Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 277 bits (708), Expect = 4e-79 Identities = 162/356 (45%), Positives = 219/356 (61%), Gaps = 12/356 (3%) Query: 14 GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPK 73 G +D L+L+I GEFLVL+G SGCGKST L +AGL DV++G I I +R+VT PK Sbjct: 16 GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75 Query: 74 DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSE 133 DR I MVFQ+YALYP MTV N+ F LK+A + AEI +V+ A++IL + L RKP Sbjct: 76 DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135 Query: 134 LSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHD 193 LSGGQRQRVA+GRA+VR+ VFL DEPLSNLDAKLR R +I L + L T +YVTHD Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195 Query: 194 QIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKDGRS 253 Q+EA+T+ DR+AV+K G++QQ+ P +Y+ P NLFVAGFIGSP+MN EV DG Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLV--EVPITDGG- 252 Query: 254 FVRAGGIAFDVTAYPAHTRLQPGQK-VVLGLRPEHVKVDEARDGEPTHQAV---VDIEEP 309 V+ G V+ G K V +G+RPEH+ + +G + + V++ E Sbjct: 253 -VKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEE 311 Query: 310 MGADNLLW----LTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAESENRL 361 +GAD ++ + + VR+ G+ G +R+ G +F + RL Sbjct: 312 LGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTSTGKRL 367 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: 392 Number of extensions: 17 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: 369 Length adjustment: 30 Effective length of query: 331 Effective length of database: 339 Effective search space: 112209 Effective search space used: 112209 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 Apr 09 2024. 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