Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Caulo:CCNA_03233 Length = 467 Score = 524 bits (1350), Expect = e-153 Identities = 253/453 (55%), Positives = 321/453 (70%), Gaps = 4/453 (0%) Query: 1 MNSQITNAKTREWQALSRDHHLPPFTDYKQLNEKG-ARIITKAEGVYIWDSEGNKILDAM 59 MN+ I N E + L HHLP D+K + E G +RI+T+A+G YI D +G++ILD M Sbjct: 1 MNAPIRNHDVAELKRLDLAHHLPAQADHKVIAELGGSRIVTRADGCYITDGDGHRILDGM 60 Query: 60 AGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFF 119 AGLWCVNVGYGR+EL AA QM ELP+YN FF+TA PP V+LA IA+ + HVFF Sbjct: 61 AGLWCVNVGYGRKELADAAYEQMLELPYYNTFFKTATPPTVKLAAKIAEKMGGHLTHVFF 120 Query: 120 TGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFP 179 SGSEANDTV R+VRHYW KGQP + V I RWN YHGSTVAGVSLGGMK +H QGD P Sbjct: 121 NSSGSEANDTVFRLVRHYWKLKGQPNRTVFISRWNAYHGSTVAGVSLGGMKHMHVQGDLP 180 Query: 180 IPGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIV 239 IPG+ H+ QPY +GEG P F A +++E KILEVG ENVAAFI EP+QGAGGVI+ Sbjct: 181 IPGVEHVMQPYPFGEGFGEDPAAFRDRAVKEIEDKILEVGPENVAAFIGEPVQGAGGVII 240 Query: 240 PPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIP 299 PPD YWP + + KY IL + DEVICGFGR G+WFG Q+YG PDL+ +AKGL+SGY+P Sbjct: 241 PPDGYWPAVEAVCRKYGILLVCDEVICGFGRLGQWFGHQHYGIKPDLIAMAKGLSSGYLP 300 Query: 300 MGGVVVRDEIV-EVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPY 358 + V V D IV E+ +GG+F HGFTYSGHP AAVAL+NI I+ E +I + + +T PY Sbjct: 301 ISAVGVADHIVAELREKGGDFIHGFTYSGHPTCAAVALKNIEIIEREDLITRTREDTGPY 360 Query: 359 LQKRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDK--GVGMLCREHCFRNGLIM 416 L K L DHPLVGE R +G++ A+E+V+ K T RF DK G + R+ C RNGL++ Sbjct: 361 LAKALARLNDHPLVGETRSLGLIGAVEIVREKGTNHRFLDKEGEAGPIVRDICIRNGLMV 420 Query: 417 RAVGDTMIISPPLVIDPSQIDELITLARKCLDQ 449 RA+ D+++ PPL++ ++IDEL+ + K L + Sbjct: 421 RAIRDSIVCCPPLIVSHAEIDELVGIIEKSLTE 453 Lambda K H 0.320 0.138 0.425 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: 711 Number of extensions: 39 Number of successful extensions: 4 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: 456 Length of database: 467 Length adjustment: 33 Effective length of query: 423 Effective length of database: 434 Effective search space: 183582 Effective search space used: 183582 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