Align proline porter II (characterized)
to candidate CCNA_00025 CCNA_00025 major facilitator superfamily transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Caulo:CCNA_00025 Length = 550 Score = 197 bits (500), Expect = 1e-54 Identities = 120/334 (35%), Positives = 182/334 (54%), Gaps = 22/334 (6%) Query: 23 LRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLG 82 +R ++A+S G A EW+DF ++G + + K FF G + + +AALA F V F RPLG Sbjct: 11 MRTVVSASSAGTAFEWYDFFIFGSLTQVISKTFFAGLNETAGYIAALALFGVGFAFRPLG 70 Query: 83 GLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVG 142 L FG +GD+ GR+ T+++M +TF I +P+Y+ GI APILL+I + QGF++G Sbjct: 71 ALVFGKIGDQDGRKGAFLATVLLMGGATFAIAFLPTYEQAGIIAPILLIILRCLQGFALG 130 Query: 143 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVL-----ISTIVGEANFLD 197 GEY GA+I+VAE+SP KRG+ SW+ + G + GA +V+L + VG F + Sbjct: 131 GEYGGAAIYVAEHSPANKRGWATSWVQTSAAFG-LFGALLVILATRWVLGKYVGPDAFDE 189 Query: 198 WGWRIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKY 257 WGWRIPF ++L L I +++R L E+P F E EG K + E A Sbjct: 190 WGWRIPFAVSLGLLGISVWMRLKLTESPTF-------EAMKAEG--QASKAPYAE-AFGQ 239 Query: 258 WRSL----LTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSE-DHGVLIIIAIMIGMLFVQ 312 W +L L + ++ A +Y Y+ +++ L L++IA + +F Sbjct: 240 WSNLKLVILAFVSMMCAQGAVWYTSFFYVQTFMEKFLKVDPVTINELMMIATAVSAIF-Y 298 Query: 313 PVMGLLSDRFGRRPFVLLGSVALFVLAIPAFILI 346 V G LSD+ GR+P +L G + P F L+ Sbjct: 299 VVFGWLSDKVGRKPVMLGGMTLALLFYFPGFHLL 332 Score = 43.5 bits (101), Expect = 2e-08 Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 2/96 (2%) Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNISV-LVAGLTPTLAAWLV 411 +I L + + G +A+ L +FPT +RY+AL+ ++I V G P A +V Sbjct: 454 MILGVLFVFVIAATALFGPLAACLVELFPTRVRYTALSLPYHIGTGWVGGFVPFFAFAIV 513 Query: 412 ESSQNLMMPAYYLMVVAVVGLITGV-TMKETANRPL 446 + N+ +Y ++ ++T + + ET RPL Sbjct: 514 AAVGNIYAGLWYPFAFTLLSVLTTLFLLPETKERPL 549 Lambda K H 0.327 0.142 0.429 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: 632 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 550 Length adjustment: 35 Effective length of query: 465 Effective length of database: 515 Effective search space: 239475 Effective search space used: 239475 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: 52 (24.6 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