Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 284 bits (726), Expect = 3e-81 Identities = 165/363 (45%), Positives = 224/363 (61%), Gaps = 12/363 (3%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M V++R + +FG + V+ ++L++ GEF+ +G SGCGKSTLL IAGL + S G + Sbjct: 1 MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I + V P RGI MVFQSYALYP MT N++FGL +++ I +RV+ A+ + Sbjct: 61 SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQI+ LL RKP +LSGGQRQRVAIGRA+VR+ VFLFDEPLSNLDA LR ++R+EI +L Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 L+ TMIYVTHDQ+EA+TLADRI V+ +G ++Q P+ +Y+ P N FVAGFIGSP+MN Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240 Query: 241 FFRGEVEP-KDGRSFV-RAGGIAFDVT---AYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 F E DG V GG+ D+ A PA G + LG+RPEHV + A Sbjct: 241 FLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPA-----AGTPLTLGVRPEHVGL--ADG 293 Query: 296 GEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDA 355 G ++ +E G + GQ + VR+ G R G +RL+ A +F Sbjct: 294 GAGLLATILAVERLGGETHCHAALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLFGP 353 Query: 356 ESE 358 + + Sbjct: 354 DGQ 356 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: 419 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: 358 Length adjustment: 29 Effective length of query: 332 Effective length of database: 329 Effective search space: 109228 Effective search space used: 109228 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