Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 237 bits (605), Expect = 3e-67 Identities = 131/283 (46%), Positives = 184/283 (65%), Gaps = 3/283 (1%) Query: 13 FGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEP 72 F V+ +L+L I++GEFL LLG SGCGK+T+L IAGL V G+I + + ++T Sbjct: 27 FDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPA 86 Query: 73 KDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPS 132 ++R + VFQSYAL+P MTV +N++FGL++ K P AEI RV A ++Q++ +RKP Sbjct: 87 ENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPH 146 Query: 133 ELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTH 192 +LSGGQ+QRVAI RA+V + L DE LS LD KLR +++ E+K L + L T ++VTH Sbjct: 147 QLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTH 206 Query: 193 DQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGR 252 DQ EALT++DRI VM+ G I+Q P IY P+NLFVAGFIG +N F V + Sbjct: 207 DQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIG--EINMFNATVIERLDE 264 Query: 253 SFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 VRA + Y + ++PGQK+ + LRPE ++V+E D Sbjct: 265 QRVRANVEGRECNIY-VNFAVEPGQKLHVLLRPEDLRVEEIND 306 Lambda K H 0.320 0.137 0.392 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: 344 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: 361 Length of database: 378 Length adjustment: 30 Effective length of query: 331 Effective length of database: 348 Effective search space: 115188 Effective search space used: 115188 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: 49 (23.5 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