Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Pf1N1B4_3440 Succinylornithine transaminase (EC 2.6.1.81)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3440 Length = 406 Score = 203 bits (516), Expect = 1e-56 Identities = 127/330 (38%), Positives = 178/330 (53%), Gaps = 15/330 (4%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 G+ + + D G+E ID GG + +GH +P +V+A+ Q K S + LA Sbjct: 31 GAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPALRLA 90 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGA 187 L T + FFCNSG E+ EAA KLA+ R K+ +A +FHG++L Sbjct: 91 HKLVDATFAERV--FFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFT 148 Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247 ++ +S + F P + G HVP+ ++ A++ A++ D AV+LEPIQGEGGV+ Sbjct: 149 VNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVS------DKTCAVVLEPIQGEGGVL 202 Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307 YL R+LCD AL++ DEVQTGMGR+GK+FA +H V PDIL AK+LGGG Sbjct: 203 PAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGG-F 261 Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 PI A + TE++ L H TT+GGNPLACA A A I+V+ + K D Sbjct: 262 PIAAMLTTEDLAKHLVVG--THGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKFK 319 Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVD 397 Q+ +Y L E RG G+L+ D Sbjct: 320 TRLEQIGEKY-GLFTEVRGLGLLLGCVLSD 348 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: 373 Number of extensions: 17 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: 406 Length adjustment: 32 Effective length of query: 427 Effective length of database: 374 Effective search space: 159698 Effective search space used: 159698 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