Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Length = 459 Score = 170 bits (431), Expect = 8e-47 Identities = 123/384 (32%), Positives = 193/384 (50%), Gaps = 33/384 (8%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLR----AMLAK 131 L D +G+ FID GG + N GH + V++AV+ QL L++ + + + Sbjct: 65 LWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQL---DLYTHTCFQVVAYEPYVEVCE 121 Query: 132 TLAALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSA 190 L L PG K S +G E+VE A+K+A+AY G IA +G +HG++ L Sbjct: 122 RLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPG---VIAFTGGYHGRTNLTLGL 178 Query: 191 TAK-STFRKPFMPLLPGFRHVPFGNI---EAMRTALNECKKT------GDDVAAVILEPI 240 T K + ++ F P H F N ++ AL+ + + VAA I+EP+ Sbjct: 179 TGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKNDIEPERVAAFIVEPV 238 Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300 QGEGG + PP +++ ++ L D +G L+I DEVQTG GRTG FA E V PD++ AK Sbjct: 239 QGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWFASEQWPVAPDLITTAK 298 Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360 +L GG P+ + +V P T+ G+P+ACAA+LA I ++ L A+++ Sbjct: 299 SLAGG-FPLAGVVGRADVMDA--PAPGGLGGTYAGSPVACAASLAVIEAFAQEKLLARSQ 355 Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDN--------EIGYNFASEMFRQR 412 G +L+ + LA P + + RG G ++AIE +N + +E R+ Sbjct: 356 DMGALLVRSLKDLAARIP-AIGDVRGLGAMVAIELFENGDLSRPDAALTKQVVAEAARRG 414 Query: 413 VLVAGTLNNAKTIRIEPPLTLTIE 436 +++ + IRI PLT + E Sbjct: 415 LILLSCGTHGNVIRILVPLTASDE 438 Lambda K H 0.320 0.135 0.393 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: 456 Number of extensions: 22 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: 459 Length of database: 459 Length adjustment: 33 Effective length of query: 426 Effective length of database: 426 Effective search space: 181476 Effective search space used: 181476 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