Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_021560695.1:WP_027490801.1 Length = 444 Score = 240 bits (612), Expect = 8e-68 Identities = 158/405 (39%), Positives = 225/405 (55%), Gaps = 39/405 (9%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 D G F+D + G + GH +P VV AVQ+ AK S + L + LAA+ Sbjct: 52 DVDGNRFLDFMAGIAVCATGHAHPQVVKAVQDAAAKFLHISSDYWHEEMTGLGERLAAVA 111 Query: 138 P-GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA-KST 195 P G SF C SGTE+VE ALKLA+ G+ FI G FHG++ G+LS T+ K T Sbjct: 112 PLGAPAMSFICQSGTEAVEGALKLARYVT---GRPRFIGFLGGFHGRTFGSLSFTSSKYT 168 Query: 196 FRKPFMPLLPGFRHVPFGN---------------IEAMRTALNECKKTGDDVAAVILEPI 240 +K F P L G HVP+ N ++ +R L + +VAA+++EP+ Sbjct: 169 QQKGFSPTLAGVTHVPYPNPYRPLFAGDDQGAAVLDYIRM-LFQRSVPPSEVAAILIEPM 227 Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300 QGEGG + PP G+L +R LCDE G L+I DEVQ+G+GRTG+MFACEH VQPDI+ AK Sbjct: 228 QGEGGYLTPPDGFLAGLRALCDEHGILLIFDEVQSGIGRTGRMFACEHWGVQPDIITSAK 287 Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360 LG G +PIGA IA + + S H T+GGNP+ CAAA AT++ L+ L A Sbjct: 288 GLGSG-LPIGAVIAKKSIMSQW--KRGAHGNTYGGNPVTCAAANATLD-LVRGGLMDNAA 343 Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFAS---EMFRQRVLVAG 417 + GD + R+L R+YP + E RGKG+ + +E ++++ A+ E QR G Sbjct: 344 RVGDHFMARLRELQRDYP-CIGEVRGKGLWIGMELIEDDGKKTPATALCEAVVQRAFHNG 402 Query: 418 TL---NNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA 459 L T+R PPL +++ + + +A+A +R S+++A Sbjct: 403 LLLLSCGTSTVRFMPPLNVSVGEVD-------EAIALLRSSLDQA 440 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: 493 Number of extensions: 32 Number of successful extensions: 10 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: 444 Length adjustment: 33 Effective length of query: 426 Effective length of database: 411 Effective search space: 175086 Effective search space used: 175086 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 Apr 09 2024. 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