Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 305 bits (781), Expect = 1e-87 Identities = 167/366 (45%), Positives = 237/366 (64%), Gaps = 8/366 (2%) Query: 1 MTSVSVRDLSLNFGA----VTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVS 56 M ++ ++ + +GA V V+ ++ +I GEF+V++G SGCGKSTLL +AGL ++S Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 DGQIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKR 116 GQI I DR V EPK+R I MVFQ+YALYP MTV +N+++GLK+ + +EI+ RV+R Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 117 ASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEI 176 A+ IL++ LL+R P +LSGGQRQRVA+GRA+VR VFLFDEPLSNLDAKLR ++R+EI Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 177 KRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGS 236 ++LH SL+ T +YVTHDQ+EA+TL R+ VM GV +Q+ P +Y P FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 237 PSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296 P MN +G++ DG SF + G A D+ P GQ+ +LG+RPEH+ DG Sbjct: 241 PPMNLLQGKLS-ADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLL--PILDG 297 Query: 297 EPTHQAV-VDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDA 355 ++ V++ E +GA+ L+ GQ++ +R + G + SF G FD Sbjct: 298 SAAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHWFDV 357 Query: 356 ESENRL 361 +S R+ Sbjct: 358 KSTRRI 363 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: 357 Number of extensions: 18 Number of successful extensions: 3 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: 364 Length adjustment: 29 Effective length of query: 332 Effective length of database: 335 Effective search space: 111220 Effective search space used: 111220 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