Align Glucose/galactose porter (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Pedo557:CA265_RS08575 Length = 422 Score = 276 bits (705), Expect = 1e-78 Identities = 159/417 (38%), Positives = 238/417 (57%), Gaps = 23/417 (5%) Query: 14 ETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFI 73 ++SS K Y + LFF+WG L+ ILIPHLK LN QS LI F AYF+ Sbjct: 6 DSSSGKKYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFL 65 Query: 74 VSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQV 133 +++PAG ++K+ YK ++ GL+ A G LF+PAA+ Y FL ALF++ G+T+L+ Sbjct: 66 MAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLET 125 Query: 134 AANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILS----------AATDATV 183 +ANPY +LG P A SRL L +FN L VAP+ G + ILS A TDA Sbjct: 126 SANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMTDAGR 185 Query: 184 NA----EADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEGS---AWQYRH 236 N+ EA +V+ PY+ L + V+A IF + P+++ ++ + +GS A +++H Sbjct: 186 NSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIK--TKSIDGEAKGSFFGALRHKH 243 Query: 237 LVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAA 296 L + F YVGA+V V SF + G E AA ++A + VGRF G+A Sbjct: 244 LKWAVVAQFFYVGAQVCVTSFFIRMAQQG--GGFDEKTAASYLAIYGLLFTVGRFAGTAI 301 Query: 297 MRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGS 356 ++++ K LA A ++I+L + + G ++++ AIG F SIMFPTIF+L + G+G Sbjct: 302 LQFVSSHKLLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGIGD 361 Query: 357 HTSQGSGILCLAIVGGAIVPLIQGALADAIG--IHLAFLMPIICYAYIAFYGLIGSK 411 T GS L ++IVGGAI+P G+L D G I + + +P++C+ I ++GL G K Sbjct: 362 DTKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYFGLRGYK 418 Lambda K H 0.328 0.141 0.420 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: 548 Number of extensions: 30 Number of successful extensions: 6 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: 412 Length of database: 422 Length adjustment: 31 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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: 50 (23.9 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