Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 392 bits (1006), Expect = e-113 Identities = 193/440 (43%), Positives = 293/440 (66%), Gaps = 7/440 (1%) Query: 13 SNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMR 72 ++ +P L RGL RHI+LIALGG IG GLF+G ++ AGP+VLL Y +AG+ F IMR Sbjct: 2 ADNKPELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMR 61 Query: 73 QLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPD 132 +GEM+ EPV+GSFA +A++Y PF G+L+ W+YW M++ VG++E+TA G+Y+Q+WFP+ Sbjct: 62 SMGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPE 121 Query: 133 VPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLF--SGHGGE 190 + WI A ++ NL VRLYGE EFWFA+IKV II MI GL ++F G+GG+ Sbjct: 122 MAQWIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQ 181 Query: 191 KASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVV 250 NL +GGFFA GW G + +L +++ S+ G+ELIGITA EA++P+ ++ AV +V+ Sbjct: 182 SIGFSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVL 241 Query: 251 YRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNS 310 +RIL+FY+G++ V++ ++PW E+ SN SPFV+ F + A +NFV+L A+LS NS Sbjct: 242 WRILIFYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNS 301 Query: 311 GVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLL--PQKAFG 368 G+YS RML+ L+ P + +VSR GVP+ + +S AI + +NY++ PQ+ F Sbjct: 302 GMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFV 361 Query: 369 LLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLM 428 + + V ++ W +I ++ LRFR A + F+++L+P+ NY+ +AFL +L+ M Sbjct: 362 YVYSASVLPGMVPWFVILISQLRFRRAHKAAIASHPFRSILFPWANYVTMAFLICVLIGM 421 Query: 429 CTMDDMRLSAILLPVWIVFL 448 +D R+S L V I+F+ Sbjct: 422 YFNEDTRMS---LFVGIIFM 438 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: 634 Number of extensions: 31 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 458 Length of database: 461 Length adjustment: 33 Effective length of query: 425 Effective length of database: 428 Effective search space: 181900 Effective search space used: 181900 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