Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_4758 PP_4758 Major facilitator family transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Putida:PP_4758 Length = 455 Score = 338 bits (867), Expect = 2e-97 Identities = 179/405 (44%), Positives = 249/405 (61%), Gaps = 6/405 (1%) Query: 21 LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80 ++PL +I +I+++LDR NI + HL+ DLGISAAAYG GAGLFF+ YAL E+PSN+++ Sbjct: 32 VLPLFVIMFIVNYLDRVNIGFVRPHLESDLGISAAAYGFGAGLFFIGYALFEVPSNMLLQ 91 Query: 81 KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140 KVGAR W+ RIM TWGL++ AMAFVQ ET FYVLR LLG+AEAG FPGV+ Y T W Sbjct: 92 KVGARLWLTRIMFTWGLVATAMAFVQNETQFYVLRFLLGVAEAGFFPGVIYYFTRWLPAA 151 Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200 +R +A FL G A++I GP+ ALM++ G LG HGWQWM +EG+ +VA + V+ Sbjct: 152 ERGKAIAIFLSGSALASLISGPLAGALMQIQG-LGLHGWQWMLFIEGMASVALCFFVFFW 210 Query: 201 LPDRPSKAPWLSAEEARGIEQRI--AQETEEGAGEGGHSLKNWLTP-QILLAIFVYFCHQ 257 L +P A WLS E + I Q+ E G S N L QI+L +YFC Q Sbjct: 211 LDSKPQDAKWLSKAEQDALVATIDREQQAREAIGAVRPSAWNLLKDRQIVLFCLIYFCIQ 270 Query: 258 ITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317 +TIY F+LPSII + G+LS M VG S+PW+ + L A+ + + ++ V G Sbjct: 271 LTIYAATFWLPSIIKRMGDLSDMQVGFFNSIPWLISIL-AMYAFAAGSARWKFQQAWVAG 329 Query: 318 -LLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376 LL A G+ +++ GPVF+ + C +A+ F S+ + P L A + +N+ Sbjct: 330 ALLVAATGMFMSTTGGPVFAFVAVCFAAIGFKSASSLFWPIPQGYLDARIAAAVIALINS 389 Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLR 421 G LGGFV P+ G++EQ TG+ GL +A+ V+AA+A +R Sbjct: 390 VGNLGGFVAPTTFGLLEQQTGSIQGGLYGLAVTSVLAAIAIFFVR 434 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: 577 Number of extensions: 27 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: 455 Length adjustment: 33 Effective length of query: 405 Effective length of database: 422 Effective search space: 170910 Effective search space used: 170910 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