Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate GFF1917 PGA1_c19490 ABC transporter, inner-membrane protein
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Phaeo:GFF1917 Length = 294 Score = 316 bits (810), Expect = 4e-91 Identities = 143/275 (52%), Positives = 206/275 (74%) Query: 20 AKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWLVSIQN 79 A++A P ++ ++IFVG W+V SFTNSKLLP FVG DQY RL+ RW+VS++N Sbjct: 12 ARLAITPFVVIVLLIFVGCVGWSVQLSFTNSKLLPNGDFVGLDQYYRLFRTTRWIVSLKN 71 Query: 80 LAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWLLNPQY 139 + +FG + +L++GF+LA L+DQKIR E FRTI LYP++LSF+VTGL WQW LNP Sbjct: 72 MLLFGVFFVSGALILGFLLAILLDQKIRAEAFFRTIFLYPYSLSFVVTGLAWQWFLNPSL 131 Query: 140 GIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDEDIWKAA 199 G+Q+ VR LGW+SF+FD L + ++ IY I+IAA+W G+GLVM LMLAGLRG+D +IW+A+ Sbjct: 132 GLQNAVRELGWSSFTFDWLTDQSMAIYTIVIAAIWHGSGLVMALMLAGLRGVDPEIWRAS 191 Query: 200 RVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPAKYV 259 ++DGIP W+ YV I+ P++ V ++V+++ +VK +D+VVA T+GGPGIA+EVPAK+V Sbjct: 192 KIDGIPTWRVYVHIVAPILGPVIFASVVLLSLSVVKGFDIVVAMTNGGPGIATEVPAKFV 251 Query: 260 YDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLE 294 D++ + N+G A +T+ML+TV + PW Y++ Sbjct: 252 LDHILERANVGLAMAGATIMLITVISALAPWLYVQ 286 Lambda K H 0.329 0.142 0.449 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: 330 Number of extensions: 11 Number of successful extensions: 1 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: 302 Length of database: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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