Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate PfGW456L13_318 Histidine transport protein (permease)
Query= TCDB::P24207 (458 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318 Length = 468 Score = 402 bits (1033), Expect = e-116 Identities = 202/443 (45%), Positives = 285/443 (64%), Gaps = 4/443 (0%) Query: 16 EPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLG 75 E L RGL RHI+ +ALG AIGTGLF G AIQMAGPAVLL Y + G F++MR LG Sbjct: 5 EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64 Query: 76 EMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPT 135 EM V PV+GSF +A Y GP AGF+ GW Y V+VGMA++TA GIYM +WFP+V Sbjct: 65 EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSR 124 Query: 136 WIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGL-WLLFSGHGGEKA 192 WIW I+ +NL NV+++GE EFW +L+KV AI+ MI GFG+ W S G+ Sbjct: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQAT 184 Query: 193 SIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYR 252 I NLW +GGF G GLI S AV+MF+FGG+E+IG+TA EA+DP+ +P+A+N V R Sbjct: 185 DISNLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244 Query: 253 ILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGV 312 ILLFY+ +++VL++++PW ++ S SPFV IF L + A+ LN V++ A++S NS + Sbjct: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304 Query: 313 YSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMA 372 + RM+FGL+ QG+APK R+SR GVP ++++ A L VL+NYL+P+ F L+ + Sbjct: 305 FGAGRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPENVFLLIAS 364 Query: 373 LVVATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMCTM 431 + + W+MI + + R +M Q + +F L+P+ IAF+ I ++ Sbjct: 365 VATFATVWVWLMILVTQVAMRRSMSAEQVAQLKFPVPLWPYAPAAAIAFMLFIFGVLGYF 424 Query: 432 DDMRLSAILLPVWIVFLFMAFKT 454 D + + I+ VWIV L +A+ T Sbjct: 425 PDTQAALIVGVVWIVLLVLAYLT 447 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: 647 Number of extensions: 26 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: 468 Length adjustment: 33 Effective length of query: 425 Effective length of database: 435 Effective search space: 184875 Effective search space used: 184875 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