Align Inositol transport system permease protein (characterized)
to candidate GFF2275 PGA1_c23070 putative ribose transport system permease protein
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Phaeo:GFF2275 Length = 333 Score = 158 bits (400), Expect = 2e-43 Identities = 106/324 (32%), Positives = 168/324 (51%), Gaps = 20/324 (6%) Query: 26 IFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLS 85 I L LI + E F V D++F M++ ++L++ Q + IG++A+G+T V++ IDLS Sbjct: 19 IVLELIFFSVAGEFFS--VSDKAF-MDTDNMLLLLKQSAPIGIIAMGMTIVMVNGNIDLS 75 Query: 86 SGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTG 145 G++ A+ A+I + +F L + + + + L G++ GAING I+ TG Sbjct: 76 VGAIYAICAIILLD-----SMTWTMFAGLGNWVIPVAWCLALLTGVVLGAINGLIVWKTG 130 Query: 146 IPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVI-------IFLVVAVI 198 + FI TLG M+ RGL Y QP S L+ +T + + LVV V Sbjct: 131 VDAFIVTLGSMLGYRGLVFMYNGEQPTSHLN--WTLVDFAEAQFLGLHTATWFLLVVTVA 188 Query: 199 FHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATG 258 + T +G+ YAIG N +AA +GI V H++I + I G LA L+ VV + + + Sbjct: 189 IWFLMNRTVHGRNAYAIGNNREAAVNAGIRVGPHMMINFMIIGFLAALSAVVFYSESGSV 248 Query: 259 QAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDII 318 G YEL I A V+GGT L GG G I T G + + ++ G +G D +++ Sbjct: 249 NPNDGQLYELWVITAVVLGGTKLTGGAGSIVSTFGGVIAIQLLRKGLAHIGADTSTVNLV 308 Query: 319 KGLIIVVAVVIDQYRN---KRKLK 339 GLI++ + +D+ N K +LK Sbjct: 309 IGLILIAVLFLDRQLNVKGKEELK 332 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: 253 Number of extensions: 14 Number of successful extensions: 4 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: 333 Length adjustment: 28 Effective length of query: 312 Effective length of database: 305 Effective search space: 95160 Effective search space used: 95160 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