Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Echvi_2790 Echvi_2790 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= reanno::pseudo5_N2C3_1:AO356_13150 (454 letters) >FitnessBrowser__Cola:Echvi_2790 Length = 434 Score = 192 bits (488), Expect = 2e-53 Identities = 130/409 (31%), Positives = 206/409 (50%), Gaps = 29/409 (7%) Query: 36 IITHAKGVYLWDSEGNKILDGMAGLWCVAVGYGREELADAASQQMRELPYYNLFFQTAHP 95 ++ A GV+L +G +++DGM+ W GY L A QQ+ + + +F H Sbjct: 29 VVKKASGVFLELEDGTRLIDGMSSWWSTIHGYQVPALNRAIQQQLENMAHV-MFGGITHR 87 Query: 96 PVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYH 155 P EL++A+ ++ P+G+ HVF++ SGS + ++M YW KGQ +K + ++GYH Sbjct: 88 PAAELTQALLEVVPQGLKHVFYSDSGSVAVEVAMKMALQYWHSKGQGSKNRFATVRSGYH 147 Query: 156 GSTVAGASL-GGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDMSPEEFGVWAANQLEEKIL 214 G T S+ +T MH + + + + P G + PEE + E++L Sbjct: 148 GDTWHDMSVCDPVTGMHSIFNNRLSPQIFLPAPQSTFHG-QLIPEEL------EEVERVL 200 Query: 215 EIGVDNVGAFIAEPI-QGAGGVIVPPDSYWPRMKEILAKYDILFVADEVICGFGRTGEWF 273 + + AFI EPI QGAGG+ Y +K KYDIL +ADE+ GFGRTG+ F Sbjct: 201 SSHHEEIAAFILEPIVQGAGGMRFYHPDYLNSLKTHCEKYDILLIADEIATGFGRTGKLF 260 Query: 274 GTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVLNEG--GDFNHGFTYSGHPVAAA 331 +H + P +M I K LT GY+ + DV +++G G F HG T+ G+P+A A Sbjct: 261 ACEHAAITPDIMCIGKALTGGYMSFAATLCTADVAHTISDGSPGVFMHGPTFMGNPLACA 320 Query: 332 VALENIRIL--RDEKI-IERVHSETAPYLQKRLRELNDHPLVGEVRGVGLLGAIELVQDK 388 AL ++ +L +D K I+ + S +L L L V EVR +G +G +E+ Sbjct: 321 TALASLELLLAKDWKAEIQAIES----HLNDALAGLQTLEAVKEVRVLGAIGVVEM---- 372 Query: 389 ATRKRYEGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVISKAEIDEL 437 + + K + + GL +R G + PP VI+ AE+ +L Sbjct: 373 --KAEVDMKAIQAALTK----RGLWLRPFGKLIYTMPPFVITPAELQQL 415 Lambda K H 0.320 0.139 0.431 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: 491 Number of extensions: 30 Number of successful extensions: 6 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: 454 Length of database: 434 Length adjustment: 32 Effective length of query: 422 Effective length of database: 402 Effective search space: 169644 Effective search space used: 169644 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