Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 209 bits (532), Expect = 1e-58 Identities = 143/381 (37%), Positives = 210/381 (55%), Gaps = 33/381 (8%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133 L D +G FID GG + N GHR+P ++ AV+ QL + H+ ++ P + LA+ L Sbjct: 34 LWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFT-HTCAMVTPYESFVTLAERL 92 Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 AL PG K + F +G E+VE A+K+A+A+ G IA SGAFHG++L A++ T Sbjct: 93 NALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPG---VIAFSGAFHGRTLLAMALTG 149 Query: 193 KST-FRKPFMPLLPGFRHVPFGN------IEAMRTALNECKKTGDD---VAAVILEPIQG 242 K ++ F P H PF N ++ AL + K+ D VAA+I+EP+QG Sbjct: 150 KVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQLFKSDVDATRVAAIIVEPVQG 209 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG + PP +L A+RK+CDE G L+I+DE+QTG RTGKMFA EH V+PD++ +AK+L Sbjct: 210 EGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKMFAIEHSGVEPDLMTMAKSL 269 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 GG P+ A E+ P T+ G+PLA AALA ++V+ E+ L ++ Sbjct: 270 AGG-FPLSAVTGKAEIMDAPI--PGGIGGTYAGSPLATTAALAVLDVIEEEKLIQRSNDL 326 Query: 363 GDMLLDGFRQLA-REYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV-------- 413 G+ + FR +A R ++ + R G ++A+E V + A+E+ + V Sbjct: 327 GERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEPAAELTKALVAKAAEKGL 386 Query: 414 --LVAGTLNNAKTIRIEPPLT 432 L GT N IRI PLT Sbjct: 387 VLLSCGTYGN--VIRILVPLT 405 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: 433 Number of extensions: 19 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: 459 Length of database: 428 Length adjustment: 32 Effective length of query: 427 Effective length of database: 396 Effective search space: 169092 Effective search space used: 169092 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