Align Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= SwissProt::A0A1D8PPI5 (571 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 233 bits (593), Expect = 2e-65 Identities = 138/440 (31%), Positives = 229/440 (52%), Gaps = 20/440 (4%) Query: 51 SSINDEFGEVKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTICF 110 S N GE+KR LK RH+ +IA+GG IGTGLF+ + ++ + GP M ++ + I F Sbjct: 2 SGQNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSM-ILGYAICGFIAF 60 Query: 111 SVTQSLGEMATYIPISGSFAQFVTRWVSKSCGAANGWLYWFSWAVTFGLELSVVGQVIQF 170 + + LGEM P++GSF+ F + G +GW W + + ELS VG+ + + Sbjct: 61 MIMRQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHY 120 Query: 171 WTDAVPLAAWISIFFVILTIFNFFPVKFYGEVEFWIASIKIIAVFGWI-IYAFIMVCGAG 229 W +P + FFV++ N VKF+GE EFW A IK++A+ I + A+++ G+G Sbjct: 121 WWPEIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSG 180 Query: 230 KTGPVGFRYWRNGYAWGDGILVNNNGKYVAAFVSGLINSIFTFQGTELVAVTAGEAS--P 287 W +G + +G V+ V L +F+F G E++ TA EA Sbjct: 181 GPEATVANLWTHGGFFPNG---------VSGLVMALAFIMFSFGGLEMLGFTAAEADKPK 231 Query: 288 RALRSAIRKVMFRILVFYVLCMLFMGLLVPYND--PKLTQDGGFTRNSPFLIAMENSGTK 345 + AI +V++RIL+FYV ++ + L P+++ + GG +SPF+ G+ Sbjct: 232 TVIPKAINQVIYRILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSD 291 Query: 346 VLPHIFNAVIVTTIISAGNSNIYSGSRILYGLAQAGVAPKFFLRTNKGGVPFFAVAFTAA 405 V ++ N V++T +S NS Y +R+L G+A+ G AP + +K GVP ++ +AA Sbjct: 292 VAANLLNFVVLTAALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAA 351 Query: 406 FGALGYLACSSQGNKAFTWLLNITATAGLISWGFISVSHIRFMKTLQRRGISRDTLPFKA 465 + L A L+++ +I+W IS SH++F + L R G FKA Sbjct: 352 VTFVAVLLNYLMPQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTG---QKPLFKA 408 Query: 466 FFMPFSAYYGMVVCFIVVLI 485 + P+ Y +V+ F+V+++ Sbjct: 409 LWYPYGNY--VVLAFVVLIL 426 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: 699 Number of extensions: 44 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: 571 Length of database: 472 Length adjustment: 35 Effective length of query: 536 Effective length of database: 437 Effective search space: 234232 Effective search space used: 234232 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