Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 339 bits (870), Expect = 7e-98 Identities = 179/365 (49%), Positives = 245/365 (67%), Gaps = 7/365 (1%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + +A+ K + G ++ +D+ I DGEF VL+GPSGCGKST+LRM+AGLE+I+GG Sbjct: 1 MASVQIRAVKKQF-GSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGE 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + IGGTVVN++ ++R++AMVFQNYALYPHM+V DN+AF L K+ A +D RV++ A Sbjct: 60 ILIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAAD 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L LL+R PR +SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR Q+R +IK L Sbjct: 120 ILGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKEL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 HQRL+TT++YVTHDQ+EAMT+AD++++M+DG + Q G P +LY YP NLF AGFIG+PAM Sbjct: 180 HQRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAM 239 Query: 241 NFLSGTVQRQDGQLFIETAH-QRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAAS 299 NF+ T++R +E A R + V VRP+H+ I AA Sbjct: 240 NFIPATLRRNATGAEVEFADGTRVPAPYGAALQGNDGQKVTYGVRPEHLSIG-----AAG 294 Query: 300 LTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVES 359 V +VE GAD + +R GD +LT++ G + L D H+FD ES Sbjct: 295 QGIATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFDAES 354 Query: 360 GENLS 364 G++L+ Sbjct: 355 GKSLA 359 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: 397 Number of extensions: 11 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: 361 Length adjustment: 30 Effective length of query: 376 Effective length of database: 331 Effective search space: 124456 Effective search space used: 124456 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