Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 405 bits (1041), Expect = e-117 Identities = 230/503 (45%), Positives = 324/503 (64%), Gaps = 9/503 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL + + KSF AL + L + GE+HAL+GENGAGKSTL+K+LS HA D G + Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 66 DGRPVALRD-PGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124 G+ + RD P + GI IYQE + P +SVA N+++G E R RLGL+D + +R+ Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121 Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 A+L LG L++AEQQ VEIA+A+ +R++IMDEPTAALS RE ++L Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 ++ L+ +++IY+SHR+ EV A+ DR TV+RDG FV +++ +V++MVGR + Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 Query: 245 SEFYQHQRIAPADAAQLP----TVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300 EF + +R P A L T R A G +R SF R GE++G AGLVGAGRT+ Sbjct: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300 Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360 LARL+FGADP + G +L++ +P+ + PR A++AGI VPEDRK QG FL ++ N ++ Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360 Query: 361 NVASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419 + LG V R+ + Q+L +K+A ET +GKLSGGNQQKVLL R + + Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420 Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479 PKVLI+DEPTRG+DI AK+E++Q++ LA GVAVVVISSEL EV+ + DR++V REG+I Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480 Query: 480 TGELAGAAITQENIMR-LATDTN 501 +L T+E +M +AT T+ Sbjct: 481 VADLDAQTATEEGLMAYMATGTD 503 Score = 85.9 bits (211), Expect = 3e-21 Identities = 64/222 (28%), Positives = 111/222 (50%), Gaps = 7/222 (3%) Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHI-DQPRAAMRAGIAYVP 340 V GEV G GAG++ L ++L A G + G+ + D P + GIA + Sbjct: 26 VGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIY 85 Query: 341 EDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVG 400 ++ LF +++VA N M + RLGLV L A+A + L + + +P+ PV Sbjct: 86 QEFN---LFPELSVAEN--MYLGREPRRLGLVDWSRLRADAQALLNDLGLPL-NPDAPVR 139 Query: 401 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSE 460 L+ QQ V +A+ + + +++I+DEPT + ++ ++ L ++ V+V+ +S Sbjct: 140 GLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHR 199 Query: 461 LPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502 L EV +CDR VMR+G A + +++RL +V Sbjct: 200 LGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 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: 743 Number of extensions: 41 Number of successful extensions: 9 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: 515 Length adjustment: 35 Effective length of query: 486 Effective length of database: 480 Effective search space: 233280 Effective search space used: 233280 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