Align Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= SwissProt::A0A1D8PPI5 (571 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 258 bits (658), Expect = 5e-73 Identities = 157/468 (33%), Positives = 257/468 (54%), Gaps = 31/468 (6%) Query: 58 GEVKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTICFSVTQSLG 117 GE+KR LK RH+ +IA+GG IGTGLF+ + +L + GP M ++ + I F + + LG Sbjct: 9 GELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSM-ILGYAIAGFIAFLIMRQLG 67 Query: 118 EMATYIPISGSFAQFVTRWVSKSCGAANGWLYWFSWAVTFGLELSVVGQVIQFWTDAVPL 177 EM P++GSF+ F ++ G +GW YW + + EL+ VG+ +QFW VP Sbjct: 68 EMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVP- 126 Query: 178 AAWIS--IFFVILTIFNFFPVKFYGEVEFWIASIKIIAVFGWI-IYAFIMVCGAGKTGPV 234 +W+S +FFV++ + N VK +GE+EFW A IK++A+ G I + +++ G G Sbjct: 127 -SWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTGGPQAS 185 Query: 235 GFRYWRNGYAWGDGILVNNNGKYVA-AFVSGLINSIFTFQGTELVAVTAGEASP--RALR 291 W +G + +G +G +A AF+ +F+F G ELV +TA EAS + + Sbjct: 186 VSNLWDHGGFFPNGY----SGLLMAMAFI------MFSFGGLELVGITAAEASEPGKVIP 235 Query: 292 SAIRKVMFRILVFYVLCMLFMGLLVPYND--PKLTQDGGFTRNSPFLIAMENSGTKVLPH 349 AI +V++R+L+FYV + + L P++ L G SPF+ G+ H Sbjct: 236 KAINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAH 295 Query: 350 IFNAVIVTTIISAGNSNIYSGSRILYGLAQAGVAPKFFLRTNKGGVPFFAVAFTAAFGAL 409 I N V++T +S NS +Y SR+LYGLA+ G APK ++ NK GVP A+ +A L Sbjct: 296 ILNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLL 355 Query: 410 GYLACSSQGNKAFTWLLNITATAGLISWGFISVSHIRFMKTLQRRGISRDTLPFKAFFMP 469 L ++A L + + +I+W IS++H++F K + ++GI FK+F+ P Sbjct: 356 SVLVNYLAPHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGI---VPGFKSFWFP 412 Query: 470 FSAYYGMVVCFIVVLIQGFTVFWDFNASDFFTAYISVILFVVLWVGFH 517 FS Y + + F+V+++ + AS F ++ ++V++ GF+ Sbjct: 413 FSNY--LCLAFMVMIVCVMLMIPGIRASVF-----AIPVWVLIIFGFY 453 Lambda K H 0.327 0.140 0.445 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: 757 Number of extensions: 42 Number of successful extensions: 6 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: 571 Length of database: 467 Length adjustment: 35 Effective length of query: 536 Effective length of database: 432 Effective search space: 231552 Effective search space used: 231552 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 (21.7 bits) S2: 52 (24.6 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