Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF767 PGA1_c07810 aminotransferase class-III
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Phaeo:GFF767 Length = 457 Score = 333 bits (855), Expect = 5e-96 Identities = 183/456 (40%), Positives = 270/456 (59%), Gaps = 12/456 (2%) Query: 4 KNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCV 63 +N Q +W S H ++F + R++T G ++ D +GN++LD AGL+CV Sbjct: 3 RNDQLDQWDRDSFFHPSTHLAEFAR-GNLPQRVVTGGTGCHIEDRDGNRMLDAFAGLYCV 61 Query: 64 AIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSE 123 +GYGR E+A+A + Q REL YY+ + + LAK I D AP+ M+ V+F SGS+ Sbjct: 62 NVGYGRPEIAEAIADQARELAYYHSYVGHGTEASITLAKMIMDRAPDHMSKVYFGLSGSD 121 Query: 124 GNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVH 183 N+T ++++ +Y I G+P KK IISR GYHGS + SL G+ H + DLP+ +VH Sbjct: 122 ANETNIKLIWYYNNILGRPEKKKIISRWRGYHGSGLMTGSLTGLELFHNKFDLPLAQVVH 181 Query: 184 IPQPYWF-GEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSY 242 PY+F E + +F +LE I G DT+ AFI EP+ G GG++ PP Y Sbjct: 182 TESPYYFRREDLSQSEADFVAHCVAELEALIAREGADTIAAFIGEPVLGTGGIVPPPAGY 241 Query: 243 WPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLI 302 WP I+ +L ++DIL VADEV+ GFGR G FGSD YG++PD++TIAKGLTS Y P+ G I Sbjct: 242 WPAIQAVLERHDILLVADEVVTGFGRLGTMFGSDHYGMRPDLITIAKGLTSAYAPLSGSI 301 Query: 303 VRDEVVEVLNEGGDFN----HGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQ 358 V D++ +VL G D N HG+TYS HP+ AA + N++++ + ++E+ A A YL Sbjct: 302 VSDKMWQVLERGTDENGPIGHGWTYSAHPIGAAAGVANLKLIDQLGLVENAGAIGA-YLN 360 Query: 359 KRLRE-LNDHPLVGEVRGVGLLGAIELVQDKATRARY-VGKGVG-MICRQFCFDNGLIMR 415 +R+ L DHP VG++RG G+L A+E V D+ R + +G I + + +I R Sbjct: 361 DEMRKALGDHPNVGDLRGEGMLCAVEFVADRDDRRFFDASDKIGPQIAAKLLEQDSVIAR 420 Query: 416 AV--GDTMIIAPPLVITKAEIDELVTKARKCLDLTL 449 A+ GD + APP +T+ E D +V + + L Sbjct: 421 AMPQGDILGFAPPFCLTRDEADRVVAATHRAVTAVL 456 Lambda K H 0.320 0.140 0.428 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: 638 Number of extensions: 38 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: 454 Length of database: 457 Length adjustment: 33 Effective length of query: 421 Effective length of database: 424 Effective search space: 178504 Effective search space used: 178504 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