Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_3940 PP_3940 Putative metabolite transport protein NicT
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Putida:PP_3940 Length = 437 Score = 265 bits (678), Expect = 2e-75 Identities = 148/419 (35%), Positives = 232/419 (55%), Gaps = 15/419 (3%) Query: 11 QALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYAL 70 +AL + +L+P L Y+ ++LDR N+ AK + DL S AAYGLGAGLFF+ Y + Sbjct: 18 KALYSKITWRLIPFLCFCYLAAYLDRINVGFAKLQMLEDLQFSTAAYGLGAGLFFVGYII 77 Query: 71 SEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVM 130 E+PSNLI+ +VGA+ WIARIM+TWGL+SA FV T FY+LR LLG AEAG PGV+ Sbjct: 78 FEVPSNLILQRVGAKLWIARIMITWGLLSACTMFVTSTTQFYILRFLLGAAEAGFLPGVL 137 Query: 131 LYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALM-RMDGMLGWHGWQWMFMLEGLP 189 YLT W+ +R R F++G+ +++IGGP+ +M D + G HGWQW+F+LE +P Sbjct: 138 YYLTMWYPTYRRGRIIALFMIGLPLSSVIGGPISGWIMGHFDQVQGLHGWQWLFLLEAIP 197 Query: 190 AVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAG------EGGHSLKNWLT 243 +V + + LP+ +A WLSA++ + +A + EG +G +LK W+ Sbjct: 198 SVLLGILTFWALPNHFQQAKWLSADDKAQLAADLAADDAEGKDSKHSFRDGFFNLKVWML 257 Query: 244 PQILLAIFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRF 303 I +I ++ Y + F++P+ I G T +GLLT++P +AA G L+I Sbjct: 258 GGIDFSIL------LSAYAMGFWMPTFIRDAGVSDTFHIGLLTAIPSLAALAGMLMIGAS 311 Query: 304 ATTPGRCRRLLVTGLLTMALGLGIASV--SGPVFSLLGFCLSAVMFFVVQSIIFLYPASR 361 + R ++ + A+ + +++ V +++ F +++ + F PA+ Sbjct: 312 SDRHRERRWHIIVPFIIGAIAMASSTLFSQNLVMTVVLFAIASAAIIGAVPVFFSLPATF 371 Query: 362 LKGVALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420 LKG A A G + + G V S+MGV+ TG + L V A L+++ + L Sbjct: 372 LKGTAAATGFALACSVANIAGLVSNSLMGVVTDLTGTSHAALWVFAGCLILSCFLVIAL 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: 536 Number of extensions: 23 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: 437 Length adjustment: 32 Effective length of query: 406 Effective length of database: 405 Effective search space: 164430 Effective search space used: 164430 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