Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Koxy:BWI76_RS08745 Length = 459 Score = 398 bits (1023), Expect = e-115 Identities = 191/436 (43%), Positives = 284/436 (65%), Gaps = 3/436 (0%) Query: 16 EPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLG 75 +P L RGL+ RHI+ IALG AIGTGLF G AI+ AGPAVLL Y + G F++MR LG Sbjct: 6 KPHLLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMRALG 65 Query: 76 EMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPT 135 EM V PVSGSF+ +A +Y GP AGF++GW Y V+V +A++TA GIYM W+PDVP Sbjct: 66 EMAVRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPDVPR 125 Query: 136 WIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGHGG--EKAS 193 WIW + I A+NL +VR++GE EFW +LIKV+AII MI G ++F G G Sbjct: 126 WIWVLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNAFPATG 185 Query: 194 IDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRI 253 ++NLW +GGF GW G+I SL ++MF+FGG+E+IG+TAAEA++P+K IP+A+N + RI Sbjct: 186 LENLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIPLRI 245 Query: 254 LLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVY 313 +LFY+ +L +L+A++PW SPFV+IF L A+ LN +++ AS+S NS ++ Sbjct: 246 VLFYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINSDIF 305 Query: 314 SNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMAL 373 RM++G++ +G APK R++ GVP ++++ G V++NYL+P++ F L+ +L Sbjct: 306 GAGRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQVFVLIASL 365 Query: 374 VVATLLLNWIMICLAHLRFRAAMRRQGR-ETQFKALLYPFGNYLCIAFLGMILLLMCTMD 432 + W+MI LAH R + + R F L+P L + F+G+++ ++ ++ Sbjct: 366 AAFATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAVLGMVE 425 Query: 433 DMRLSAILLPVWIVFL 448 + R++ I VW+ L Sbjct: 426 ETRIALIAGLVWLGLL 441 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: 636 Number of extensions: 29 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: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 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