Align ProY of 457 aas and 12 TMSs (characterized)
to candidate Pf6N2E2_5633 Aromatic amino acid transport protein AroP
Query= TCDB::P0AAE2 (457 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Length = 472 Score = 367 bits (942), Expect = e-106 Identities = 195/457 (42%), Positives = 279/457 (61%), Gaps = 13/457 (2%) Query: 6 KLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEM 65 +LKRGL RHI+ +ALG AIGTGLF GSA +K AGPS++L Y I G A++IMR LGEM Sbjct: 10 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69 Query: 66 SVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWI 125 V P A SFS +A + G AG+++GW ++V ++++TA G Y+ W P +P W+ Sbjct: 70 IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129 Query: 126 WVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQPTGIH 185 + ++I +NL +VKVFGE EFWF+ KV I+ MI G +++ G+GG + Sbjct: 130 SAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLV--SGHGGPQASVT 187 Query: 186 NLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245 NLWS+GGFF NG G+VM++ ++MF++GG+E++G TA EA P+ IP+AIN V RIL+ Sbjct: 188 NLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILI 247 Query: 246 FYVGTLFVIMSIYPWNQV---------GTAGSPFVLTFQHMGITFAASILNFVVLTASLS 296 FY+G L V++S+ PW+ + +GSPFV F +G AA ILNFVVLTA+LS Sbjct: 248 FYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALS 307 Query: 297 AINSDVFGVGRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENV 356 NS + RML GMAEQG APK+ SK +RG+P ++L L AV LNY++P++ Sbjct: 308 VYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVAVLLNYLIPQHA 367 Query: 357 FLVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFII 416 ++ SL V W MI S FR+ + L FK L F++FI+ Sbjct: 368 LELLMSLVVATLVINWAMISYSHFKFRQHMNQTHQTPL-FKALWYPYGNYICLAFVVFIL 426 Query: 417 GLIGYHPDTRISLYVGFAWIVVLLI-GWMFKRRHDRQ 452 G++ P ++S+Y W+V + + W+ +R RQ Sbjct: 427 GVMLLIPGIQVSVYAIPVWVVFMAVCYWIKNKRSARQ 463 Lambda K H 0.329 0.143 0.449 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: 521 Number of extensions: 25 Number of successful extensions: 5 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: 457 Length of database: 472 Length adjustment: 33 Effective length of query: 424 Effective length of database: 439 Effective search space: 186136 Effective search space used: 186136 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