Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate SMc04393 SMc04393 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Smeli:SMc04393 Length = 370 Score = 327 bits (838), Expect = 3e-94 Identities = 174/369 (47%), Positives = 241/369 (65%), Gaps = 8/369 (2%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M+ + + +L ++GA+ +L +NL+I+ G FLVL+G SGCGKSTLLN IAGL ++ G I Sbjct: 1 MSFLKITNLRKSYGALEILKDINLEIEEGGFLVLVGPSGCGKSTLLNTIAGLEPITSGDI 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I R+V+ P R I MVFQSYALYP MTV N++FG+++ +P E EK +K+ +++ Sbjct: 61 AINGRSVSGLHPSKRDIAMVFQSYALYPNMTVAGNIAFGMEIRGVPKEEREKAIKQVADM 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQI LL RKPS+LSGGQRQRVA+GRALVR+ VFLFDEPLSNLDAKLR ++R EIKRLH Sbjct: 121 LQIGHLLDRKPSQLSGGQRQRVAMGRALVRNPQVFLFDEPLSNLDAKLRVDMRTEIKRLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 +K T++YVTHDQIEA+TLA +IAV+K GV+QQ P IYN P N+FVA F+GSP+MN Sbjct: 181 HRMKTTIVYVTHDQIEAMTLATKIAVLKDGVLQQFGTPAEIYNNPANMFVADFMGSPAMN 240 Query: 241 FFRGEVEPKDGRSFVRAGGIAFDV--TAYPAHTRLQ--PGQKVVLGLRPEHVKVDEARDG 296 + ++E + V + A P + L G++VV G+RPE + + D Sbjct: 241 LLKAQIETAGSQVSVTLARPNAEPLRLAVPHNGALSAYAGKEVVFGIRPEALTDPDGADR 300 Query: 297 EPTH----QAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASI 352 + ++++ EP G+D G+ + R+ R PG T RL+F++ A Sbjct: 301 NAQFVAEGECLIEVVEPAGSDTFAVTRLGGKEIVARLRADARIAPGQTSRLAFNLDKAVF 360 Query: 353 FDAESENRL 361 FD +SE R+ Sbjct: 361 FDPQSEKRI 369 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: 397 Number of extensions: 10 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: 370 Length adjustment: 30 Effective length of query: 331 Effective length of database: 340 Effective search space: 112540 Effective search space used: 112540 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