Align Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= SwissProt::Q59WU0 (568 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 234 bits (598), Expect = 4e-66 Identities = 147/465 (31%), Positives = 236/465 (50%), Gaps = 32/465 (6%) Query: 56 EVKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTLAYSVTQSLGE 115 E+KR LK RH+ +IA+GG IGTGLF+ + +L + GP M ++ + +A+ + + LGE Sbjct: 10 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSM-ILGYAICGFIAFMIMRQLGE 68 Query: 116 MTTYIPVSGSFAQFITRWVSKSCGAANGWLYWFSWAITFALELSVVGQVIQYWTDAVPLA 175 M PV+GSF+ F ++ G +GW W + + EL+ VG+ I YW +P Sbjct: 69 MIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTW 128 Query: 176 GWISIFFVLLTTFNLFPVKYYGEVEFWIASTKVIAIVGWL-IYAFCMVCGAGKTGPVGFR 234 + FFVL+ NL VK +GE EFW A KV+AIVG + + ++ +V G G Sbjct: 129 ASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNGGPQAAVSN 188 Query: 235 YWRNGYAWGDGMIVSNNGKYAISFINGLINAVFTFQGTELVAVTAGEAS--PRAIRSAIK 292 W +G + +G+ A++FI +F+F G E++ TA EA I AI Sbjct: 189 LWSHGGFFPNGV---TGLVMAMAFI------MFSFGGLEMLGFTAAEADKPKTVIPKAIN 239 Query: 293 KVMFRILVFYVLCMLFIGLLVPYND--PKLTQDGGFTRNSPFLIAMENSGTKVLPHIFNA 350 +V++RIL+FY+ ++ + L P++ L G SPF+ G+ HI N Sbjct: 240 QVIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNF 299 Query: 351 VIVTTIISAGNSNVYSGSRILYGLAQAGVAPKFFLKTNKGGVPYFAVLFTAAFGALGYLA 410 V++T +S NS Y SR+L G+A+ G APK K +K GVP ++L +AA + L Sbjct: 300 VVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLL 359 Query: 411 CSEDGNKAFTWLLNIIATAGLIAWGFISVSHVRFMNVLRKRGLSRDILPYKAFFMPYSAY 470 + A L++++ +I W IS SH +F + K ++ +KA + PY Y Sbjct: 360 NYLIPHSALELLMSLVVATLVINWAMISYSHFKFRQHMNK---TKQTPLFKALWYPYGNY 416 Query: 471 ----YAIIIIFIVVLIQGFTVFWDFNASDFFTAYISVILFVVLWI 511 + + I+ +++LI G + Y + V +W+ Sbjct: 417 ICLAFVLFILGVMLLIPGIQT----------SVYAIPVWLVFMWV 451 Lambda K H 0.326 0.141 0.448 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: 742 Number of extensions: 41 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: 568 Length of database: 473 Length adjustment: 35 Effective length of query: 533 Effective length of database: 438 Effective search space: 233454 Effective search space used: 233454 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