Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Pf6N2E2_5326 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5326 Length = 396 Score = 223 bits (567), Expect = 1e-62 Identities = 144/389 (37%), Positives = 219/389 (56%), Gaps = 16/389 (4%) Query: 65 AVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD- 123 A+ + G L D G+E++D + G + NVGH +P +V+A+ Q A LH+ L Sbjct: 19 ALSFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQ-AGLLLHTSNLYSI 77 Query: 124 PLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFH 181 + LA+ L L+ L+ +FF NSG E+ E ALKLA+ Y +G + + AFH Sbjct: 78 DWQQRLAQKLTQLSG--LERAFFNNSGAEANETALKLARLYGWHKGIEQPLVVVMDNAFH 135 Query: 182 GKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQ 241 G++LG + A+ + R F L F VPFG++ A+ A+ + + + AV++EPIQ Sbjct: 136 GRTLGTMCASDGPSVRLGFNRLPGDFIKVPFGDLAALE-AIQQAH--AERIVAVLVEPIQ 192 Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301 GE GV L PPGYL A+R+LC L++LDE+QTG+GRTG+ FA +HE + PD++ LAK Sbjct: 193 GESGVQLAPPGYLKALRELCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 252 Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361 LG GV PIGA +A + + P H +TFGGNPLAC + ++ +Q L A Sbjct: 253 LGNGV-PIGACLARGKAAELF--TPGSHGSTFGGNPLACRVGCTVLEIIEQQALVDNARH 309 Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNN 421 +GD LL R + P+ V RG+G+++ IE + + A R L+ + Sbjct: 310 QGDQLLGRLRIELADNPN-VLAIRGQGLMIGIEL--KQPVRDLALRAARDHGLLI-NITR 365 Query: 422 AKTIRIEPPLTLTIEQCELVIKAARKALA 450 +TIR+ PPLT+ + E++++ + LA Sbjct: 366 GQTIRLLPPLTIDGREVEMIVRGVSRCLA 394 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: 434 Number of extensions: 23 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: 396 Length adjustment: 32 Effective length of query: 427 Effective length of database: 364 Effective search space: 155428 Effective search space used: 155428 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