Align Inositol transport system permease protein (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 163 bits (413), Expect = 5e-45 Identities = 111/319 (34%), Positives = 164/319 (51%), Gaps = 26/319 (8%) Query: 30 LIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSV 89 LI + L +FG ++ + F + L L++ QV I+G++A + VI+T GIDLS G++ Sbjct: 45 LIVLVLSVIVFGLLLGSKFF--SPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAI 102 Query: 90 LALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPF 149 + LS+++ F LP + VA GL G + G ING ++A +PPF Sbjct: 103 MVLSSVVMGQ-----------FTFRYGLPPEVAVACGLICGTICGFINGWLVARMKLPPF 151 Query: 150 IATLGM---------MVSARGLARYYTEGQ--PVSMLSDSYTAIGHGAMP--VIIFLVVA 196 I TLGM + SA R T P+ L IG VI +++ Sbjct: 152 IVTLGMWQIVLASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVFTYGVIFMVILV 211 Query: 197 VIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAA 256 V+ LR+T +G++ YA+G + +AA SG+ V R LI VY ++GL+ AG R Sbjct: 212 VLLAYVLRHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIG 271 Query: 257 TGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQD 316 + G +++I A VIGG SL GG G I GT GALI+GV G +G DA Sbjct: 272 SVSPTSGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTY 331 Query: 317 IIKGLIIVVAVVIDQYRNK 335 ++ GL+I+ AV +DQ+ K Sbjct: 332 LLIGLLIIAAVAVDQWIRK 350 Lambda K H 0.325 0.140 0.394 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: 278 Number of extensions: 18 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: 340 Length of database: 353 Length adjustment: 29 Effective length of query: 311 Effective length of database: 324 Effective search space: 100764 Effective search space used: 100764 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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