Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_3391 PP_3391 putative Tartrate MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Putida:PP_3391 Length = 438 Score = 265 bits (676), Expect = 3e-75 Identities = 145/403 (35%), Positives = 222/403 (55%), Gaps = 3/403 (0%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 ++MPL II ++ S+ DR NI+ AK + +LG+S AAYGL A +FF+ Y L E+PS+L + Sbjct: 29 RIMPLAIICFLFSYFDRINISFAKTQMQQELGLSDAAYGLAASMFFVGYVLFEVPSSLGL 88 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 + GA WI RIMV+WGL +AA+ F + + Y LR L+G+ EAG P ++ YL WF R Sbjct: 89 KRYGAPAWICRIMVSWGLATAALVFAYTQYTLYFLRFLIGVMEAGFGPAILFYLACWFPR 148 Query: 140 EQRARATGYFLLGVCFANIIGGP-VGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198 + A+ G + L V A +GGP G L MDG+LG GW W+F++ GLP V +V Sbjct: 149 KHLAKMNGLWFLAVPLAGAVGGPAAGFLLGTMDGVLGLAGWHWLFLMSGLPCVLLGLLVL 208 Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258 KL A WLS EE + + +AQ+ G + LT ++ + F+Y+ + Sbjct: 209 WKLDRDIEAAKWLSREEKDLLAENLAQDKRTAKPILGSIWRVLLTREVAIMAFIYYVVKT 268 Query: 259 TIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTGL 318 Y + F++P +I G + VG+L++LP+ A +G +L+ R + G +R LV L Sbjct: 269 ASYGLNFWMPHLIKSSGVQDMLWVGVLSALPYAVACIGMVLLTRHSDRTGERKRYLVYCL 328 Query: 319 LTMALGLGIASV--SGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376 L A+G +A + P + L+ F+ I + P S G+A+A G +N+ Sbjct: 329 LAAAVGYLLACLFSDSPFAMMTALVLATAGTFIAIPIFWTIPQSTFSGLAIATGTAAINS 388 Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALR 419 G L G V P ++G I T + G+ IA +++VA L +R Sbjct: 389 VGQLSGIVAPVMVGKINDLTDSTYMGMLSIAPLILVACLVVMR 431 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: 508 Number of extensions: 26 Number of successful extensions: 3 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: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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