Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 376 bits (966), Expect = e-109 Identities = 191/443 (43%), Positives = 274/443 (61%), Gaps = 5/443 (1%) Query: 15 QEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQL 74 Q L RGL RHI+ +ALG AIGTGLF G AIQ AGPAVLL Y + G +++MR L Sbjct: 4 QSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRAL 63 Query: 75 GEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVP 134 GEM V PV+GSF +A GP AGFL GW Y ++V +A++TA GIYM +WFPDVP Sbjct: 64 GEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDVP 123 Query: 135 TWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHG----GE 190 WIW +I +NL++V+++GE EFW +L+KV AI+ MIG G+ ++ G G G Sbjct: 124 RWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGGV 183 Query: 191 KASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVV 250 I NLW +GGF G G+I S AV+MF+FGG+E+IGITA EARDP++ IP+A+N V Sbjct: 184 ATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAVP 243 Query: 251 YRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNS 310 RILLFY+ +L VL++LYPW + S SPFV IF L A+ LN V++ A++S NS Sbjct: 244 LRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAINS 303 Query: 311 GVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLL 370 ++ RML+G++VQ AP+ VSR+GVP ++++ V++NY++P+ F L+ Sbjct: 304 DIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFTLI 363 Query: 371 MALVVATLLLNWIMICLAHLRFRAAM-RRQGRETQFKALLYPFGNYLCIAFLGMILLLMC 429 ++ + W+MI L+ + R M R + +F +P AF+ I ++ Sbjct: 364 ASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVLG 423 Query: 430 TMDDMRLSAILLPVWIVFLFMAF 452 R + ++ VW++ L +A+ Sbjct: 424 WFPQTRAALLVGAVWLLLLVVAW 446 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: 639 Number of extensions: 30 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: 466 Length adjustment: 33 Effective length of query: 425 Effective length of database: 433 Effective search space: 184025 Effective search space used: 184025 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