Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 209 bits (532), Expect = 9e-59 Identities = 132/296 (44%), Positives = 173/296 (58%), Gaps = 8/296 (2%) Query: 2 TSVSVRDLSLNFGAVTV-LDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGL-LDVSDGQ 59 T++++R F T+ L L+LDI GE +VLLG SGCGK+T L IAGL + G Sbjct: 5 TTITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGV 64 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119 + D +VT + RG+GMVFQSYAL+P MTV +N+++GL+V +I A +RV Sbjct: 65 VMFGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLA 124 Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179 ++ + P +R+ +LSGGQRQRVA+ RA+ V L DEPL+ LDAKLR LR +I +L Sbjct: 125 MMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQL 184 Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 +SL T +YVTHDQ EA+ L DRI VM G I Q P IY AP N FVA FIG +M Sbjct: 185 LRSLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIG--TM 242 Query: 240 NFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 N +E R V G + TA A P + L RPE V + +A D Sbjct: 243 NRLPAVLEADAWR--VPGGLVPRHGTA--ASLAAAPSPRAELLFRPEDVALAQAED 294 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: 331 Number of extensions: 12 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: 357 Length adjustment: 29 Effective length of query: 332 Effective length of database: 328 Effective search space: 108896 Effective search space used: 108896 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