Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_022949003.1 H035_RS0110875 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000421465.1:WP_022949003.1 Length = 430 Score = 174 bits (440), Expect = 7e-48 Identities = 126/399 (31%), Positives = 197/399 (49%), Gaps = 18/399 (4%) Query: 14 AMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSI 73 A D H HP+++ A + A+GV + A +L+D MA WC GY + Sbjct: 9 AFDRDHLWHPYSNLP--AHYPVWPVASAQGVRLKLADERELIDGMASWWCAIHGYNHPRL 66 Query: 74 ADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMV 133 A AQL + + F THEPAI L ++ +L P +++VF SGS A + L+M Sbjct: 67 NAAVEAQLGKMA-HVMFGGLTHEPAIELGERLVNLTPTPLDKVFLCDSGSVAVEVALKMA 125 Query: 134 RRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGG--MGFMHQQGDLPIPGIVHIDQPYWF 191 +YW +G KK ++ + YHG T+ ++ G H D +P + P Sbjct: 126 LQYWQARGNSGKKRFLALRGGYHGDTLGAMTVCDPVTGMHHLFSDF-LPRQLFAPHPSC- 183 Query: 192 GEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDSYWNEIKRI 250 G PEA Q L A++LE ++AA I EP QGAGG+ Y ++++ Sbjct: 184 GFHDPWDPEAI-----QPL-AELLERRHHELAAVILEPIVQGAGGMRFYHPEYLKAVRQL 237 Query: 251 LEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVAD 310 ++Y +L I DE+ +GFGRTG FA Q + PD++ + K +T GY+ + + + +A+ Sbjct: 238 CDEYEVLLIADEIATGFGRTGRLFACQHADIAPDILCVGKAITGGYLTLAATLTTPNIAE 297 Query: 311 VL-ISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKV-RTDTGPYLQDRLQTLSA 368 + + G F HG T+ +P+A AVA +I +L E +V R +TG L+ L + Sbjct: 298 TIGQGEAGCFMHGPTFMANPLACAVASASIDLLLESDWQSRVKRIETG--LRRGLAPCAE 355 Query: 369 HPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCR 407 V EVR +G +G +E+ V S + AG+ R Sbjct: 356 LASVKEVRVLGAIGVVEMREPVDLAVITPSFVDAGVWLR 394 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: 488 Number of extensions: 23 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: 430 Length adjustment: 32 Effective length of query: 428 Effective length of database: 398 Effective search space: 170344 Effective search space used: 170344 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