Align proline porter II (characterized)
to candidate AO356_06425 AO356_06425 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_06425 Length = 437 Score = 239 bits (609), Expect = 2e-67 Identities = 129/423 (30%), Positives = 217/423 (51%), Gaps = 10/423 (2%) Query: 25 KAITAASLGNAMEWFDFGVYGFVA-YALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 + TA+ +G A+E++DF VY A +G VFFP + QM+++ TF + FL RPLG Sbjct: 20 RVATASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQMLSSFLTFGIAFLARPLGS 79 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 FG GD+ GR+ L ++++M + T IG++P Y +IG WAPILL + + QG +GG Sbjct: 80 ALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYASIGAWAPILLCLLRFGQGLGLGG 139 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E+ GA++ E +P KR + G + G GF+ G+ + ++ + + F DWGWRIP Sbjct: 140 EWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTLAMSLDDEQFRDWGWRIP 199 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F ++ L I+GLY+R L ETP F + + Q+ KV E+ ++YW L Sbjct: 200 FLLSAVLVIVGLYVRLKLHETPVFANAMAR---------QERVKVPLVELFSQYWAPTLL 250 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFG 323 ++ +Y+ + SY L YS + + ++ ++ M P+ SDR+G Sbjct: 251 GAAAMVVCYALFYISTVFSLSYGVSTLGYSRETFLGLLCFAVLFMAAATPLSAWASDRYG 310 Query: 324 RRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTH 383 R+P +++G + L+ G + L + ++ M + LP +FPTH Sbjct: 311 RKPILIIGGLLAIASGFLMEPLLTHGSTGGVALFLCIELFLMGVTFAPMGALLPELFPTH 370 Query: 384 IRYSALAAAFNISVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKETAN 443 +RY+ +AA+N+ +V A + + L Y+ A++ +I + +KET + Sbjct: 371 VRYTGASAAYNLGGIVGASAAPFFAQKLVAMGGLSYVGGYVSAAALLSVIAVLCLKETRH 430 Query: 444 RPL 446 L Sbjct: 431 NDL 433 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: 40 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: 500 Length of database: 437 Length adjustment: 33 Effective length of query: 467 Effective length of database: 404 Effective search space: 188668 Effective search space used: 188668 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: 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