Align proline porter II (characterized)
to candidate BPHYT_RS23435 BPHYT_RS23435 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS23435 Length = 469 Score = 254 bits (648), Expect = 6e-72 Identities = 152/448 (33%), Positives = 247/448 (55%), Gaps = 28/448 (6%) Query: 6 KVKPITLRDVTIIDDGKLRKAITAASLGNAMEWFDFGVYGFVAYAL-GKVFFPGADPSVQ 64 +V P + LR+ A+++G A E++DF VYG A + G+ FFP ADP + Sbjct: 4 RVNPARPQATAPASTAMLRRVAFASTIGTAAEYYDFFVYGTAAVLVFGQKFFPSADPLIG 63 Query: 65 MVAALATFSVPFLIRPLGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGI 124 +AA AT++V FL RPLGG+ FG GD+ GR+K L +TI+I+ + TF IGL+P Y +IGI Sbjct: 64 TLAAFATYAVGFLARPLGGIVFGHFGDRVGRKKALIVTILIVGLGTFAIGLLPDYQSIGI 123 Query: 125 WAPILLLICKMAQGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVV 184 WAPI L++ ++ QGF VGGE GA + AEY+P +RGF S + G+ AGF++ +G+ Sbjct: 124 WAPIALIVIRVLQGFGVGGEQAGAVLLTAEYAPPARRGFFASLVQLGAPAGFLIPSGLFA 183 Query: 185 LISTIVGEANFLDWGWRIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQD 244 L+ + +A LDWGWRIPF + L +GLY+R EE+P F + + + + Sbjct: 184 LLGATLTQAQLLDWGWRIPFLASALLVAVGLYIRLRTEESPIFAT-IQR-----TKAVAS 237 Query: 245 GPKVSFKEIATKYWRSLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGV------ 298 P V E+ ++ +++ +G + + M Y L Y + HG+ Sbjct: 238 RPVV---EVVRQFGPTIVKGVGAKLIEACAFAM-------YTMIVLAYGKAHGIAQGMLL 287 Query: 299 -LIIIAIMIGMLFVQPVMGLLSDRFGRRPFVLLGSVALFVLAIPAFILINS-NVIGLIFA 356 +I+A+ + ++ + P+ G LSDR GRR + G++ L +P F+ I+S N + Sbjct: 288 ETVIVAVALELVTI-PLAGALSDRIGRRTTFIAGALLHVALVVPFFMAIDSGNRAAIQLV 346 Query: 357 GLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLVESSQ 415 +L ++V + A+ P +FP +R S +A + I S+L +G+ LA L++ + Sbjct: 347 MILAISVGHSLCYAPQAALFPELFPARVRCSGIALIWQIGSLLGSGVLGLLAVKLIQLTH 406 Query: 416 -NLMMPAYYLMVVAVVGLITGVTMKETA 442 N + Y+ V+ +V ++ + ETA Sbjct: 407 GNSLALIVYVAVLGIVSAVSLFALPETA 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: 581 Number of extensions: 28 Number of successful extensions: 4 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: 469 Length adjustment: 34 Effective length of query: 466 Effective length of database: 435 Effective search space: 202710 Effective search space used: 202710 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