Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 193 bits (491), Expect = 8e-54 Identities = 123/350 (35%), Positives = 187/350 (53%), Gaps = 24/350 (6%) Query: 70 AGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAM 128 AG L+D G+ ++D GG + +GH + V++AVQ Q+ K H+ L Sbjct: 18 AGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAEA 77 Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFT---FIATSGAFHGKSL 185 LA L + PG L +F + G+E+ EAA+KLA+ Y RG T IA ++HG +L Sbjct: 78 LADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNTL 137 Query: 186 GALSATAKSTFRKPFMPLL-------PGFRHVPFGNIEAM----RTALNECKKT-----G 229 GAL+A + R+ F PLL P + +V G+ E+ + NE + Sbjct: 138 GALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLGP 197 Query: 230 DDVAAVILEPIQGE-GGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEH 288 + V A + EP+ G G + GY +R++CD++G L+ILDEV GMGRTG +FACE Sbjct: 198 ETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACEA 257 Query: 289 ENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNP--FLHTTTFGGNPLACAAALAT 346 + V PDILC+AK LG G PIGA + + +++ + F H T+ G+P+A AA LA Sbjct: 258 DGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLAV 317 Query: 347 INVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFV 396 + LL++ L ++ + G+ L ++P V + RG+G+ IE V Sbjct: 318 VRALLDRGLVQRSAEMGETLHAALVARFGQHPH-VGDLRGRGLFRGIELV 366 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: 493 Number of extensions: 27 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: 440 Length adjustment: 33 Effective length of query: 426 Effective length of database: 407 Effective search space: 173382 Effective search space used: 173382 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