Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 206 bits (523), Expect = 1e-57 Identities = 118/287 (41%), Positives = 172/287 (59%), Gaps = 5/287 (1%) Query: 9 LSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVT 68 +S FG T ++ ++L I GEF LLG+SGCGK+TLL +AG + G+I I ++VT Sbjct: 28 ISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVT 87 Query: 69 WEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLK 128 P +R + M+FQSYAL+P M+V N++FGLK + I+ +V A E++Q+ Sbjct: 88 EVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFSG 147 Query: 129 RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMI 188 RKP +LSGGQRQRVA+ R L ++ V L DEPL+ LD KLR ++E+ + + T + Sbjct: 148 RKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFV 207 Query: 189 YVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEP 248 VTHDQ EA+T++ RI VM +G I+Q+ P+ IY P FVA FIG + N F+G V Sbjct: 208 MVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIG--AANMFQGSVRG 265 Query: 249 KDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 +G + + D++ A + G V + +RPE V + ARD Sbjct: 266 GEGALAIACPELEHDLSVTEAGA-VAAGTPVTVMVRPEKVMI--ARD 309 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: 341 Number of extensions: 15 Number of successful extensions: 1 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: 379 Length adjustment: 30 Effective length of query: 331 Effective length of database: 349 Effective search space: 115519 Effective search space used: 115519 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