Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 394 bits (1012), Expect = e-114 Identities = 230/508 (45%), Positives = 322/508 (63%), Gaps = 17/508 (3%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 LL + N+ K FPGV AL V+L G V ALMGENGAGKSTLMKI++G Y D GE Sbjct: 32 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD-AGELR 90 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL--VARGDMVRA 130 + G+ V + P +A G+A+I+QEL+L P++S+AENI++GR Q GL + +M R Sbjct: 91 LRGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE-QLNGLHMIDHREMHRC 149 Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 A L RL + P V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++ E LF Sbjct: 150 TAKLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 209 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 ++I L+ +G I+YI+H+M E+ +AD V V RDG ++G + +L+ MMVGR+ Sbjct: 210 SIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 269 Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310 LS + +++LSVRD+ K SFDL AGE+LG+AGL+G+GRT +A + Sbjct: 270 LSQLFPVREKPI--GDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAI 327 Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370 FG GE+R+ G +V + P AI+ G A LTEDRKL GLF SV EN+ Sbjct: 328 FGITPSDGGEIRL-----DGEVVRI--SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 380 Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430 + V +G G + + A R + L ++ + + LSGGNQQK +L+R L Sbjct: 381 EMAVLPH-YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 439 Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490 PR+LILDEPTRG+D+GAK+EIYRLI+ LA G+A++MISSELPEV+G+ DRV+VM EG Sbjct: 440 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 499 Query: 491 TLAGEVRPAGSAAETQERIIALATGAAA 518 L G + + TQER++ LA+G +A Sbjct: 500 DLMGTL---DRSEATQERVMQLASGMSA 524 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: 637 Number of extensions: 30 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: 526 Length adjustment: 35 Effective length of query: 505 Effective length of database: 491 Effective search space: 247955 Effective search space used: 247955 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