Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 299 bits (765), Expect = 1e-85 Identities = 166/361 (45%), Positives = 223/361 (61%), Gaps = 9/361 (2%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA++ + L K + G ++ +DL + D EFVV +GPSGCGKST+LR+IAGLE++S GT Sbjct: 1 MANLKIKNLQKGFEGFS-IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + + G + ++ +R++AMVFQ YALYPHMSV N++F L ++ +V E A Sbjct: 60 IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAAR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L LLERKP+ +SGGQ+QR AI RAI++ P +FLFDEPLSNLDA LR Q+R ++ RL Sbjct: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ L+ T +YVTHDQ+EAMTLAD+V+++ GRI Q GSP ELY P NLF AGF+GTP M Sbjct: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFS--RLRHAMAVKLAVRPDHVRIAGEREPAA 298 FL G V R + Q E L S L AV L +RP+H+ IA + Sbjct: 240 GFLKGKVTRVESQ-SCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTL 298 Query: 299 SLTCPVSVELVEILGADALL-TTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDV 357 ++T V E LG+D + LT + D Q G TL L LD H+FD Sbjct: 299 TVTADVG----ERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDT 354 Query: 358 E 358 + Sbjct: 355 D 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: 349 Number of extensions: 15 Number of successful extensions: 3 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