Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate PfGW456L13_4790 D-serine/D-alanine/glycine transporter
Query= TCDB::P24207 (458 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4790 Length = 473 Score = 408 bits (1049), Expect = e-118 Identities = 197/437 (45%), Positives = 286/437 (65%), Gaps = 3/437 (0%) Query: 19 LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78 L R L RHI+L+ALG IG GLFLG AI+MAGPA++L Y + G+ +IMR LGEM Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 79 VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138 V PV+GSF+ +A Y GP AGFL+GWNYW ++++ +AE+TA +YM WFPDVP WIW Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196 A A I + ++NL+ V+ +GE EFWFALIK++ II M+ G G+ G+ G I N Sbjct: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVALGISN 197 Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256 LW +GGF G G+++SL ++MF++ G+E+IG+TA EA++P+K+IP A+ V +RILLF Sbjct: 198 LWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316 Y+G+L V+L++YPW E+ + SPFVM F L A +NFV++ A+LS N G++S Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376 RML+ L+ G AP + S GVP +L+LS L VL+NYL+P+K F + A+ Sbjct: 318 RMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLNYLVPEKVFVWVTAIATF 377 Query: 377 TLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTMDDMR 435 + W+MI LA L+FR + + +++ LYP +YL +AFL +++ LM D R Sbjct: 378 GAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437 Query: 436 LSAILLPVWIVFLFMAF 452 ++ + P ++V L + F Sbjct: 438 VALYVGPAFLVLLTVLF 454 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: 684 Number of extensions: 35 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: 473 Length adjustment: 33 Effective length of query: 425 Effective length of database: 440 Effective search space: 187000 Effective search space used: 187000 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