Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 246 bits (629), Expect = 5e-70 Identities = 145/334 (43%), Positives = 203/334 (60%), Gaps = 14/334 (4%) Query: 1 MTSVSVR--DLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58 M SV VR + L++G+ VL ++LDI GEF LG SGCGK+TLL IAG G Sbjct: 14 MESVGVRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRG 73 Query: 59 QIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRAS 118 + I R+++ R +GMVFQSYAL+P MTV +N++FGL+ ++P AEIE+RV A Sbjct: 74 AVTIGGRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAAL 133 Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178 +++ ++ L R+PS+LSGGQ+QRVA+ R +V + V L DEPLSNLDAKLR ++R E+ Sbjct: 134 DLVGLKHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLS 193 Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238 L + L T I+VTHDQ EA T+ DRIAVM+ G++QQ+ P +Y+ P NLFVAGF+G + Sbjct: 194 LQRKLGLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLG--T 251 Query: 239 MNFFRGEVEPKD-GRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDE----A 293 N G+V D G +FV GG+ P ++PG L RP+++ + + Sbjct: 252 ANVLEGQVRAVDGGTAFVMGGGVPI-----PLPHGVEPGAAGKLMFRPQNLFIRQDGGPP 306 Query: 294 RDGEPTHQAVVDIEEPMGADNLLWLTFAGQSMSV 327 R G VV E +GA + GQ + V Sbjct: 307 RAGHVRLMGVVRHREFLGASIRYAVDIGGQQVQV 340 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: 390 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 331 Effective length of database: 341 Effective search space: 112871 Effective search space used: 112871 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