Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 379 bits (972), Expect = e-109 Identities = 219/505 (43%), Positives = 314/505 (62%), Gaps = 16/505 (3%) Query: 12 MEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEI 71 M +L + K FPGV A+D VD V E+ +L+GENGAGKSTLIKIL+ DAG + Sbjct: 1 MTLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTV 60 Query: 72 LVNGERVEFH-SPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDE 130 G+ ++ +P+ + GI+ I+QE NL ++VAEN++L E R VD Sbjct: 61 TFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR------LGLVDW 114 Query: 131 NYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190 + + ++ LL+ +G +PDA VR LT A++QMVEI KA+ R+I MDEPT++L+ Sbjct: 115 SRLRADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGR 174 Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250 E +RL II LK+R +SV++VSHRL EV + DR VMRDG+ + + +V +++ Sbjct: 175 EVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVR 234 Query: 251 MMVGREVEFFPHGIETRPGEIALEVRN-------LKWKDKVKNVSFEVRKGEVLGFAGLV 303 +MVGR VEF PG + L+V L ++ VSF R GE++G AGLV Sbjct: 235 LMVGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLV 294 Query: 304 GAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTV 363 GAGRT+ L+FG + +G + V+ + + +++P DAI+ GI L+PEDRK QG L ++ Sbjct: 295 GAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSI 354 Query: 364 KDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLA 423 + N+ LPSLK +S G +DER E ++ E Y ++L IK LSGGNQQKV+L Sbjct: 355 RRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLG 414 Query: 424 KWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVV 483 + +A +LI DEPTRGID+GAKAE+H+++ +LA G AV++ISSEL E++ +SDRIVV Sbjct: 415 RAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVV 474 Query: 484 MWEGEITAVLDNREKRVTQEEIMYY 508 EG I A LD + T+E +M Y Sbjct: 475 FREGVIVADLD--AQTATEEGLMAY 497 Lambda K H 0.319 0.138 0.381 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: 647 Number of extensions: 29 Number of successful extensions: 8 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: 520 Length of database: 515 Length adjustment: 35 Effective length of query: 485 Effective length of database: 480 Effective search space: 232800 Effective search space used: 232800 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 (21.7 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