Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 212 bits (540), Expect = 1e-59 Identities = 131/357 (36%), Positives = 208/357 (58%), Gaps = 17/357 (4%) Query: 1 MATLELRNVNKTYG--PGLPD--TLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLET 56 MA ++L+++ +Y P PD ++ ++ G L+GPSGCGKST++N I+GL Sbjct: 1 MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60 Query: 57 ISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116 S G +L D ++ +SP+DR+IA VFQ +Y +M+V DN+AF LK K+P ++I V Sbjct: 61 PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120 Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRP-KIYLFDEPLSNLDAKLRVEMR 175 ++++L+IE L +K L+ ++Q+V+MGR L R LFDEPL+ +D +L+ ++R Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180 Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235 ++K +H++ T VYVTHDQ+EA T DK+AVM G I QFGTP +++ P + FV F Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240 Query: 236 IGSPPMNFIPLRLQRKD---GRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQII 292 IGSP MN I ++ + G + L+S Q +Q + +GIRPE + Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTVVSLESWQVDV-----LQRT--RSTNIKIGIRPEFVE 293 Query: 293 LANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQF 349 +++ ++ T AEV E G +V V L+ K+ R + + A ++G + L F Sbjct: 294 VSSVASD--DTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSF 348 Lambda K H 0.319 0.138 0.393 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: 319 Number of extensions: 17 Number of successful extensions: 2 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: 386 Length of database: 366 Length adjustment: 30 Effective length of query: 356 Effective length of database: 336 Effective search space: 119616 Effective search space used: 119616 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 (21.7 bits) S2: 50 (23.9 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