Align Putrescine importer PuuP (characterized)
to candidate PP_2802 PP_2802 Amino acid permease family protein
Query= SwissProt::P76037 (461 letters) >FitnessBrowser__Putida:PP_2802 Length = 443 Score = 350 bits (897), Expect = e-101 Identities = 179/421 (42%), Positives = 263/421 (62%), Gaps = 3/421 (0%) Query: 18 LRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISDGHVPASYLLALAGVLFTAISYGKLV 77 LR+SL + V++ GLA+L P+ VF T+G+++ S +YL+A GV+FTA+SYG+LV Sbjct: 10 LRRSLGPFSVLLFGLAFLAPLIVFGTYGVITQASGNTTAMAYLVAATGVVFTALSYGRLV 69 Query: 78 RQFPEAGSAYTYAQKSINPHVGFMVGWSSLLDYLFLPMINVLLAKIYLSALFPEVPPWVW 137 R FP AGSAYTY +K +N ++GFMVGW++LLDY F+PM+ LL YL+ FPEVP WVW Sbjct: 70 RVFPVAGSAYTYTRKMLNANLGFMVGWAALLDYFFIPMLIWLLGASYLNMAFPEVPQWVW 129 Query: 138 VVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIFLVVQGLHKGEGVGTVWSLQPF 197 + F+ + N+ + + FN L ++VQ+ I+ VFI L V + G G + S +PF Sbjct: 130 ITGFIVSTSLLNVLGIQVANRFNVLLMVVQLVIIAVFIGLCVHYIVAANGPGGLLSAKPF 189 Query: 198 ISENAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPKAIFLTAVYGGVIFIAAS 257 +++ + GA I +SFLGFDA++TLSEET D R +P+AI L A+ GG +++ +S Sbjct: 190 FNQDVPFATSMAGAAIAAYSFLGFDALSTLSEETRDPGRTLPRAILLVALIGGSVYVGSS 249 Query: 258 FFMQLFFPDISRFKDPDAALPEIALYVGGKLFQSIFLCTTFVNTLASGLASHASVSRLLY 317 +FM L P F+ D A EIA +GG LF ++ L V A+G++ ASV RLLY Sbjct: 250 YFMYLAHPS-PTFELVDGAAFEIARMIGGDLFFAVVLTGIIVAHFAAGMSFQASVGRLLY 308 Query: 318 VMGRDNVFPERVFGYVHPKWRTPALNVIMVGIVALSALFFDLVTATALINFGALVAFTFV 377 +GRDN P R+FG +HP+++TPA N+++ G+ + + TAT+L+NFGA +AFT V Sbjct: 309 ALGRDNQLPRRLFGALHPRYKTPAFNILLCGVFGTAGFGLTIATATSLVNFGAFLAFTAV 368 Query: 378 NLSVFNHFWRRKGMNKSWKDHFHYLLMPLVGALTVGVLWVNLESTSLTLGLVWASLGGAY 437 NL + + K +L PL+G +T G + V+L+ +L +G W LG Y Sbjct: 369 NLCALRLTFDAR--VKDGAGLLRGVLFPLIGLVTAGWMLVSLDKDALIMGGCWLGLGLVY 426 Query: 438 L 438 L Sbjct: 427 L 427 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: 667 Number of extensions: 32 Number of successful extensions: 3 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: 443 Length adjustment: 33 Effective length of query: 428 Effective length of database: 410 Effective search space: 175480 Effective search space used: 175480 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