Align proline porter II (characterized)
to candidate AO353_05775 AO353_05775 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05775 Length = 446 Score = 261 bits (666), Expect = 5e-74 Identities = 145/423 (34%), Positives = 240/423 (56%), Gaps = 21/423 (4%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 R+A A+ G+ +EW+D+GVYGF+A +GK FF DP+ ++A+ A F++ F IRPLGG Sbjct: 13 RRAFIGATSGHLIEWYDYGVYGFLAVYIGKAFFVSDDPTSSLLASFAAFALSFFIRPLGG 72 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 LFFG L DK GR+K L +V+M+ ST +GL+P+Y T+GI APILL++ + QGFS GG Sbjct: 73 LFFGPLADKIGRRKTLITVLVMMAGSTVLLGLLPTYATLGIAAPILLVLIRCVQGFSAGG 132 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E + F++EY+ +RGF WL ++ G +LG V ++ ++G WGWRIP Sbjct: 133 EIGTITSFISEYAGPGRRGFATCWLMVTAVLGLLLGGAVANGMTWVMGADLMQAWGWRIP 192 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F IA PLG+I +Y+R LE++P F R G + K +E+ W+ + Sbjct: 193 FLIAAPLGLISMYIRLKLEDSPEFLAL-------QRAG--ETSKAPLREV--WQWKRAIA 241 Query: 264 CIGLVIATNVT-YYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRF 322 + +I + + +Y++LT+ +Y+S L + +L + + V P G +D++ Sbjct: 242 LVFFIITLHSSIFYLVLTFASTYMSSILKFDSGTTLLYVFVASLSAAVVMPFGGAFTDKY 301 Query: 323 GRRPFVL----LGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPA 378 GR+PF+L L ++A++ L A ++ I L+ +A++ + + + Sbjct: 302 GRKPFLLVVGTLATLAMYWLFKSAPTATPASFI----YPLMTVAILFGLYASSTYALMSE 357 Query: 379 MFPTHIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVT 437 + PT IR + +A A+NI V V G P ++ WL++ + ++ P Y+ + VV LI V Sbjct: 358 LLPTRIRSTGIAVAYNIPVAVFGGSAPLISTWLIKVTGDITSPWYFYIGTGVVSLIALVL 417 Query: 438 MKE 440 +++ Sbjct: 418 LRK 420 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: 588 Number of extensions: 35 Number of successful extensions: 6 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: 446 Length adjustment: 33 Effective length of query: 467 Effective length of database: 413 Effective search space: 192871 Effective search space used: 192871 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