Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_085637119.1 MGEO_RS10860 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_002115805.1:WP_085637119.1 Length = 350 Score = 310 bits (794), Expect = 4e-89 Identities = 169/364 (46%), Positives = 236/364 (64%), Gaps = 19/364 (5%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M +VS++D+ +FGA V+ +N+DI GEF+V++G SGCGKSTLL +AGL V+ G++ Sbjct: 1 MATVSLKDIKKSFGATDVIHGINMDISDGEFIVIVGPSGCGKSTLLRMVAGLETVTSGEV 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I + +EP DR I MVFQ+YALYP M+V +N+ +GLK+A++P +I +V+ A+++ Sbjct: 61 LIGGQRANEKEPMDRDIAMVFQNYALYPHMSVRQNMGYGLKIARMPKDQINAKVEEAAKL 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQ+ PLL RKP +LSGGQRQRVA+GRA+VR+ VFLFDEPLSNLDAKLR ++R+EIK L Sbjct: 121 LQLTPLLDRKPRQLSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLEIKELQ 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 L T +YVTHDQ+EA+T+ADR+ VM GV +Q+ P+ +Y P LF A FIGSP+MN Sbjct: 181 SKLGITSLYVTHDQVEAMTMADRMIVMNGGVAEQIGTPLEVYETPRTLFAAQFIGSPAMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFD-VTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPT 299 F E +RAG + D V P+ P V LG+RPEH+ +E Sbjct: 241 VFDAE---------IRAGNVMIDGVAITPSAGADGP---VKLGIRPEHLVPEE----NGP 284 Query: 300 HQAVVDIEEPMGADNLLWLTF-AGQSMSVRIAGQRRY-PPGSTVRLSFDMGVASIFDAES 357 Q V I EP+GA+ LL G+ +++ + G G+ +R + G+ +FDA S Sbjct: 285 FQVKVMITEPLGANTLLHGRLPGGEDVTISLPGVHNVSATGADMRFAAQPGMTHVFDATS 344 Query: 358 ENRL 361 RL Sbjct: 345 GMRL 348 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: 377 Number of extensions: 14 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: 350 Length adjustment: 29 Effective length of query: 332 Effective length of database: 321 Effective search space: 106572 Effective search space used: 106572 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 24 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