Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847 Length = 367 Score = 305 bits (781), Expect = 1e-87 Identities = 167/364 (45%), Positives = 234/364 (64%), Gaps = 15/364 (4%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA++ + L K + G ++ +DL + D EFVV +GPSGCGKST+LR+IAGLE++SGGT Sbjct: 1 MANLKIKNLQKGFEGFS-IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + + G + ++ +R++AMVFQ YALYPHMSV N++F L AE++++V E A Sbjct: 60 IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAAR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L +LERKP+ +SGGQ+QR AI RAI++ P +FLFDEPLSNLDA LR Q+R ++ RL Sbjct: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ L+ T +YVTHDQ+EAMT+AD+V+++ G+I Q GSP +LY P NLF AGF+GTP M Sbjct: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 Query: 241 NFLSGTVQRQDGQ----LFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296 FL G V R +GQ L L+G + L AV L +RP+H+ +A Sbjct: 240 GFLKGKVTRVNGQSCEVLLDAGTRITLPLSG---ANLSVGGAVTLGIRPEHLELA----Q 292 Query: 297 AASLTCPVSVELVEILGADAL--LTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHV 354 T V+ ++ E LG+D + T G + LT V D + G TL+L LD H+ Sbjct: 293 PGDCTLQVTADVSERLGSDTFCHVLTSSG-EALTMRVRGDLASRYGETLSLHLDAEHCHL 351 Query: 355 FDVE 358 FD + Sbjct: 352 FDAD 355 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: 354 Number of extensions: 15 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: 406 Length of database: 367 Length adjustment: 30 Effective length of query: 376 Effective length of database: 337 Effective search space: 126712 Effective search space used: 126712 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