Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Koxy:BWI76_RS23390 Length = 375 Score = 311 bits (796), Expect = 3e-89 Identities = 174/377 (46%), Positives = 236/377 (62%), Gaps = 14/377 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA++ L K Y+ G +H +DL I DGEF+V++GPSGC KST LRM+AGLE ISGG Sbjct: 1 MAEVIFNKLEKVYSNGFKAVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGGE 60 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 +RIG +VN+L + R +AMVFQNYALYPHM+V +N+AFGL+ K P +I+ +V E A Sbjct: 61 VRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAAK 120 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L LE LL+R PR +SGGQ QR A+ RAI+K P VFLFDEPLSNLDAKLRA +R I L Sbjct: 121 ILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISDL 180 Query: 181 HQRLR-----TTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235 H++L+ TTVYVTHDQ EAMT+ DR+ +M+ G I+Q +P LY P+N+F AGFI Sbjct: 181 HKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHKPKNMFVAGFI 240 Query: 236 GTPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRL--RHAMAVKLAVRPDHVRIAGE 293 G P MN + Q G+L + L S++ V VRP+ V I+ Sbjct: 241 GAPEMNIRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQQVFFGVRPEFVSISD- 299 Query: 294 REPAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADR---LPQPG--ATLTLALD 348 EP A +C + VE +G + + + D LTA VP+D + + G + D Sbjct: 300 -EPFAEGSCTGEMVRVENMGHEFFVYLKVADYELTARVPSDEAKPMIEKGLHRKVHFKFD 358 Query: 349 QHELHVFDVESGENLSL 365 ++ H+FD ++ +N+SL Sbjct: 359 LNKCHIFDAKTEQNISL 375 Lambda K H 0.321 0.137 0.403 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: 363 Number of extensions: 10 Number of successful extensions: 4 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: 406 Length of database: 375 Length adjustment: 31 Effective length of query: 375 Effective length of database: 344 Effective search space: 129000 Effective search space used: 129000 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: 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