Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)
Query= TCDB::P24207 (458 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 397 bits (1019), Expect = e-115 Identities = 199/447 (44%), Positives = 288/447 (64%), Gaps = 7/447 (1%) Query: 15 QEPT--LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMR 72 Q+P L RGL RHI+ +ALG AIGTGLF G AIQMAGPAVLL Y + G F++MR Sbjct: 2 QQPAKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61 Query: 73 QLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPD 132 LGEM V PV+GSF +A Y GP AGF+ GW Y V+VGMA++TA GIYM +WFP+ Sbjct: 62 ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121 Query: 133 VPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWL--LFSGHG 188 V WIW ++ +NL NV+++GE EFW +L+KV AI+ MI GFG+ L + + G Sbjct: 122 VDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181 Query: 189 GEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQ 248 + I NLW +GGF G GLI S AV+MF+FGG+E+IG+TA EA+DP++ +P+A+N Sbjct: 182 AQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINA 241 Query: 249 VVYRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVY 308 V RILLFY+ +++VL++++PW ++ S SPFV IF NL + A+ LN V++ A++S Sbjct: 242 VPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAI 301 Query: 309 NSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFG 368 NS ++ RM++GL+ QG+APK R+SR GVP ++++ + L VL+NYL+P+ F Sbjct: 302 NSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFL 361 Query: 369 LLMALVVATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLL 427 L+ ++ + W+MI + R +M Q + +F +P+ IAF+ I + Sbjct: 362 LIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGV 421 Query: 428 MCTMDDMRLSAILLPVWIVFLFMAFKT 454 + D + + I+ VWIV L +A+ T Sbjct: 422 LGYFPDTQAALIVGVVWIVLLVLAYLT 448 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: 652 Number of extensions: 28 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: 469 Length adjustment: 33 Effective length of query: 425 Effective length of database: 436 Effective search space: 185300 Effective search space used: 185300 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