Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Cola:Echvi_0508 Length = 431 Score = 263 bits (672), Expect = 8e-75 Identities = 154/430 (35%), Positives = 251/430 (58%), Gaps = 16/430 (3%) Query: 14 LNKTPLFQFILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAI 73 ++K L+ FILL+ LF LWG A + D L+ FK + S+++ ++ +Q AFYG YF +A+ Sbjct: 10 VSKATLWPFILLTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQLAFYGAYFCLAL 69 Query: 74 PASLVIKKTSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAAN 133 PA++ IKK +YK +L+GL L+ VG LF+PAS +Y FL A++ +A GLS LET+AN Sbjct: 70 PAAIYIKKYTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVLAGGLSILETSAN 129 Query: 134 TYSSMIGPKAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLE-KQMAGMNAEQVHN 192 Y ++GP+A AT RLN++Q+F P+G+ G++L K+ + S+ E + + M AEQ+ Sbjct: 130 PYIMVMGPEASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEADERSRMTAEQLQQ 189 Query: 193 FKVLMLENTLEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNAR 252 + L+ + Y + + LVV+ VL T+ PT + + S + L+ L N Sbjct: 190 VRQEELDAVMGTYVGVALFLVVMWVLIKFTKMPTA----SEGGLQDSLGNGLKRLLGNKN 245 Query: 253 FRRGIVAQFLYVGMQVAVWSFTIRLALELGDINERDASTFMVYSFACFFIGKFIANILMT 312 + G++AQF YVG Q+ +WS+TIR + D+NE DAS + + + F + +F+ LM Sbjct: 246 YVFGVLAQFFYVGAQIGIWSYTIRYVMMELDMNESDASNYYLAAIVLFTVSRFLFTALM- 304 Query: 313 RFNPEKVLILYSVIGALFLAYV-----ALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDT 367 +F +L+ S IGA+ L V + S + V ++ +S++F TIY + Sbjct: 305 KFVRPSLLMAISAIGAIGLTMVVIFGHGMVGSIALVCISGCMSLMF----PTIYGLAAEG 360 Query: 368 VDNEHTEMAGAVIVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVYFWRESK 427 + ++ T++ G+ ++MAI+G A+ P IQG V+D S+ LSF V C++ V Y K Sbjct: 361 LGDD-TKLGGSGLIMAILGGAIFPFIQGLVSDSLDSIHLSFFVPAACYLVVVAYGLFHYK 419 Query: 428 VRGNLAEVAA 437 + + +AA Sbjct: 420 HKKEIPAMAA 429 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: 410 Number of extensions: 14 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: 431 Length adjustment: 32 Effective length of query: 406 Effective length of database: 399 Effective search space: 161994 Effective search space used: 161994 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