Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008 Length = 485 Score = 342 bits (878), Expect = 1e-98 Identities = 201/470 (42%), Positives = 290/470 (61%), Gaps = 14/470 (2%) Query: 37 LMGENGAGKSTLMKVLSGVHAPD--QGEILLDGRPVALRD-PGASRAAGINLIYQELAVA 93 L+GENGAGKST++K+L+G D QG + +G + D P + GI IYQE + Sbjct: 1 LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60 Query: 94 PNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVE 153 ++SVA N+++G E R G +D M S VL LG + +LS+AEQQ VE Sbjct: 61 ADMSVAENMYLGRE-PLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVE 119 Query: 154 IARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRV 213 IA+AL ++++IMDEPTAALS RE ++L ++ L+ +G++IIY+SH++ EV A DR Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179 Query: 214 TVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGG 273 T+ RDG+++ ++ + IV++MVGR + EF + L R AGG Sbjct: 180 TIFRDGAYITSGDVCDVSVDDIVRLMVGRDV-EFVRKPLTGAPGEVMLKVQSVSRTAAGG 238 Query: 274 -------KIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVH-I 325 + S DVRAGE++GFAGLVGAGRTELAR++FGAD G I + GR V Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPF 298 Query: 326 DQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGL-VRSRSLGGVARAA 384 PR + AG+A VPEDRK Q FL ++ N ++ R G+ + R+ + + Sbjct: 299 KSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDY 358 Query: 385 IQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLV 444 +RL +K+++ +G LSGGNQQKV+LAR + + PKVLI+DEPTRG+D+ AK+E++QL+ Sbjct: 359 QKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418 Query: 445 HRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIM 494 +A GVAV+VISSELPEV+ + DR++ REG ITG ++ T+E +M Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLM 468 Score = 89.4 bits (220), Expect = 3e-22 Identities = 67/238 (28%), Positives = 115/238 (48%), Gaps = 13/238 (5%) Query: 22 LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVA-LRDPGASRA 80 L DM + +R GEI G GAG++ L +V+ G D+G I ++GR V+ + P A Sbjct: 247 LLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFKSPREGIA 306 Query: 81 AGINLIYQEL---------AVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQL 131 AG+ L+ ++ ++ N+S+ + +G R + + D A + D R Sbjct: 307 AGVALVPEDRKQQACFLSHSIRWNMSLPS---LGGLQRWGMFIDDRAETQLIQDYQKRLR 363 Query: 132 GAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRD 191 S G LS QQ+V +AR + + +++I+DEPT + ++ ++ + Sbjct: 364 IKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLLFDMAR 423 Query: 192 EGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQ 249 G+A+I IS + EV A++DR+ R+G G + DE E ++ M S F Q Sbjct: 424 AGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQGVSSSFSQ 481 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: 675 Number of extensions: 33 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 485 Length adjustment: 34 Effective length of query: 487 Effective length of database: 451 Effective search space: 219637 Effective search space used: 219637 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