Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_012383166.1 BIND_RS00765 acetylornithine transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000019845.1:WP_012383166.1 Length = 405 Score = 227 bits (579), Expect = 5e-64 Identities = 134/394 (34%), Positives = 218/394 (55%), Gaps = 18/394 (4%) Query: 66 VEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPL 125 + ++ G L T G+ F+D GG + ++G+ +P ++ A+ Q K S P Sbjct: 14 IAFERGEGAWLTSTTGERFLDFGGGIAVASLGYSHPHLIKALHEQGDKLWHTSNLFQIPQ 73 Query: 126 RAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHG 182 LA+ L A++ + FF NSG E++E +K A+ Y + G K I GAFHG Sbjct: 74 AERLAERLTAVSFAD--FVFFTNSGAEAMEGVIKTARKYHAACGHPEKNRIITFQGAFHG 131 Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242 ++L ++A + F P LPGF +VPFG++EA++ A+ + A+++EPIQG Sbjct: 132 RTLATIAAAGNEKYLDGFEPRLPGFDNVPFGDLEAVKAAIKP------ETGAILIEPIQG 185 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGG+ + P +L A+RKLCDE G L++LDEVQ+G+GR+GK+FA E V+PD++ +AK + Sbjct: 186 EGGIRVVSPDFLQALRKLCDEQGLLLLLDEVQSGVGRSGKLFAYEWAGVEPDVMAIAKGI 245 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 GGG P+GA +AT E + H +T+GGNPLA + A ++++LE + A E Sbjct: 246 GGG-FPLGAFMATREAAKGMVVG--THGSTYGGNPLATSIGNAVLDIVLEPSFLAHVEAT 302 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA 422 G +L L +P+++ E RG G++ I+ + A+ + V+ AG Sbjct: 303 GVLLQQRLVALRERHPEVIAELRGAGLMRGIKVTLPVADFAAAARAEKLLVIPAGD---- 358 Query: 423 KTIRIEPPLTLTIEQCELVIKAARKALAAMRVSV 456 +R+ PPL + E+ + I+ A AA++ + Sbjct: 359 NVVRLLPPLIIGEEEVDGAIERLDAACAALKARI 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: 447 Number of extensions: 25 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: 405 Length adjustment: 32 Effective length of query: 427 Effective length of database: 373 Effective search space: 159271 Effective search space used: 159271 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 24 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