Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 321 bits (823), Expect = 2e-92 Identities = 184/378 (48%), Positives = 246/378 (65%), Gaps = 14/378 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + LAK Y V+ ++L I DGEFVV +GPSGCGKST+LRMIAGLE+IS G Sbjct: 1 MAAVSIRNLAKRYDDNE-VMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGD 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L IG +N++PA +R VAMVFQ+YALYPHMS+YDN+AFGL+ + AEID V+ A Sbjct: 60 LDIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAK 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L+++ LL+RKPRA+SGGQ+QR AI RAI + PSVFLFDEPLSNLDA LR ++R + +L Sbjct: 120 ILHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H L+TT +YVTHDQ+EAMTLAD+++++ +GRI Q GSP +LY +P N F AGFIG+P M Sbjct: 180 HDDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKM 239 Query: 241 NFLSGTV---QRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPA 297 NF+ GTV Q Q+ + +WA S L+ V L VRP+H+ IA + + A Sbjct: 240 NFIDGTVAAIQADGVQVQLPGGGLQWAAVDG--STLQVGQKVTLGVRPEHLNIA-QGQAA 296 Query: 298 ASLTCPVSVELVEILGADALLTTRC-GDQTLTALVPADRLPQP-GATLTLALDQHELHVF 355 C +E+LG + L G + L D L P G+ L LA D H+F Sbjct: 297 LQARCTA----LELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLF 352 Query: 356 DVESGENLSLPDAALTAP 373 + G+ L +++ AP Sbjct: 353 GAD-GQALPRLASSVAAP 369 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: 416 Number of extensions: 16 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: 372 Length adjustment: 30 Effective length of query: 376 Effective length of database: 342 Effective search space: 128592 Effective search space used: 128592 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