Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 15422 b1302 GABA aminotransferase, PLP-dependent (NCBI)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Keio:15422 Length = 421 Score = 198 bits (503), Expect = 3e-55 Identities = 141/403 (34%), Positives = 217/403 (53%), Gaps = 30/403 (7%) Query: 69 QAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM 128 Q+ TL D +G E+ID G + N GHR+P +V+AV+ QL +Q H+ + P + Sbjct: 27 QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQL-QQFTHTAYQIVPYESY 85 Query: 129 --LAKTLAALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKS 184 LA+ + AL P G+ K +FF +G E+VE A+K+A+A+ G IA SG FHG++ Sbjct: 86 VTLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAHTGRPG---VIAFSGGFHGRT 141 Query: 185 LGALSATAK-STFRKPFMPLLPGFRHVPF-GNIEAMRT-----ALNECKKT---GDDVAA 234 ++ T K + ++ F P HVP+ ++ + T A+ K+ VAA Sbjct: 142 YMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAA 201 Query: 235 VILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPD 294 +I EP+QGEGG + P + A+R+LCDE G +MI DEVQ+G RTGK+FA +H +PD Sbjct: 202 IIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPD 261 Query: 295 ILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQN 354 ++ +AK+L GG MP+ + + P T+ GNPLA AAA A +N++ +++ Sbjct: 262 LMTMAKSLAGG-MPLSGVVGNANIMDA--PAPGGLGGTYAGNPLAVAAAHAVLNIIDKES 318 Query: 355 LPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFA--SEMFRQR 412 L +A Q G L + A+E + RG G ++A+EF D + G A ++ +QR Sbjct: 319 LCERANQLGQRLKNTLID-AKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQR 377 Query: 413 VLVAGTL-----NNAKTIRIEPPLTLTIEQCELVIKAARKALA 450 L G L IR PLT+ Q + +K + AL+ Sbjct: 378 ALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 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: 434 Number of extensions: 19 Number of successful extensions: 6 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: 421 Length adjustment: 32 Effective length of query: 427 Effective length of database: 389 Effective search space: 166103 Effective search space used: 166103 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