Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate RR42_RS33945 RR42_RS33945 MFS transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__Cup4G11:RR42_RS33945 Length = 446 Score = 294 bits (752), Expect = 4e-84 Identities = 163/420 (38%), Positives = 246/420 (58%), Gaps = 16/420 (3%) Query: 23 RHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLFFLTYAVLEIPSNLF 82 R L+P L + Y++++IDR+ +G AK M+ +G+S ++GLGAGLFF+ Y + E+PSNL Sbjct: 34 RKLIPFLALIYVVAYIDRSVVGFAKLHMNAAVGISDASYGLGAGLFFIGYFLCEVPSNLA 93 Query: 83 LTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAGLYPGIIYYLTLWFG 142 L R GARRW ARI+ TWG+I+ MA + ++FYV+R LLGAAEAGLYPGI+Y+LT WF Sbjct: 94 LERFGARRWFARILFTWGVITMAMALINSASTFYVLRFLLGAAEAGLYPGILYFLTKWFP 153 Query: 143 REERAKATGLFLLGVCLANIIGAPLGGLLLSLDGMSGWHGWQWMFFIEGLPAIALAFVVW 202 RA+ GL +L +A I+ P+ G +LS G+ G WQ +F + GLPA+ L Sbjct: 154 MRHRARIIGLLVLAQPIALIVTGPIAGWVLSTSGLFGLTNWQTLFVLSGLPAVLLCLPTL 213 Query: 203 RRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKT------ALTTRVFLLLV 256 R LP+ P+ ARWL D A +E+E + T F+LK AL + LLL Sbjct: 214 RILPESPSQARWLAPAD----RAWIERELAADQST---FALKAHGNPLGALKDKRVLLLA 266 Query: 257 LIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILLPRFA-RTEQR 315 L++ S+YGLS +LP II +G +T GLL+A+P++ A G L+PR + R +R Sbjct: 267 LLFLPFPLSIYGLSLWLPTIIKQFG-VTDATTGLLSAVPYLFAVVGLYLVPRHSDRKGER 325 Query: 316 SRSMLMAGYLVMATGMAIGAIAGHGVALLGFSLAAFMFFAMQSIIFNWLPSIMSGHMLAG 375 +++ + T A + + L L AF +++Q++++ ++G A Sbjct: 326 YWHIIVVSAMGAITMAASAWVQTPALQFLFICLTAFSIYSIQAVVWALPGQFLTGASAAV 385 Query: 376 SFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVGALASLLIKSSSSSTPA 435 +N L GG+LGP+ +G +D TG SGL+F A+L+ L + +++ S+ TPA Sbjct: 386 GIATINSLANLGGYLGPYGIGLIKDATGKLASGLYFLAAMLVFAVLMTFVVR-SALETPA 444 Lambda K H 0.328 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: 551 Number of extensions: 27 Number of successful extensions: 2 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: 445 Length of database: 446 Length adjustment: 32 Effective length of query: 413 Effective length of database: 414 Effective search space: 170982 Effective search space used: 170982 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