Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 305 bits (782), Expect = 9e-88 Identities = 168/362 (46%), Positives = 233/362 (64%), Gaps = 14/362 (3%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+ +++R +G V+ ++L I GEF V +G SGCGKSTLL IAGL + S+G I Sbjct: 1 MSGITLRGAVKRYGETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I R+VT +P +RG+ MVFQ+YALYP MTV +N+ FGLK+ +P AEI+ +V ASEI Sbjct: 61 HIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 L++ L RKP LSGGQRQRVAIGRA+VR +VFLFDEPLSNLDA+LR E+RVEI RLH Sbjct: 121 LKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 + + TMIYVTHDQ+EA+TLAD+I V+++G ++Q+ P+ +Y P+N+FVAGFIGSP+MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTH 300 F G +E V G+ P V +G+RP+H+ ++ DG Sbjct: 241 FLDGRIE----NDAVHLAGL----PPLPVPGAAGRSGPVTVGVRPQHIALEPGGDG---- 288 Query: 301 QAVVDIEEPMGADNLLWLTFA-GQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESEN 359 +V++ E +G + L+L A G ++V + G+ V LS +F+AE+ Sbjct: 289 -YLVELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFEAETGQ 347 Query: 360 RL 361 RL Sbjct: 348 RL 349 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: 369 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: 351 Length adjustment: 29 Effective length of query: 332 Effective length of database: 322 Effective search space: 106904 Effective search space used: 106904 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