Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate N515DRAFT_4327 N515DRAFT_4327 phospholipid/cholesterol/gamma-HCH transport system ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Dyella79:N515DRAFT_4327 Length = 270 Score = 108 bits (271), Expect = 1e-28 Identities = 81/243 (33%), Positives = 120/243 (49%), Gaps = 12/243 (4%) Query: 4 VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63 + VRDL FG V + L+LD+ GE L ++G SG GKS LL I GL + GQ+ + Sbjct: 15 IQVRDLVNRFGTQAVHEHLDLDVRRGEILGVVGGSGTGKSVLLRTIVGLRRPTSGQVQVF 74 Query: 64 DRNVTWEEPKDRG-----IGMVFQSYALYPQMTVEKNLSFGL---KVAKIPPAEIEKRVK 115 +++ P+ R G++FQ+ AL+ V +N++ L K P AE VK Sbjct: 75 GQDLLRLPPEQRSRIERRFGVLFQNGALFSSQNVVENIAMPLIEHAGLKRPEAEALGTVK 134 Query: 116 RASEILQIQPLLKRK-PSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRV 174 A + + P + K PSELSGG +R A+ RAL D +V DEP + LD + Sbjct: 135 LA--LAGLPPGTEHKYPSELSGGMVKRAALARALALDPEVLFLDEPTAGLDPISAAAFDQ 192 Query: 175 EIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI 234 I L +L T+ VTHD T+ DR+AV+ + D + + E+ +V + Sbjct: 193 LILTLRDALGLTVFLVTHDLDTLYTICDRVAVLSQKKV-LACDRLDVVAQNEDPWVQSYF 251 Query: 235 GSP 237 P Sbjct: 252 HGP 254 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: 259 Number of extensions: 10 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: 270 Length adjustment: 27 Effective length of query: 334 Effective length of database: 243 Effective search space: 81162 Effective search space used: 81162 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: 48 (23.1 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