Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 213 bits (543), Expect = 7e-60 Identities = 128/361 (35%), Positives = 188/361 (52%), Gaps = 15/361 (4%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135 L+ +G+ ++D G + +GH +P A+ Q A S P LA+ + Sbjct: 25 LIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSNLYGSPQGEALAQRI-- 82 Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSATA 192 + FF NSG E++E A+K A+ Y G + I AFHG+S+GA+SAT Sbjct: 83 VDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITFKNAFHGRSIGAISATD 142 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252 + R F PLLPGF +V F ++E K D+ A ++E +QGEGG+ Sbjct: 143 QPKMRDGFEPLLPGFDYVKFNDLEGA------IAKIDDETAGFLVETVQGEGGMTAGTVE 196 Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312 ++ +RK CDE G L+ILDE+Q G GRTGKM+A EH + PDIL AK +G G P+GA Sbjct: 197 FIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGIGNG-FPLGAC 255 Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372 +ATEE + H +T+GGNPLA AA A ++V+LE E+ G+ L GF Q Sbjct: 256 LATEEAAKGMTFG--THGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMGERLRAGFEQ 313 Query: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432 L + L E RGKG+++ I+ + + +F + + L+ R+ PPL Sbjct: 314 LIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLT-VAAGENVFRVLPPLV 372 Query: 433 L 433 + Sbjct: 373 I 373 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: 474 Number of extensions: 22 Number of successful extensions: 6 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: 398 Length adjustment: 32 Effective length of query: 427 Effective length of database: 366 Effective search space: 156282 Effective search space used: 156282 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