Align Glucose/galactose porter (characterized)
to candidate AO353_25100 AO353_25100 glucose transporter
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25100 Length = 425 Score = 342 bits (876), Expect = 2e-98 Identities = 187/389 (48%), Positives = 244/389 (62%), Gaps = 13/389 (3%) Query: 31 LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90 LFF+ G IT LND+L+P LK++F L+YT++ML+Q FF AYFI ++PAG L+ RI Y R Sbjct: 29 LFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMRA 88 Query: 91 IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150 V+GL++ A GC LFIPA ++ FLGALFVLA GVT +QV ANP +++LG TA S Sbjct: 89 AVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAPS 148 Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNA------------EADAVRFPYLLLA 198 RLTL AFNSLGTTVAP GA+LIL + +A EA + Y + Sbjct: 149 RLTLGHAFNSLGTTVAPYLGAILILGSLNAVDTSALSPAELTSFLSQEASVISNTYASIT 208 Query: 199 LAFTVLAIIFAILKPPDVQEDEPA-LSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSF 257 L ++A+I + + P L+ + + LG IF+YVGAEV++GS Sbjct: 209 LFICMVALIVWLKRNELQPSTRPERLNPLAALNLLKQPRFALGTASIFLYVGAEVTIGSL 268 Query: 258 LVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILL 317 + ++L PT L A HVA++WGGA+VGRFIGSA MR GK LAF A I+LL Sbjct: 269 ITDYLMLPTTLALPAEAAGKHVAFYWGGALVGRFIGSALMRTFAPGKLLAFAATAVIVLL 328 Query: 318 FITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPL 377 I+ T G +A WS+LA+GLFNSIMFPTIF+LA GLG ++GSG+ C AIVGGA +P Sbjct: 329 TISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLFCCAIVGGAFIPP 388 Query: 378 IQGALADAIGIHLAFLMPIICYAYIAFYG 406 + G AD + +A +P CYA IA YG Sbjct: 389 LTGYAADLSTLAMALSVPATCYACIAIYG 417 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: 554 Number of extensions: 27 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: 412 Length of database: 425 Length adjustment: 32 Effective length of query: 380 Effective length of database: 393 Effective search space: 149340 Effective search space used: 149340 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