Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 199 bits (507), Expect = 7e-56 Identities = 123/342 (35%), Positives = 186/342 (54%), Gaps = 22/342 (6%) Query: 3 SVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFI 62 S+ +R+++ FG LD ++L I GE + LLG SGCGK+TLL IAG+ +GQ+ Sbjct: 2 SIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMF 61 Query: 63 KDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVA--KIPP--AEIEKRVKRAS 118 + T ++R +G VFQ YAL+ M V +N++FGL+V K P +EI KRV Sbjct: 62 EGSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLL 121 Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178 ++Q+ L R P++LSGGQRQR+A+ RAL + V L DEP LD K+R ELR ++R Sbjct: 122 SLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRR 181 Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238 LH + + ++VTHDQ EAL +ADR+ VM G I+Q+ P +Y+ P + FV F+G + Sbjct: 182 LHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLG--N 239 Query: 239 MNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEP 298 +N F V A A + GQ+ V +RP + +D E Sbjct: 240 VNVFHSRVH---------------GAWAEVARDDVPAGQEAVAFIRPHDIDIDTVATPE- 283 Query: 299 THQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGST 340 + +A V + +G + + G+ + V + +R+ G T Sbjct: 284 SLEAKVSYVQTIGPLVRVEVIHQGELVEVELTRERQQVLGLT 325 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: 312 Number of extensions: 12 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: 360 Length adjustment: 29 Effective length of query: 332 Effective length of database: 331 Effective search space: 109892 Effective search space used: 109892 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 Apr 09 2024. 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