Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate RR42_RS10975 RR42_RS10975 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Cup4G11:RR42_RS10975 Length = 443 Score = 281 bits (719), Expect = 3e-80 Identities = 148/403 (36%), Positives = 234/403 (58%), Gaps = 5/403 (1%) Query: 17 MFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSN 76 +F ++MP L++ Y++++LDR N+ AK + DL S +GLGAGLFF+ Y L E+PSN Sbjct: 28 VFWRIMPFLMLCYVIAYLDRVNVGFAKLQMAQDLAFSETVFGLGAGLFFIGYFLFEVPSN 87 Query: 77 LIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYW 136 L+MHK+GAR WIARIM+TWG+ISA FV+ T+FY++R LLG+AEAG +PGV+LYLTYW Sbjct: 88 LLMHKLGARVWIARIMITWGIISALFVFVKTPTTFYIMRFLLGLAEAGFYPGVILYLTYW 147 Query: 137 FNREQRARATGYFLLGVCFANIIGGPVGAALM-RMDGMLGWHGWQWMFMLEGLPAVAFAW 195 + +RA+ F+ G+ A ++G P+ +M G GWQWMF++E LPA+ Sbjct: 148 YPANRRAKMIALFMSGIPVAGMLGNPLSGWIMDAFHDYGGMRGWQWMFLIEALPALLIGI 207 Query: 196 VVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEE-GAGEGGHSL-KNWLTPQILLAIFVY 253 V L + +APWL A E R +++ I ++ + GA GHSL + ++ +Y Sbjct: 208 VTVFVLKNGIDQAPWLDANEKRVLKRNIEEDARQAGASGTGHSLGAVFKDSRVWWMCMIY 267 Query: 254 FCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRL 313 FC Y + F++P+++ G +++GLL+++P+I A + + A R Sbjct: 268 FCFVTGQYALTFWMPTLVKTSGVTGNLNIGLLSAIPFICAIVVMNFLGHSADARRERRWH 327 Query: 314 LVTGLLTMALGLGIAS--VSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGL 371 L+ L A+G IA+ V ++ L+A + + P + L G+A A G+ Sbjct: 328 LIVPALMGAVGFAIAASFTHNTVVAIAALSLAAAGVLTCAPLFWSLPTAFLSGLAAASGI 387 Query: 372 GFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAA 414 VN+ G L GFV P ++G + T + + + V++ +LV+ A Sbjct: 388 AVVNSVGNLAGFVAPYMVGYLTDLTHSTQSSMYVLSGMLVLGA 430 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: 605 Number of extensions: 33 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: 443 Length adjustment: 32 Effective length of query: 406 Effective length of database: 411 Effective search space: 166866 Effective search space used: 166866 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