Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 400 bits (1027), Expect = e-116 Identities = 236/505 (46%), Positives = 324/505 (64%), Gaps = 17/505 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 LL + N+ K FPGV AL V+L G V ALMGENGAGKSTLMKI++G Y D GE Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD-AGELR 84 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL--VARGDMVRA 130 + G+ V D P +A G+A+I+QEL+L P++S+AENI++GR Q GL V G+M R Sbjct: 85 LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE-QLNGLHMVDHGEMHRC 143 Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 A L RL P V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++ E LF Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 ++I L+ +G I+YI+H+M E+ +AD V V RDG ++G + +L+ MMVGR+ Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 263 Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310 LS + Q + +++LSVRD++ KG SFDL AGE+LG+AGL+G+GRT +A + Sbjct: 264 LSQLFP-VREQPIG-DLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAI 321 Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370 FG T GE+ + G V + P AI+ G A LTEDRKL GLF SV EN+ Sbjct: 322 FGVTPSTGGEILL-----DGQPVRI--SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 374 Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430 + V +G G + + A R + L ++ + + LSGGNQQK +L+R L Sbjct: 375 EMAVLPH-YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433 Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490 PR+LILDEPTRG+D+GAK+EIYRLI+ LA G+A++MISSELPEV+G+ DRV+VM EG Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 493 Query: 491 TLAGEVRPAGSAAETQERIIALATG 515 L G + G A TQER++ LA+G Sbjct: 494 DLMGTLN-RGEA--TQERVMQLASG 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: 630 Number of extensions: 27 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