Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_2830 PP_2830 Major facilitator family transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Putida:PP_2830 Length = 450 Score = 578 bits (1491), Expect = e-170 Identities = 285/421 (67%), Positives = 341/421 (80%), Gaps = 1/421 (0%) Query: 5 PSARTPQALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLF 64 P+ Q LN L+ KLMPLLI+ Y++SFLDRTNIALAK + +DLG+SAAAYGLGAGLF Sbjct: 29 PATTHEQRLNGLLLRKLMPLLIVVYVMSFLDRTNIALAKASMGIDLGLSAAAYGLGAGLF 88 Query: 65 FLTYALSEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAG 124 FLTYAL+E+PSNLIMH+VGARFWI RIM+TWGL+SA MAFVQGETSFY++RLLLG+AEAG Sbjct: 89 FLTYALAEVPSNLIMHRVGARFWITRIMITWGLLSAGMAFVQGETSFYIMRLLLGVAEAG 148 Query: 125 LFPGVMLYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFM 184 LFPGVMLYLTYWF+REQRARATGYFLLGVC ANI+ GP+G AL+ +DG+LGWHGWQW+F+ Sbjct: 149 LFPGVMLYLTYWFDREQRARATGYFLLGVCVANILSGPLGGALLELDGVLGWHGWQWLFV 208 Query: 185 LEGLPAVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTP 244 LEGLPAVA A+VVW+KLPD P+ APWL+A +A+ IE+R+A E + A + + + Sbjct: 209 LEGLPAVALAYVVWKKLPDGPASAPWLTAADAQDIERRLAAE-QAAAPQQSKLGQMFRDR 267 Query: 245 QILLAIFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA 304 QI LAI VYF HQITIYTVIFFLP II Y LS VGLLT++PWIAAA+GA +PR A Sbjct: 268 QIWLAIAVYFVHQITIYTVIFFLPGIIGTYAALSPFQVGLLTAVPWIAAAIGAATLPRLA 327 Query: 305 TTPGRCRRLLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKG 364 T+P RCR LL GLLTMA GL +AS++ L+GF L+A+M FVVQSIIF++P+SRL G Sbjct: 328 TSPRRCRTLLFLGLLTMAAGLLLASLTNSFIGLIGFSLTALMLFVVQSIIFVFPSSRLSG 387 Query: 365 VALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGH 424 ALA GL FV CGL GGFVGPSVMG+IEQ+TG+ NGL +IA +LV AAL + RLR G Sbjct: 388 SALAAGLAFVTTCGLFGGFVGPSVMGLIEQTTGSTRNGLWIIAALLVCAALVSTRLRQGQ 447 Query: 425 E 425 E Sbjct: 448 E 448 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: 668 Number of extensions: 29 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: 438 Length of database: 450 Length adjustment: 32 Effective length of query: 406 Effective length of database: 418 Effective search space: 169708 Effective search space used: 169708 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