Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate CCNA_02439 CCNA_02439 transporter, major facilitator superfamily
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Caulo:CCNA_02439 Length = 430 Score = 290 bits (742), Expect = 6e-83 Identities = 153/413 (37%), Positives = 237/413 (57%), Gaps = 4/413 (0%) Query: 5 PSARTPQALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLF 64 PS+ +A + +LMPL + Y+++++DR N++ AK + LG+S AAYGLGA LF Sbjct: 4 PSSALERATVGRVTRRLMPLFCLMYLIAYIDRQNVSYAKLDMVSALGLSEAAYGLGASLF 63 Query: 65 FLTYALSEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAG 124 F+ Y L E P+NLI+ +VGAR W ARIM +WGL++ A+ F Q FYVLR LLG+AEAG Sbjct: 64 FIGYFLFEAPANLILARVGARVWFARIMFSWGLVTLALGFTQNAAMFYVLRFLLGVAEAG 123 Query: 125 LFPGVMLYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFM 184 FPGV+ LT W+ + RAR G F++ FAN +G +G L+ MDG LG GWQW+F+ Sbjct: 124 FFPGVLYVLTLWYPQAHRARMVGLFMIASAFANAVGAAIGGLLLGMDGFLGLAGWQWVFL 183 Query: 185 LEGLPAVAFA-WVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLT 243 + G PAV A +V+WR LP PS A WL E + +A E + + K Sbjct: 184 VTGAPAVLLAPYVLWR-LPSGPSDARWLPDVEKSWLASTLAAERGGEVDDHRGAWKAIFD 242 Query: 244 PQILLAIFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRF 303 P++L+ +Y ++ Y + ++LP+I+ +G +T++ G + +PW+ A+ +PR Sbjct: 243 PRVLMLAGLYIGMPLSAYGLSYWLPTIVKSFGVSNTVN-GFINVIPWLLVAVALWFVPRH 301 Query: 304 ATTPGRCRRLLVTGLLTMALGLGIASV-SGPVFSLLGFCLSAVMFFVVQSIIFLYPASRL 362 A G + +L A+ L ++ + G C++A F Q + + P S L Sbjct: 302 AARHGASAWHIAGPVLLAAVALSLSVILPGAALKFTMLCIAAPAIFAAQPVFWSLPPSFL 361 Query: 363 KGVALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAAL 415 G A G+ +NA G LGGF+ +++ V+ +TG+ + + +A VL+V +L Sbjct: 362 SGPRAAAGIATINAVGNLGGFIAQNLVPVVRDATGSELAPMLALAAVLLVTSL 414 Lambda K H 0.327 0.141 0.438 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: 579 Number of extensions: 31 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: 438 Length of database: 430 Length adjustment: 32 Effective length of query: 406 Effective length of database: 398 Effective search space: 161588 Effective search space used: 161588 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 (21.7 bits) S2: 51 (24.3 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