Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 405 bits (1040), Expect = e-117 Identities = 240/518 (46%), Positives = 329/518 (63%), Gaps = 18/518 (3%) Query: 1 MSDMSDTSTKAP-LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKIL 59 M+ D S P LL + N+ K FPGV AL V+L G V ALMGENGAGKSTLMKI+ Sbjct: 13 MTFQPDVSLDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKII 72 Query: 60 SGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR 119 +G Y D GE + G+ V D P +A G+A+I+QEL+L P++S+AENI++GR Q Sbjct: 73 AGIYQPD-AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE-QLN 130 Query: 120 GL--VARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEP 177 GL V G+M R A L RL P V +LSIA+RQ+VEIA+AV +++ IL+MDEP Sbjct: 131 GLHMVDHGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEP 190 Query: 178 TTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL 237 T+ ++ E LF++I L+ +G I+YI+H+M E+ +AD V V RDG ++G + Sbjct: 191 TSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSM 250 Query: 238 SQAALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAG 297 +L+ MMVGR+LS + Q + E++LSVRD++ KG SFDL AGE+LG+AG Sbjct: 251 DGDSLISMMVGRELSQLFP-VREQPIG-ELVLSVRDLSLDGIFKGVSFDLHAGEILGIAG 308 Query: 298 LVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKL 357 L+G+GRT +A +FG T GE+R+ G V + P AI+ G A LTEDRKL Sbjct: 309 LMGSGRTNVAEAIFGVTPSTGGEIRL-----DGQPVRI--SDPHMAIEKGFALLTEDRKL 361 Query: 358 QGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSG 417 GLF SV EN+ + V +G G + + A R + L ++ + + LSG Sbjct: 362 SGLFPCLSVLENMEMAVLPH-YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSG 420 Query: 418 GNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEV 477 GNQQK +L+R L PR+LILDEPTRG+D+GAK+EIYRLI+ LA G+A++MISSELPEV Sbjct: 421 GNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEV 480 Query: 478 VGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATG 515 +G+ DRV+VM EG L G + + TQER++ LA+G Sbjct: 481 LGMSDRVMVMHEGDLMGTL---DRSEATQERVMQLASG 515 Lambda K H 0.320 0.136 0.382 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: 635 Number of extensions: 28 Number of successful extensions: 10 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: 540 Length of database: 517 Length adjustment: 35 Effective length of query: 505 Effective length of database: 482 Effective search space: 243410 Effective search space used: 243410 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