Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 343 bits (880), Expect = 4e-99 Identities = 189/372 (50%), Positives = 245/372 (65%), Gaps = 11/372 (2%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M ++ + ++ +FG+ VL ++L ID GEFL+L+G SGCGKSTL+N IAGL V+ G+I Sbjct: 1 MAALEINNVCKDFGSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGEI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I +VTW+ P +R I MVFQSYALYP MTV +N+SFGL++ K+P AE E V+R +++ Sbjct: 61 RIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVADL 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQI LL+RKPS+LSGGQRQRVA+GRAL R+ V+LFDEPLSNLDAKLR ++R EIK+LH Sbjct: 121 LQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 Q L T++YVTHDQIEA+TLAD IAVM+ G I QL P +YN P +LFVAGF+GSPSMN Sbjct: 181 QRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYP-AHTRLQP------GQKVVLGLRPEHVKVDEA 293 F + G +R + P R P G++V+LGLRPEH D+A Sbjct: 241 FISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTEDDA 300 Query: 294 RDGEPTHQAV----VDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGV 349 R GE + + EP GAD LL L + R+ + R G + L DMG Sbjct: 301 RLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEATARVGPKCRVKAGERLTLRIDMGR 360 Query: 350 ASIFDAESENRL 361 A +FD E+E RL Sbjct: 361 AVMFDRETEKRL 372 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: 395 Number of extensions: 16 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: 373 Length adjustment: 30 Effective length of query: 331 Effective length of database: 343 Effective search space: 113533 Effective search space used: 113533 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