Align Glucose/galactose porter (characterized)
to candidate 353142 BT3616 fucose permease (NCBI ptt file)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Btheta:353142 Length = 418 Score = 238 bits (607), Expect = 2e-67 Identities = 150/417 (35%), Positives = 225/417 (53%), Gaps = 27/417 (6%) Query: 18 QKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLP 77 + Y L + LFF+W + L +I L +LN ++ + ++ AYFI +P Sbjct: 3 KNTYTIPLALVFSLFFLWAISSNLLPTMIRQLMKTCELNTFEASFTETAYWLAYFIFPIP 62 Query: 78 AGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANP 137 +KR SYK GI+ GL++AA+G LF PAA + Y +L F++A+G+ L+ AANP Sbjct: 63 IAMFMKRYSYKAGIIFGLLLAAVGGLLFFPAAMLKEYWAYLCIFFIIATGMCFLETAANP 122 Query: 138 YVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILS--------------AATDATV 183 YVT+LG PETA RL L Q+FN LG +A +F + LILS A + Sbjct: 123 YVTVLGAPETAPRRLNLAQSFNGLGAFIAAMFLSKLILSGTHYTRETLPVDYPGGWQAYI 182 Query: 184 NAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQED--EPALSDKKEG----SAWQYRHL 237 E DA++ PYL+LAL +A++F K P + ++ EPA S KKE + HL Sbjct: 183 QLETDAMKLPYLILALLLLAIAVVFVFSKLPKIGDEGAEPA-SGKKEKLIDFDVLKRSHL 241 Query: 238 VLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM 297 G I F Y G + ++ S + + T AGL E A + ++GR+IG+ M Sbjct: 242 RWGVIAQFFYNGGQTAINSLFLVYCC--TYAGLPEDTATTFFGLYMLAFLLGRWIGTGLM 299 Query: 298 -RYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGS 356 ++ G L + A + I+L + + G I ++++LAI F SIM+PT FSLAL GLG+ Sbjct: 300 VKFRPQGMLLVY-ALMNILLCGVVMLWGGMIGLYAMLAISFFMSIMYPTQFSLALKGLGN 358 Query: 357 HTSQGSGILCLAIVGGAIVPLIQGAL--ADAIGIHLAFLMPIICYAYIAFYGLIGSK 411 T GS L +AIVG A +P + + ++A+ +P+IC+A+ A+YG G K Sbjct: 359 QTKSGSAFLVMAIVGNACLPQLTAYFMHVNEHIYYVAYGIPMICFAFCAYYGWKGYK 415 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: 533 Number of extensions: 34 Number of successful extensions: 5 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: 418 Length adjustment: 31 Effective length of query: 381 Effective length of database: 387 Effective search space: 147447 Effective search space used: 147447 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 Apr 09 2024. 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