Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF2392 PGA1_c24230 acetylornithine aminotransferase ArgD
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Phaeo:GFF2392 Length = 394 Score = 219 bits (558), Expect = 1e-61 Identities = 129/365 (35%), Positives = 201/365 (55%), Gaps = 20/365 (5%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-PLRAMLAKTLA 134 L++ G+ F+D G + +GH +P +V A+ +Q A+ H L P + LA L Sbjct: 24 LIEADGRRFLDLAAGIAVNALGHAHPALVKALTDQ-AETLWHVSNLYHIPQQQALADRLV 82 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191 + FF NSGTES E A+K+A+ Y +G + + SG+FHG+S +SA Sbjct: 83 EHSFADTV--FFTNSGTESCELAVKMARKYFHDKGQPERVEILTFSGSFHGRSSAGISAA 140 Query: 192 AKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPP 251 F P+LPGF+H+ FG+++ + A+ D AA+++EP+QGEGG+ P Sbjct: 141 GSEKMTAGFGPMLPGFKHLMFGDLDGVTDAIT------DQTAAILIEPVQGEGGIRPVPD 194 Query: 252 GYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGA 311 L A+R++CDE G L+ILDEVQ G+GRTGK+FA E + PDI+ +AK +GGG P+GA Sbjct: 195 AELKALRQICDEHGLLLILDEVQCGVGRTGKLFAHEWAGITPDIMMVAKGIGGG-FPLGA 253 Query: 312 TIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371 +ATEE S + H +T+GGNPL CA A ++ + + A+ +K +L Sbjct: 254 VLATEEAASGM--TAGTHGSTYGGNPLGCAVGCAVMDHVTDPEFLAEVSRKAGLLRQKLE 311 Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431 L +P + + RG G+++ ++ V + + + V+ +N +R+ PPL Sbjct: 312 GLVASHPQVFEAVRGSGLMLGLKCV--AANTDVVAAGYEAEVVTVPAADN--VVRLLPPL 367 Query: 432 TLTIE 436 TLT E Sbjct: 368 TLTDE 372 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: 394 Number of extensions: 24 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 459 Length of database: 394 Length adjustment: 32 Effective length of query: 427 Effective length of database: 362 Effective search space: 154574 Effective search space used: 154574 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