Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >MicrobesOnline__882:208056 Length = 542 Score = 234 bits (596), Expect = 7e-66 Identities = 141/447 (31%), Positives = 235/447 (52%), Gaps = 17/447 (3%) Query: 7 QTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIG 66 +T ++L + H PF+ + P II A G +L D++GN+ LDG++ LW G Sbjct: 57 RTARLRSLDAAHVWHPFTQMRDWMGSEPCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHG 116 Query: 67 YGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGND 126 + + +A +Q+ + + L P +ELA ++ IAP G+ VF++ SGS + Sbjct: 117 HRHPHIDEAIRRQLDRVAHSTLL-GLGGTPSIELAARLTAIAPAGLTRVFYSDSGSTAVE 175 Query: 127 TMLRMVRHYW--AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184 L++ Y A +G + +++ N YHG T+ SLGGM+ H + V Sbjct: 176 AALKIAFQYHRQAPEGDARRTRVMAFSNAYHGDTIGSVSLGGMSLFHGIYGPLLFDPVRA 235 Query: 185 PQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244 P P+ + D+ PE G+ ++E + G + + +QGA G+++ P + Sbjct: 236 PAPHCYRCPADLRPETCGMACLGEVERLMRHHGHELCAVVVEPLVQGAAGMLVQPRGWLR 295 Query: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304 ++++ ++ + VADEV GFG+TG F + G+ PDM+ +AKG+T GY+P+ +V Sbjct: 296 GLRDLCDRHGVFMVADEVAVGFGKTGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLVT 355 Query: 305 DEVVE-VLNEGGDFN---HGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360 + + + L DF HG TY+G+ +A A AL ++ + EE+ +E +R L Sbjct: 356 EHIHDGFLGGYADFRTFFHGHTYTGNALACAAALASLDVFEEERTLETLRPR-IERLATL 414 Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARY-----VGKGVGMICRQFCFDNGLIMR 415 L LND P VG++R VG++ IELV D+ TR Y +G V + R+ G+I+R Sbjct: 415 LAPLNDLPHVGDIRRVGVMTGIELVADRETRTPYRPEERIGHRVTLEARR----RGVIVR 470 Query: 416 AVGDTMIIAPPLVITKAEIDELVTKAR 442 +GD M++ PPL IT+ E++ LV R Sbjct: 471 PLGDVMVLMPPLSITETELETLVHTVR 497 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: 639 Number of extensions: 33 Number of successful extensions: 7 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: 542 Length adjustment: 34 Effective length of query: 420 Effective length of database: 508 Effective search space: 213360 Effective search space used: 213360 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: 52 (24.6 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