Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate GFF3691 PS417_18890 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__WCS417:GFF3691 Length = 453 Score = 327 bits (837), Expect = 6e-94 Identities = 167/403 (41%), Positives = 247/403 (61%), Gaps = 14/403 (3%) Query: 21 LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80 ++PL +I +IL+++DR NI + H++ DLGI AAAYG GAGLFF+ YAL E+PSN+++ Sbjct: 28 VLPLFVIMFILNYIDRVNIGFVRTHMEHDLGIGAAAYGFGAGLFFIGYALFEVPSNMLLQ 87 Query: 81 KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140 KVGAR W+ RIM TWG+++ MAF+Q ET FY+LR LLG+AEAG FPGV+ Y T W Sbjct: 88 KVGARLWLTRIMFTWGIVATLMAFIQNETHFYILRFLLGVAEAGFFPGVIYYFTRWLPGA 147 Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200 +R +A FL G A++I GP+ AL++++G G+HGWQWMF +EGL +VA + VW Sbjct: 148 ERGKAIAIFLSGSAVASLISGPLSGALLQIEG-FGFHGWQWMFAIEGLASVALGFFVWFW 206 Query: 201 LPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWL-----TPQILLAIFVYFC 255 L +P A W++ EE + I QE + E ++K L QILL +YFC Sbjct: 207 LDSKPHDAQWMTREEQDALVNAIDQEQRD--REALTTVKPTLGKLLKDRQILLFCALYFC 264 Query: 256 HQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCR---R 312 Q+TIY F+LPSII K G+L+ + VG S+PW+ + + + FA+ G+ + Sbjct: 265 IQLTIYAATFWLPSIIKKMGDLTDVQVGFFNSIPWL---ISIIAMYAFASLSGKFKFQQA 321 Query: 313 LLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLG 372 + LL A G+ +++ GP+F+ + C +A+ F S+ + P L A + Sbjct: 322 WVAAALLIAAAGMFMSTTGGPIFAFVAICFAAIGFKSASSLFWPIPQGYLDVRIAAAVIA 381 Query: 373 FVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAAL 415 +N+ G LGGFV P+ G +EQ+TG+ GL +A ++AA+ Sbjct: 382 LINSIGNLGGFVAPTTFGFLEQTTGSIQGGLYGLAGTSLLAAI 424 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: 562 Number of extensions: 30 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: 453 Length adjustment: 32 Effective length of query: 406 Effective length of database: 421 Effective search space: 170926 Effective search space used: 170926 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