Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 170 bits (430), Expect = 6e-47 Identities = 104/280 (37%), Positives = 157/280 (56%), Gaps = 14/280 (5%) Query: 15 AVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEE--- 71 ++ +D+++ +++ GE L L+G SGCGK+TLL IAG + G I + V + Sbjct: 20 SLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSL 79 Query: 72 -PKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRK 130 P+ R +GMVFQ YAL+P +TV N+ FGL+ K A ++A ++ ++ L +R Sbjct: 80 PPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAV----ARQALALVGLEGLERRY 135 Query: 131 PSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYV 190 P ELSGGQ+QRVA+ RAL + L DEPLSNLD ++R LR E++ + + + T I V Sbjct: 136 PHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILV 195 Query: 191 THDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKD 250 THDQ EAL++ DR+AVM+ G +Q+ P ++ P + FVA F+ NF E + Sbjct: 196 THDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS--QANFLATEYQGDA 253 Query: 251 GRS----FVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPE 286 R+ F GG+ T + + V+L PE Sbjct: 254 WRTVLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPE 293 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: 317 Number of extensions: 20 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: 368 Length adjustment: 29 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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