Align proline porter II (characterized)
to candidate AO353_04405 AO353_04405 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04405 Length = 438 Score = 241 bits (614), Expect = 5e-68 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++A TF + FL RPLG Sbjct: 21 RVATASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQMLSAFLTFGIAFLARPLGS 80 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 FG GD+ GR+ L ++++M + T IG++P Y++IG WAPILL + + QG +GG Sbjct: 81 ALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYESIGAWAPILLCVLRFGQGLGLGG 140 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E+ GA++ E +P KR + G + G GF+ G+ + ++ + + F WGWRIP Sbjct: 141 EWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTLAMTLNDEQFRSWGWRIP 200 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F ++ L ++GLY+R L ETP F + + Q+ K+ E+ ++YW +L Sbjct: 201 FLLSAVLVMVGLYVRLKLHETPVFANAMAR---------QERVKIPLVELFSQYWAPMLL 251 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFG 323 ++ +Y+ + SY L YS + + ++ ++ M P+ SDRFG Sbjct: 252 GAAAMVVCYALFYISTVFSLSYGVSTLGYSRETFLGLLCFAVLFMAAATPLSAWASDRFG 311 Query: 324 RRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTH 383 R+P +++G V + L+ + L + ++ M + LP +FPT Sbjct: 312 RKPVLIIGGVLAILSGFTMEPLLTHGTTWGVALFLCIELFLMGVTFAPMGALLPELFPTR 371 Query: 384 IRYSALAAAFNISVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKETAN 443 +RY+ +AA+N+ +V A + + L Y+ AV+ LI + +KET + Sbjct: 372 VRYTGASAAYNLGGIVGASAAPFFAQKLVAMGGLSWVGGYVSAAAVISLIAVLCLKETRH 431 Query: 444 RPL 446 L Sbjct: 432 NDL 434 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: 631 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: 438 Length adjustment: 33 Effective length of query: 467 Effective length of database: 405 Effective search space: 189135 Effective search space used: 189135 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