Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 224 bits (572), Expect = 3e-63 Identities = 130/381 (34%), Positives = 215/381 (56%), Gaps = 18/381 (4%) Query: 66 VEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPL 125 V ++ G L + G+ F+D G + +GH +P +V+A++ Q K S P Sbjct: 15 VIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPG 74 Query: 126 RAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGK---FTFIATSGAFHG 182 + +A+ L + +FFCN+G E++E +K+A+ Y G+ +A +G+FHG Sbjct: 75 QERVAERL--IKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGSFHG 132 Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242 +++ L+A + + F P+ GF HVP+G++EA R A+ G + AA+++EP+QG Sbjct: 133 RTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAI------GSNTAALLVEPVQG 186 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG+ P YL +R L D+FG L+++DEVQTG+GRTGK+FA E + PD++ LAK L Sbjct: 187 EGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKGL 246 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 GGG P+GA +ATE+ S + P H TFGGNPLA A A A ++ ++ + + Sbjct: 247 GGG-FPVGAVLATEKAASCM--TPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAV 303 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA 422 +L LAR YP + + RG+G+++ ++ V + F +++F +L G +N Sbjct: 304 AALLRGRLDDLARRYPGAIAQVRGQGLMLGLKTV--PVNTEFNAKLFAAGLLAVGAGDN- 360 Query: 423 KTIRIEPPLTLTIEQCELVIK 443 +R+ PPL + + E ++ Sbjct: 361 -VVRLVPPLIIGEAEVERAVE 380 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: 440 Number of extensions: 27 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: 388 Length adjustment: 32 Effective length of query: 427 Effective length of database: 356 Effective search space: 152012 Effective search space used: 152012 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: 50 (23.9 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