Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 414 bits (1063), Expect = e-120 Identities = 223/507 (43%), Positives = 320/507 (63%), Gaps = 10/507 (1%) Query: 3 QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 62 Q+P+L++ GI K+F AL + LTI PGE+HALMGENGAGKSTLMKVL G+H PD+G+ Sbjct: 4 QSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQ 63 Query: 63 ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122 I++ +PV + P ++A GI I+QEL++A +SVA N+++G R R GL+D A + + Sbjct: 64 IIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEA 123 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 +T+A+L +L GF A G LSIA QQ VEIARAL ++ VI DEPTA+L++ E L Sbjct: 124 KTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVL 183 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 F V+ L+++G+ I YISHRM E++ + DR++VLRDG + G + E + E + QMM+GR Sbjct: 184 FEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGR 243 Query: 243 --SLSEFYQHQRIAPADAAQLPTVMQVRALAGGKI-RPASFDVRAGEVLGFAGLVGAGRT 299 LS H + ++VR L+ G + +F+VR GEV+GF GLVGAGRT Sbjct: 244 KLDLSRNEAHHELG-------EVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRT 296 Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359 E+A LFG + G I L+G V I P A+ GI+ VPEDRKGQGL L M N T Sbjct: 297 EIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMT 356 Query: 360 MNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419 + V + + +L+++ + VG LSGGNQQK+++ +WL + Sbjct: 357 LPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMR 416 Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479 P VLI+DEPTRG+D+ +K+EI+ L+ LA+QG AV+VISSE+PEV+ + DR++ M G I Sbjct: 417 PNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRI 476 Query: 480 TGELAGAAITQENIMRLATDTNVPRTA 506 +T+EN++ + + + A Sbjct: 477 MRTFTSEEVTEENLIAAISGLDTEKVA 503 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: 681 Number of extensions: 38 Number of successful extensions: 7 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: 521 Length of database: 503 Length adjustment: 35 Effective length of query: 486 Effective length of database: 468 Effective search space: 227448 Effective search space used: 227448 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