Align Proline-specific permease (ProY) (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= TCDB::P37460 (456 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 370 bits (949), Expect = e-107 Identities = 191/457 (41%), Positives = 283/457 (61%), Gaps = 12/457 (2%) Query: 6 KLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEM 65 +LKRGL RHI+ +ALG AIGTGLF GSA +K AGPS++L Y I G A++IMR LGEM Sbjct: 10 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 69 Query: 66 SVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWI 125 V P A SFS +A + G AG+++GW Y ++V +A++TA G Y+ W+P VP W+ Sbjct: 70 IVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPSWV 129 Query: 126 WVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIH 185 +++ IN+M+VKVFGE+EFWF+ KV II MI G ++ G GG + Sbjct: 130 SAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLF--SGTGGPQASVS 187 Query: 186 NLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245 NLW +GGFF NG+ G++M++ +MF++GG+E++GITA EA +P K IP+AIN V R+L+ Sbjct: 188 NLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQVVYRVLI 247 Query: 246 FYVGTLFVIMSIYPWNQV---------GTNGSPFVLTFQHMGITFAASILNFVVLTASLS 296 FYVG L V++S+YPW+Q+ GSPFV F +G AA ILNFVVLTA+LS Sbjct: 248 FYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNFVVLTAALS 307 Query: 297 AINSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENV 356 NS V+ RML+G+AEQG APK K +++G+P + + V + L +V +NY+ P Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLVNYLAPHEA 367 Query: 357 FLVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFII 416 ++ +L + + W MI L+ + FR+ + + + FK + L F+V I+ Sbjct: 368 LELLFALVVASLMINWAMISLTHLKFRKIMSQQGI-VPGFKSFWFPFSNYLCLAFMVMIV 426 Query: 417 ALIGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQL 453 ++ P R S++ W++++ + + +DR L Sbjct: 427 CVMLMIPGIRASVFAIPVWVLIIFGFYRMRMAKDRAL 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: 597 Number of extensions: 32 Number of successful extensions: 4 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: 456 Length of database: 467 Length adjustment: 33 Effective length of query: 423 Effective length of database: 434 Effective search space: 183582 Effective search space used: 183582 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