Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate Pf6N2E2_691 D-galactarate permease
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_691 Length = 465 Score = 327 bits (839), Expect = 4e-94 Identities = 174/433 (40%), Positives = 253/433 (58%), Gaps = 24/433 (5%) Query: 21 LMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIMH 80 ++PL+++ +I++++DR NI + HL+ DLGI AAAYGLGAGLFF+ YAL E+PSN+++ Sbjct: 24 VLPLVVVMFIVNYIDRVNIGFVRSHLETDLGIGAAAYGLGAGLFFVGYALFEVPSNMLLQ 83 Query: 81 KVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNRE 140 + GAR W+ RIM TWG + AMAFV+GETSFYVLR +LG AEAG FPG++ Y T W Sbjct: 84 RYGARAWLTRIMFTWGAAAMAMAFVRGETSFYVLRFILGAAEAGFFPGIIYYFTQWLPAN 143 Query: 141 QRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWRK 200 +R +A FL G A++I GPV AL+ + GM G HGWQWMF++EG ++ VW Sbjct: 144 ERGKAMAIFLSGSAIASVISGPVSGALLHISGM-GLHGWQWMFLIEGFASIVLCGFVWFW 202 Query: 201 LPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWL-----TPQILLAIFVYFC 255 L PS+A WLS+EE + IA+ E+ A E +K + QI L F+YF Sbjct: 203 LQSHPSQAKWLSSEEKTVLIAAIAE--EQRAREAAQVIKPSIFKLLADRQIALFCFIYFS 260 Query: 256 HQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCR---R 312 +TIY F+LPS+I K G L VGLL S+PWI + + + FA G+ + Sbjct: 261 IALTIYGATFWLPSMIKKMGNLGDFQVGLLNSIPWI---ISIIAMYGFAALAGKWKFQQA 317 Query: 313 LLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLG 372 + L+ A G+ +++ GP+F+ + C +A+ F ++ + P L A + Sbjct: 318 WVAVTLVVAAFGMFMSTTGGPIFAFVAICFAAIGFKAASALFWPIPQGYLDARIAAAVIA 377 Query: 373 FVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLR----------M 422 +N+ G LGGFV P+ G +EQ+TG+ GL +A +VAA+ R + Sbjct: 378 LINSIGNLGGFVAPTAFGFLEQTTGSIEGGLYGLAATSLVAAVVIFFARTAPKRDTPNSL 437 Query: 423 GHEPERGAQASEA 435 PE A+AS++ Sbjct: 438 SGRPEAVAEASQS 450 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: 575 Number of extensions: 24 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: 465 Length adjustment: 33 Effective length of query: 405 Effective length of database: 432 Effective search space: 174960 Effective search space used: 174960 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