Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 383 bits (984), Expect = e-111 Identities = 207/494 (41%), Positives = 309/494 (62%), Gaps = 9/494 (1%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 L+ GI KSF AL+++ PG++HALMGENGAGKSTL+K+L G + P G++ + Sbjct: 11 LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 70 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLG-HLPARFGLVNRGVLRQQALT 134 + +A + S A+G+ +I+QEL + P ++VA N+F+G L R GL++ +R + Sbjct: 71 GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 130 Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 +L+ L + GRLS+ ++Q VEIA+AL + ++ DEPT++LS RE ++L ++ Sbjct: 131 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 190 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 RLRDEG ++Y+SHRM EV+ + + VTV +DG +V E+ +++V MVGR + Sbjct: 191 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVR-DEIDSERIVQMMVGRSLS 249 Query: 255 DIYDYRPRERGDVA-----LQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRL 309 + Y ++ D A +QV+ L G G P SF V GE+LG GLVGAGRTEL RL Sbjct: 250 EFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELARL 308 Query: 310 LSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369 L G + + G ++L + + + PR A+ AG+ PEDRK +G+ +V N ++ Sbjct: 309 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 368 Query: 370 SHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVL 429 H+ LG L+R G A I+ L VK + LSGGNQQK +L RWL + KVL Sbjct: 369 RHTRLG-LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 427 Query: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489 +LDEPTRG+DI AK+EIYQ++H LA+ G+AV+V+SS+L EV+GI DR+LV+ EG + GEL Sbjct: 428 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 487 Query: 490 SRDQANESNLLQLA 503 + + N+++LA Sbjct: 488 AGAAITQENIMRLA 501 Score = 91.3 bits (225), Expect = 7e-23 Identities = 66/237 (27%), Positives = 122/237 (51%), Gaps = 20/237 (8%) Query: 287 VHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPE 346 + GEI L G GAG++ L+++LSG+ +G ++L + + LR P + AAG+ L + Sbjct: 33 IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 92 Query: 347 DRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKV---KTPTAGQ 403 + + P SV N+ + + + LG L+ R D ++ L + AG+ Sbjct: 93 EL---AVAPNISVAANVFMGSE-LRTRLG-LIDHAAMRSRTDAVLRQLGAGFGASDLAGR 147 Query: 404 KIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVV 463 LS QQ+ + R L +++++DEPT + +++ ++ L +G+A+I + Sbjct: 148 ----LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYI 203 Query: 464 SSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR--------QRVADA 512 S + EV ++DR+ VL +G+ GEL RD+ + ++Q+ + R QR+A A Sbjct: 204 SHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQRIAPA 260 Lambda K H 0.320 0.138 0.391 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: 650 Number of extensions: 32 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: 514 Length of database: 502 Length adjustment: 34 Effective length of query: 480 Effective length of database: 468 Effective search space: 224640 Effective search space used: 224640 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