Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_086510079.1 BZY95_RS11580 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >NCBI__GCF_002151265.1:WP_086510079.1 Length = 474 Score = 374 bits (959), Expect = e-108 Identities = 195/423 (46%), Positives = 272/423 (64%), Gaps = 12/423 (2%) Query: 35 RIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMRELPYYNLFFQTAH 94 R+IT KG+++ D +G + +DG AGL+CV IGYGR E+A+A +Q EL YY+ + ++ Sbjct: 34 RVITGGKGIHIVDKDGREFIDGFAGLYCVNIGYGRTEVAEAIYQQALELSYYHTYVGHSN 93 Query: 95 PPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRINGY 154 P + L++ I +A GM+ V++ GS+ N+T L++VR+Y + G+P KK +ISR GY Sbjct: 94 EPQIALSEKIIALAGPGMSKVYYGLGGSDANETQLKIVRYYNNVLGRPQKKKVISRQRGY 153 Query: 155 HGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWF---GEGGDMTPEEFGIWAANQLEE 211 HGS +A SL G+ H+Q DLP+ GI+H PY++ E M+ EF + A +LEE Sbjct: 154 HGSGLATGSLTGLKAFHDQFDLPLAGILHTEAPYYYHRAAEQEGMSEREFSQFCAQKLEE 213 Query: 212 KILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVADEVICGFGRTGE 271 IL G DTV AFI EP+ G GG++ PP+ YW I+ +LAKYD+L +ADEV+CGFGR G Sbjct: 214 MILAEGPDTVAAFIGEPVLGTGGIVPPPEGYWEAIQAVLAKYDVLLIADEVVCGFGRIGA 273 Query: 272 WFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEG----GDFNHGFTYSGHP 327 FGS YG+KPD++T+AKGLTS Y P+ G+IV D V VL +G G HG+TYSGH Sbjct: 274 DFGSHHYGIKPDLITVAKGLTSAYQPLSGVIVGDRVWSVLEQGTGQYGPIGHGWTYSGHA 333 Query: 328 VAAAVALENIRILREEKIIEHVRAETAPYLQKRLR-ELNDHPLVGEVRGVGLLGAIELVQ 386 + A AL N+ I+ E + + AET YLQ+R++ +HP+VG VRGVG+L A+E Sbjct: 334 LGCAAALANLAIIEREGLTRNA-AETGAYLQQRMQAAFGEHPIVGNVRGVGMLAALEFSV 392 Query: 387 DKATRARY-VGKGVGMICRQFCFDNGLIMRAV--GDTMIIAPPLVITKAEIDELVTKARK 443 D A RA + VG D LI RA+ GD + APPLV T AEIDE+V +A + Sbjct: 393 DPARRAHFDAAHKVGPRIAAAALDENLIARAMPQGDILGFAPPLVATPAEIDEIVARAER 452 Query: 444 CLD 446 ++ Sbjct: 453 AVN 455 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: 633 Number of extensions: 32 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: 454 Length of database: 474 Length adjustment: 33 Effective length of query: 421 Effective length of database: 441 Effective search space: 185661 Effective search space used: 185661 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 24 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