Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate H281DRAFT_06342 H281DRAFT_06342 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__Burk376:H281DRAFT_06342 Length = 473 Score = 340 bits (873), Expect = 5e-98 Identities = 187/453 (41%), Positives = 264/453 (58%), Gaps = 9/453 (1%) Query: 9 ISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGY 68 I +L D H +HP + RG V+E A G ++ DA GN+LLDA +GLWCVNVGY Sbjct: 3 IQSLIEADRQHLIHPVINYRAHEARGVTVLESASGAFLRDAAGNELLDAFSGLWCVNVGY 62 Query: 69 GRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDT 128 G++SI +AA AQ++ LP+ ++F EPAI LA K+AS+AP + V+FT GS+A D+ Sbjct: 63 GQQSIVEAATAQMKKLPYATSYFHFGSEPAIELAQKLASVAPASLQHVYFTLGGSDAVDS 122 Query: 129 NLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQP 188 +R + Y++ G PSKK II+ + YHGS+ GA L + H+ DLP+P H+ P Sbjct: 123 AIRFITHYFNATGRPSKKHIIALQRGYHGSSSMGAGLTALPAFHRNFDLPLPNQHHLPSP 182 Query: 189 YWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIK 248 Y + A + ALEAK+ ELG D VAAF EP QG+GGVI+PP + ++ Sbjct: 183 YAY-RSNFADDAALIAASVAALEAKVAELGADNVAAFFCEPIQGSGGVIVPPFGWLKAMR 241 Query: 249 RILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRV 308 K ILF+ DEVI+GFGRTG FA Q ++PDL+T+AKG+T+GY PMG V++SD + Sbjct: 242 ESCRKLGILFLADEVITGFGRTGPLFACQGESVEPDLMTVAKGLTAGYAPMGAVLMSDEI 301 Query: 309 ADVLISDGGE--FAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTL 366 + E HG TYS HPV+AA+ LE +R+ E L+ P L L Sbjct: 302 YQGIADGDAEAIVGHGHTYSAHPVSAAIGLEVLRLYHEGGLLAN-GAARAPRFARGLDAL 360 Query: 367 SAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI- 425 HPLVG+ R G++GA+ELV++K S +F + A E+ L+ RA GD ++ Sbjct: 361 LEHPLVGDSRHRGLLGALELVSNKDSKAQFDPALKLSERIAAAAYENRLIFRAFGDNILG 420 Query: 426 ISPPLCITRDEIDELIFKASQALSLTLEKIAAR 458 +P L T + D + + L TL+ + A+ Sbjct: 421 FAPALSYTESDFDMMF----ERLEKTLDDVLAQ 449 Lambda K H 0.321 0.137 0.408 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: 538 Number of extensions: 15 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: 460 Length of database: 473 Length adjustment: 33 Effective length of query: 427 Effective length of database: 440 Effective search space: 187880 Effective search space used: 187880 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