Align Putrescine importer PuuP (characterized)
to candidate AO356_01520 AO356_01520 porin
Query= SwissProt::P76037 (461 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01520 Length = 449 Score = 272 bits (695), Expect = 2e-77 Identities = 153/440 (34%), Positives = 247/440 (56%), Gaps = 11/440 (2%) Query: 7 LNIAAQPGKTRLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISDGHVPASYLLALAGV 66 ++I A K L++ L L +V+ G+ ++ P+ F +G V+ + G VP +Y++ + + Sbjct: 1 MSIEAFGYKQELKRGLSLTDLVVYGMIFMIPIAPFGVYGYVNAEAPGMVPLAYIIGMVAM 60 Query: 67 LFTAISYGKLVRQFPEAGSAYTYAQKSINPHVGFMVGWSSLLDYLFLPMINVLLAKIYLS 126 LFTA+SYG + R FP AGS Y+YAQ+ +NPHVGF+ GW LLDYL +P + + A + L+ Sbjct: 61 LFTALSYGSMARAFPVAGSVYSYAQRGLNPHVGFIAGWLMLLDYLLIPPLLYVYAAMALN 120 Query: 127 ALFPEVPPWVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIFLVVQGLHKGE 186 L+P++P +++ F+ T NL+ + A N +F+L Q+ ++ +F+F LH G Sbjct: 121 HLYPDIPKVGFILAFLVSATFVNLRGITFTARMNIIFLLAQLVVLGIFLFYAWNALHGGA 180 Query: 187 GVGTVWSLQPFISENAHLIPIITGATIVCFSFLGFDAVTTLSEETP-DAARVIPKAIFLT 245 G G + + E+ + ++ +I SFLGFDA++TL+EE D R + KA +T Sbjct: 181 GHGQLTLAPLYSPEHFNFALLMQAVSIAVLSFLGFDAISTLAEEIKGDPGRSVGKAALVT 240 Query: 246 AVYGGVIFIAASFFMQLFFPDISRFKDPDAALPEIA-LYVGGKLFQSIFLCTTFVNTLAS 304 + G IF+ ++ + FK D A EIA L G L + T +A Sbjct: 241 LLVMGAIFVVQTWIATDLAAGMG-FKSADTAFYEIAELAAGSWLATLTAVATALAWGVAV 299 Query: 305 GLASHASVSRLLYVMGRDNVFPERVFGYVHPKWRTPALNVIMVGIVAL--SALFFDLV-T 361 + S A+VSRLL+ M RD P +V VHPK TP +++ +V +++L LF + V T Sbjct: 300 AITSQAAVSRLLFGMARDGQLP-KVLAKVHPKHNTPYMSIYLVAVLSLLICYLFINAVDT 358 Query: 362 ATALINFGALVAFTFVNLSVFNHFWRRKGMNKSWKDHFHYLLMPLVGALTVGVLWVNLES 421 T+L+NFGAL F ++++V NH+WRR+ + +++ PLVG + V + N+ Sbjct: 359 LTSLVNFGALSGFMLLHITVINHYWRRQRSGQL----IRHVICPLVGFVIVAAIMYNMGV 414 Query: 422 TSLTLGLVWASLGGAYLWYL 441 + LGL+W + G YL L Sbjct: 415 AAQKLGLIWIAAGVVYLCLL 434 Lambda K H 0.328 0.141 0.437 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: 618 Number of extensions: 42 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: 461 Length of database: 449 Length adjustment: 33 Effective length of query: 428 Effective length of database: 416 Effective search space: 178048 Effective search space used: 178048 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: 51 (24.3 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