Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_041243352.1 GLOV_RS11140 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000020385.1:WP_041243352.1 Length = 449 Score = 241 bits (616), Expect = 3e-68 Identities = 144/448 (32%), Positives = 240/448 (53%), Gaps = 10/448 (2%) Query: 12 LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71 LQ+ D + HPFT D VI R EG ++ D+ G++ LD +A +W G+ Sbjct: 6 LQSWDKQYVWHPFTQMQDWLAEEPLVIVRGEGSWLIDSDGSRYLDGVASMWTNVHGHSHP 65 Query: 72 SIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLR 131 ++ A Q L ++ E +I LA ++ +AP + +VF++ +GS A + L+ Sbjct: 66 ALNKALADQAARLE-HSTLLGLAGEQSILLAKQLIEIAPAGLRKVFYSDNGSTAVEVGLK 124 Query: 132 MVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWF 191 M +Y KG P + + ++AYHG T+ S+GG+ H + + PY + Sbjct: 125 MAYQYHCHKGEPQRSRFLRLQHAYHGDTIGSMSVGGISIYHDTFKPLLFSTIEAPAPYCY 184 Query: 192 GEGRDMS-PEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDSYWNEIKR 249 S P A G+ +ALE + E E +A + EP QGAGG+++ P Y +++ Sbjct: 185 RCPMGQSDPAACGMACLEALEQLMCEHRE-YLAGMLMEPLLQGAGGMLVHPAGYLKGVRQ 243 Query: 250 ILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVA 309 + ++Y +L I DEV +GFGRTG+ FA Q G+ PD++ I+KG+ +GY+P+ + ++ + Sbjct: 244 LCDRYGVLLITDEVATGFGRTGSMFACQQEGVTPDIMAISKGLCAGYLPLAATLATEEIY 303 Query: 310 DVLISDGGE---FAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTL 366 + + E F HG T++G+P+A AVAL ++ + EE L++ V L LQ L Sbjct: 304 QAFLGNYAELKTFFHGHTFTGNPLACAVALRSLELFEETGLLESV-GQRSKQLTALLQQL 362 Query: 367 SAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGM-LCREACIESGLVMRAVGDTMI 425 HP VG +R G+ IELV DK + + E G+ +C+EA G+ R +G+T++ Sbjct: 363 EDHPHVGNLRQCGLAAGIELVQDKATKAAYPWEEKRGVRVCQEA-RRHGVFSRPLGNTVV 421 Query: 426 ISPPLCITRDEIDELIFKASQALSLTLE 453 + PPL IT DE+ L+ ++A+ + + Sbjct: 422 VFPPLAITEDELAFLMEGLNKAIRVVTD 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: 484 Number of extensions: 33 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: 460 Length of database: 449 Length adjustment: 33 Effective length of query: 427 Effective length of database: 416 Effective search space: 177632 Effective search space used: 177632 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