Align Probable lysine/arginine permease CAN3; Basic amino acids permease CAN3 (characterized)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease
Query= SwissProt::A0A1D8PPG4 (566 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423 Length = 466 Score = 218 bits (555), Expect = 4e-61 Identities = 139/437 (31%), Positives = 219/437 (50%), Gaps = 28/437 (6%) Query: 50 DSHGEVKRDLKARHVAMIGIGSTIGTGLFISTGHLLSQTGPVMSLISFLFVTTICFSVTQ 109 DS+G + + K RHV M+ I IG GLF+ +GH ++ GP + ++++LF + V + Sbjct: 8 DSNGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAV-MLAYLFSGLLVVLVMR 66 Query: 110 SLGEMATYIPVSGSFVQFITRWVSKSCGAANGWLYGWSWAITFGLELSIVGQVIQFWTDA 169 LGEMA P +GSF + + + + G GWLY W W + +E G V+ W A Sbjct: 67 MLGEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPA 126 Query: 170 IPLAAWISIFFVLLTALNLFPVKFYGEIEFWMASIKLTAVIGWIIYAFCMVCGAGKTGPV 229 I + S+ VLL NLF V YGE EFW A K+ A+IG+I F ++ G Sbjct: 127 IDAWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMG------- 179 Query: 230 GFRYWRNGYAWGDGMIVSNNGKYA----IAFINGLINAVFTFQGTELVAITAGEASPKA- 284 + A G ++ +G +A A + I +F+F GTE V I A E+ A Sbjct: 180 ---WIPEREASGLSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQ 236 Query: 285 -LKSAIRKVMFRILVFYVLCMLFIGLLVPYNDPKLTEDGGFTRNSPFLIAMENSGTKVLP 343 + A R V++RI VFY+L + + +VP+NDP L G + R A+E Sbjct: 237 NIAKATRSVIWRIGVFYLLSIFVVISVVPWNDPLLASVGSYQR------ALELMNIPHAK 290 Query: 344 HIFNAVIVTTIISAGNSTVYAGSRIFYGLAESGVAPKIFLSTTKAGVPYVAVLFTAAFGA 403 + + V++ + S NS++Y SR+ Y L G APK T+ AGVP AV+ + GA Sbjct: 291 FLVDMVVLIAVASCMNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGA 350 Query: 404 LGYLVVSNDGTVVFNWLLNIAATAGLVAWGFISVSHIRFMQVLKQRGISRDTLPFKAFFM 463 L +F +LL + L+ + I++S +R ++L+++ I LPF+ + Sbjct: 351 GVTLFSYFMPAGLFQFLLASSGAIALLVYLVIAISQLRMRRMLQRQNIE---LPFRMWLF 407 Query: 464 PYSAYYAAIVVFTVALI 480 P+ + ++VF A + Sbjct: 408 PWLTW--LVIVFISAAL 422 Lambda K H 0.327 0.141 0.451 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: 722 Number of extensions: 39 Number of successful extensions: 5 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: 566 Length of database: 466 Length adjustment: 35 Effective length of query: 531 Effective length of database: 431 Effective search space: 228861 Effective search space used: 228861 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