Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF767 PGA1_c07810 aminotransferase class-III
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Phaeo:GFF767 Length = 457 Score = 317 bits (811), Expect = 7e-91 Identities = 164/420 (39%), Positives = 251/420 (59%), Gaps = 9/420 (2%) Query: 37 RIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAH 96 R++T G +I D +GN++LDA AGL+CVNVGYGR E+ +A Q REL +Y+ + Sbjct: 33 RVVTGGTGCHIEDRDGNRMLDAFAGLYCVNVGYGRPEIAEAIADQARELAYYHSYVGHGT 92 Query: 97 PPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGY 156 + LAK I D AP+ M+ V+F SGS+AN+T ++++ +Y G+P+KK +I RW GY Sbjct: 93 EASITLAKMIMDRAPDHMSKVYFGLSGSDANETNIKLIWYYNNILGRPEKKKIISRWRGY 152 Query: 157 HGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWY-GEGGDMSPDEFGVWAAEQLEKKI 215 HGS + SL G++ H + D P+ +VH PY++ E S +F +LE I Sbjct: 153 HGSGLMTGSLTGLELFHNKFDLPLAQVVHTESPYYFRREDLSQSEADFVAHCVAELEALI 212 Query: 216 LEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWF 275 G + +AAFI EP+ G GG++ PP YWP I+ +L ++DIL +ADEV+ GFGR G F Sbjct: 213 AREGADTIAAFIGEPVLGTGGIVPPPAGYWPAIQAVLERHDILLVADEVVTGFGRLGTMF 272 Query: 276 GSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG----GEFYHGFTYSGHPVA 331 GS +YG PDL+ IAKGLTS Y P+ G +V D++ +VL +G G HG+TYS HP+ Sbjct: 273 GSDHYGMRPDLITIAKGLTSAYAPLSGSIVSDKMWQVLERGTDENGPIGHGWTYSAHPIG 332 Query: 332 AAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKK 391 AA + N++++ + ++E A A + + L DHP VG+ RG GM+ A+E V ++ Sbjct: 333 AAAGVANLKLIDQLGLVENAGAIGAYLNDEMRKALGDHPNVGDLRGEGMLCAVEFVADRD 392 Query: 392 TRERF--TDKGVGMLCREHCFRNGLIMRAV--GDTMIISPPLVIDPSQIDELITLARKCL 447 R F +DK + + ++ +I RA+ GD + +PP + + D ++ + + Sbjct: 393 DRRFFDASDKIGPQIAAKLLEQDSVIARAMPQGDILGFAPPFCLTRDEADRVVAATHRAV 452 Lambda K H 0.320 0.138 0.425 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: 653 Number of extensions: 33 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: 456 Length of database: 457 Length adjustment: 33 Effective length of query: 423 Effective length of database: 424 Effective search space: 179352 Effective search space used: 179352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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