Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate Echvi_2790 Echvi_2790 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Cola:Echvi_2790 Length = 434 Score = 181 bits (459), Expect = 4e-50 Identities = 123/409 (30%), Positives = 202/409 (49%), Gaps = 29/409 (7%) Query: 38 IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97 ++ KA GV++ +G +++D M+ W GY L +A +Q+ + + +F H Sbjct: 29 VVKKASGVFLELEDGTRLIDGMSSWWSTIHGYQVPALNRAIQQQLENMA-HVMFGGITHR 87 Query: 98 PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157 P EL +A+ +V P+G+ HVF++ SGS A + ++M YW +KGQ K +GYH Sbjct: 88 PAAELTQALLEVVPQGLKHVFYSDSGSVAVEVAMKMALQYWHSKGQGSKNRFATVRSGYH 147 Query: 158 GSTVAGVSL-GGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKIL 216 G T +S+ + +H + + + + P G + P+E E++E+ +L Sbjct: 148 GDTWHDMSVCDPVTGMHSIFNNRLSPQIFLPAPQSTFHG-QLIPEEL-----EEVER-VL 200 Query: 217 EVGEENVAAFIAEPI-QGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWF 275 E +AAFI EPI QGAGG+ Y ++ KYDIL IADE+ GFGRTG+ F Sbjct: 201 SSHHEEIAAFILEPIVQGAGGMRFYHPDYLNSLKTHCEKYDILLIADEIATGFGRTGKLF 260 Query: 276 GSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG--GEFYHGFTYSGHPVAAA 333 ++ PD+M I K LT GY+ + ++ ++ G G F HG T+ G+P+A A Sbjct: 261 ACEHAAITPDIMCIGKALTGGYMSFAATLCTADVAHTISDGSPGVFMHGPTFMGNPLACA 320 Query: 334 VALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALEL---VKNK 390 AL ++ +L + +++A +L L V E R +G + +E+ V K Sbjct: 321 TALASLELLLAKDWKAEIQA-IESHLNDALAGLQTLEAVKEVRVLGAIGVVEMKAEVDMK 379 Query: 391 KTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQIDEL 439 + T + GL +R G + PP VI P+++ +L Sbjct: 380 AIQAALT-------------KRGLWLRPFGKLIYTMPPFVITPAELQQL 415 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: 505 Number of extensions: 26 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: 456 Length of database: 434 Length adjustment: 32 Effective length of query: 424 Effective length of database: 402 Effective search space: 170448 Effective search space used: 170448 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