Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Pedo557:CA265_RS08575 Length = 422 Score = 214 bits (545), Expect = 4e-60 Identities = 126/413 (30%), Positives = 218/413 (52%), Gaps = 7/413 (1%) Query: 11 DGYLNKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFL 70 D K L FIL+ LF LWG A L+ ILI K +L+N S L+ ++ + YFL Sbjct: 6 DSSSGKKYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFL 65 Query: 71 IAIPASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLET 130 +AIPA +++KK YK ++ GL + G LF PA++ +Y FL A+F I GL+ LET Sbjct: 66 MAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLET 125 Query: 131 AANTYSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQV 190 +AN Y++++G A AT RLN++ +F + A ++G + S ++++A M Sbjct: 126 SANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMTDAGR 185 Query: 191 HNFKVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASN 250 +++ + + PY + +VL+V+ +F P K + S LR+ Sbjct: 186 NSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGEAKGSFFGALRH---- 241 Query: 251 ARFRRGIVAQFLYVGMQVAVWSFTIRLALELGDINERDASTFMVYSFACFFIGKFIANIL 310 + +VAQF YVG QV V SF IR+A + G +E+ A++++ F +G+F + Sbjct: 242 KHLKWAVVAQFFYVGAQVCVTSFFIRMAQQGGGFDEKTAASYLAIYGLLFTVGRFAGTAI 301 Query: 311 MTRFNPEKVLILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDN 370 + + K+L +Y+VI L L VY + + TI+A +D + + Sbjct: 302 LQFVSSHKLLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGIGD 361 Query: 371 EHTEMAGAVIVMAIVGAAVVPAIQGYVADMF-HSLQLSFLVSMLCFVYVGVYF 422 + T+ + ++M+IVG A++P G + DM+ ++Q+ + + ++CF+ + +YF Sbjct: 362 D-TKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVI-LYF 412 Lambda K H 0.329 0.139 0.412 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: 433 Number of extensions: 22 Number of successful extensions: 2 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: 422 Length adjustment: 32 Effective length of query: 406 Effective length of database: 390 Effective search space: 158340 Effective search space used: 158340 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 (21.8 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