Align Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= SwissProt::A0A1D8PPI5 (571 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 254 bits (650), Expect = 4e-72 Identities = 155/459 (33%), Positives = 246/459 (53%), Gaps = 22/459 (4%) Query: 58 GEVKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTICFSVTQSLG 117 G +KR LK RH+ +IA+GG IGTGLF+ + +L + GP M ++ + I F + + LG Sbjct: 9 GVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSM-ILGYAIAGFIAFLIMRQLG 67 Query: 118 EMATYIPISGSFAQFVTRWVSKSCGAANGWLYWFSWAVTFGLELSVVGQVIQFWTDAVPL 177 EM P++GSF+ F + G +GW YW + + EL+ VG+ +QFW VP Sbjct: 68 EMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPT 127 Query: 178 AAWISIFFVILTIFNFFPVKFYGEVEFWIASIKIIAVFGWI-IYAFIMVCGAGKTGPVGF 236 ++FFV++ + N VK +GE+EFW A IK++A+ G I + +++V G G Sbjct: 128 WVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQASVS 187 Query: 237 RYWRNGYAWGDGILVNNNGKYVA-AFVSGLINSIFTFQGTELVAVTAGEASP--RALRSA 293 W +G + +G NG +A AF+ +F+F G ELV +TA EAS + + A Sbjct: 188 NLWSHGGFFPNG----TNGLLMAMAFI------MFSFGGLELVGITAAEASEPRKVIPKA 237 Query: 294 IRKVMFRILVFYVLCMLFMGLLVPYND--PKLTQDGGFTRNSPFLIAMENSGTKVLPHIF 351 I +V++R+L+FYV + + L P++ L G SPF+ G+ I Sbjct: 238 INQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQIL 297 Query: 352 NAVIVTTIISAGNSNIYSGSRILYGLAQAGVAPKFFLRTNKGGVPFFAVAFTAAFGALGY 411 N V++T +S NS +Y SR+LYGLA+ G APK ++ NK GVP A+ +A L Sbjct: 298 NFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCV 357 Query: 412 LACSSQGNKAFTWLLNITATAGLISWGFISVSHIRFMKTLQRRGISRDTLPFKAFFMPFS 471 + N+A L + + +I+W IS++H++F K + +RGI FKAF+ P++ Sbjct: 358 VVNYVAPNEALELLFALVVASLMINWAMISLTHLKFRKAMGQRGI---VPGFKAFWSPYT 414 Query: 472 AYYGMVVCFIVVLIQGFTVFWDFNASDFFTAYISVILFV 510 Y + + F+ ++I + AS + +ILFV Sbjct: 415 NY--LCLAFMAMIIYVMLLIPGVRASVYAIPVWVLILFV 451 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: 727 Number of extensions: 45 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 571 Length of database: 466 Length adjustment: 35 Effective length of query: 536 Effective length of database: 431 Effective search space: 231016 Effective search space used: 231016 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