Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 251 bits (640), Expect = 4e-71 Identities = 148/383 (38%), Positives = 220/383 (57%), Gaps = 29/383 (7%) Query: 80 QGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ---ELLDPLRAMLAKTLAAL 136 +G+++ID + G G+ NVGHR+P V+ A+Q+QL K +H E + + LAK L Sbjct: 35 KGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKY-MHLMVYGEYVQSPQTQLAKALTDT 93 Query: 137 TPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTF 196 P KL + NSG+E+VE ALKLAK Y G+ ++ A+HG S GALS F Sbjct: 94 LPKKLDNVYLVNSGSEAVEGALKLAKRYT---GRREILSCVNAYHGSSHGALSVGGNEIF 150 Query: 197 RKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTA 256 ++ + PLLPG RH+ F + + + ++ AA+++E +QGE G+ + Y A Sbjct: 151 KRAYRPLLPGIRHLDFNEPDQL-------DQITEETAAIMVETVQGEAGIRVGTKEYFKA 203 Query: 257 VRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATE 316 +R CDE G L+ILDE+Q G GRTGK +A +H ++ PDI+ AK +GGG MPIGA IA + Sbjct: 204 LRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGG-MPIGAFIAPQ 262 Query: 317 EVFSVLFDNPFL-HTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAR 375 + SV +NP L H TTFGG+P++CAAALATI++L ++ L E+K ++ Sbjct: 263 SIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHLNH--- 319 Query: 376 EYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTI 435 +QE R KG++MA++F E+ ++ L ++RI PPLT+T Sbjct: 320 ---PKIQEIRNKGLMMAVKFEAFEVLKPIIDRAIELGIITDWFLFCEDSMRIAPPLTITD 376 Query: 436 EQCELVIKAARKALAAMRVSVEE 458 E+ E KA A + S++E Sbjct: 377 EEIE-------KACAIILQSIDE 392 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: 421 Number of extensions: 29 Number of successful extensions: 9 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: 393 Length adjustment: 32 Effective length of query: 427 Effective length of database: 361 Effective search space: 154147 Effective search space used: 154147 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