G+ + + PR A+ AG+ PEDRK +G+ +V N ++ Sbjct: 310 LSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369 Query: 365 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423 H+ LG L+R G A I+ L VK + LSGGNQQK +L RWL + KVL Sbjct: 370 AHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVL 429 Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483 +LDEPTRG+DI AK+EIYQ++H LA+ G+AV+V+SS+L EV+GI DR+LV+ EG + GEL Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489 Query: 484 AGAAITQENIMRLA 497 + + N+++LA Sbjct: 490 SRDQANESNLLQLA 503 Score = 95.9 bits (237), Expect = 3e-24 Identities = 67/234 (28%), Positives = 120/234 (51%), Gaps = 14/234 (5%) Query: 29 IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88 + GEI L G GAG++ L ++LSG+ +G ++L G+ + LR P + AAG+ L + Sbjct: 287 VHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPE 346 Query: 89 EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGF-GASDLAG 142 + + P SV N+ + + + LG L+ R D ++ L AS Sbjct: 347 DRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIM 406 Query: 143 RLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHR 202 LS QQ+ + R L +++++DEPT + +++ ++ L +G+A+I +S Sbjct: 407 YLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSD 466 Query: 203 MAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQRIAPA 256 + EV ++DR+ VL +G+ GEL RD+ + ++Q+ + R QR+A A Sbjct: 467 LMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR--------QRVADA 512 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 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