Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 394 bits (1012), Expect = e-114 Identities = 228/504 (45%), Positives = 318/504 (63%), Gaps = 15/504 (2%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD-AGELR 85 LL + N+ K FPGV AL V+L G V ALMGENGAGKSTLMKI++G Y D GE Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 86 LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCT 145 + G+ V D P +A G+A+I+QEL+L P++S+AENI++GR L ++ +M R Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLVARGDMVRAC 128 Query: 146 AQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205 A L RL + P V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++ E LF+ Sbjct: 129 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 188 Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265 +I L+ +G I+YI+H+M E+ +AD V V RDG ++G + +L+ MMVGR+L Sbjct: 189 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 248 Query: 266 SQLFPVREKPI--GDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 323 S + ++++SVRD+ KG SFDL AGE+LG+AGL+G+GRT +A +F Sbjct: 249 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 308 Query: 324 GITPSDGGEICL-----DGQPVRI--SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENME 376 G GE+ + G V + P AI+ G A LTEDRKL GLF SV EN+ Sbjct: 309 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 368 Query: 377 MAVLPHYA-GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMT 435 + V A G G + + A R + L ++ + + LSGGNQQK +L+R L Sbjct: 369 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 428 Query: 436 NPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGD 495 PR+LILDEPTRG+D+GAK+EIYRLI+ LA G+A++MISSELPEV+G+ DRV+VM EG Sbjct: 429 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 488 Query: 496 LMGTL---DRSEATQERVMQLASG 516 L G + + TQER++ LA+G Sbjct: 489 LAGEVRPAGSAAETQERIIALATG 512 Lambda K H 0.321 0.137 0.391 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: 681 Number of extensions: 31 Number of successful extensions: 11 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: 521 Length of database: 537 Length adjustment: 35 Effective length of query: 486 Effective length of database: 502 Effective search space: 243972 Effective search space used: 243972 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