Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 211 bits (537), Expect = 2e-59 Identities = 125/328 (38%), Positives = 185/328 (56%), Gaps = 15/328 (4%) Query: 26 IDH----GEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPKDRGIGMVF 81 +DH G LLG SGCGKST+LN I+GL+ S+G + + V P+DR I VF Sbjct: 28 LDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQPSEGDVLFDGKRVNELSPRDRNIAQVF 87 Query: 82 QSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSELSGGQRQR 141 Q +Y MTV NL+F LK K+P ++I+ RV +E+L+I+ L +K L+ ++Q+ Sbjct: 88 QFPVIYDSMTVYDNLAFPLKNNKVPASKIKARVHEIAEVLEIEDKLYKKAKNLTADEKQK 147 Query: 142 VAIGRALVR-DVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTHDQIEALTL 200 V++GR LVR DV LFDEPL+ +D +L+ +LR ++K++H+ TM+YVTHDQ+EA T Sbjct: 148 VSMGRGLVREDVSAILFDEPLTVIDPQLKWKLRRKLKQIHEQFDITMVYVTHDQLEASTF 207 Query: 201 ADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEPKD---GRSFVRA 257 AD+IAVM G I Q P ++ P + FV FIGSP MN + P+ G + V Sbjct: 208 ADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFFIGSPGMNLIEVQRCPRGVCFGSTVVSL 267 Query: 258 GGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIEEPMGADNLLW 317 DV T ++ +G+RPE V+V + V+D+E+ +G ++ Sbjct: 268 ESWQVDVLQRTRSTNIK------IGIRPEFVEVSSVASDDTFEAEVLDVED-LGTYKIVT 320 Query: 318 LTFAGQSMSVRIAGQRRYPPGSTVRLSF 345 + + M VR + + GS V LSF Sbjct: 321 VQLDHEKMKVRQSEEFAASIGSKVHLSF 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: 336 Number of extensions: 13 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: 366 Length adjustment: 29 Effective length of query: 332 Effective length of database: 337 Effective search space: 111884 Effective search space used: 111884 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