Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 413 bits (1062), Expect = e-120 Identities = 199/439 (45%), Positives = 296/439 (67%), Gaps = 6/439 (1%) Query: 19 LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78 L R L RHI +ALG AIG GLFLG AI +AGP+VL Y G + F+IMR LGEM Sbjct: 5 LQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMA 64 Query: 79 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138 V +PV+GSF+ +A++Y GPFAG+L+GWNYW++ V VGMAE TA GIYM+ WFP++P WIW Sbjct: 65 VHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWIW 124 Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196 +I +NL+ V++YGE EFWF LIKV+ ++ MI G G+ L G+GG+ + N Sbjct: 125 VFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGLAN 184 Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256 LW +GG+F G+ G++L+L V++F+FGG+E IG+ A EA PE++IP+AVN V++RIL+F Sbjct: 185 LWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIF 244 Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316 Y+G+L V++A+YPW ++ + SPFV F L A +NFV++ A+LS +NS +S S Sbjct: 245 YVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGS 304 Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376 RML+ LS + AP FL +VS GVP+ +++++ A V++NYLLP++ F ++M+++ Sbjct: 305 RMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILAF 364 Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDMRL 436 + W+M+ +AH FR RR G T F +P + +C+ FL +L ++ D R+ Sbjct: 365 NTVWTWMMVLIAHYSFR---RRHG-ATAFPLRAWPLTSVVCLLFLAFVLFMLGYSADTRV 420 Query: 437 SAILLPVWIVFLFMAFKTL 455 + + W+V L +A++ L Sbjct: 421 ALYVGAGWVVLLSLAYRLL 439 Lambda K H 0.329 0.143 0.447 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: 675 Number of extensions: 44 Number of successful extensions: 3 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: 458 Length of database: 453 Length adjustment: 33 Effective length of query: 425 Effective length of database: 420 Effective search space: 178500 Effective search space used: 178500 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 (21.8 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