Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 186 bits (473), Expect = 9e-52 Identities = 129/389 (33%), Positives = 201/389 (51%), Gaps = 21/389 (5%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130 G + + D +G+EFID GG + +GH +P +V A+ +Q K S + + LA Sbjct: 29 GEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALRLA 88 Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAY---QSPRGKFTFIATSGAFHGKSLGA 187 KTL LT + FF NSG E+ EAA KLA+ Y + K I+ +FHG++L Sbjct: 89 KTLCDLTFAERV--FFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFT 146 Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247 +S + + + F P G H F ++E+++ +++ K A+++EPIQGEGGV+ Sbjct: 147 VSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEK-----TCAIVVEPIQGEGGVM 201 Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307 +L +R LCDE AL++ DEVQ+G+GR+G +A + V PDIL AK LGGG Sbjct: 202 PGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGG-F 260 Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367 P+ A + T +V + L H +T+GGN LACA A ++ + + + + + D L Sbjct: 261 PVAAMLTTAKVAASL--GVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLR 318 Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG--YNFASEMFRQRVLVAGTLNNAKTI 425 G + Y + E RG G+L+ + G +F + + V+V + A I Sbjct: 319 KGMMDIGERY-GVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMV--LVAGANVI 375 Query: 426 RIEPPLTLTIEQCELVI---KAARKALAA 451 R+ P L + EL + +AA K L A Sbjct: 376 RLAPSLIIPEPDIELALERFEAAVKKLTA 404 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: 410 Number of extensions: 23 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: 404 Length adjustment: 32 Effective length of query: 427 Effective length of database: 372 Effective search space: 158844 Effective search space used: 158844 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