Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Caulo:CCNA_03233 Length = 467 Score = 196 bits (497), Expect = 2e-54 Identities = 134/427 (31%), Positives = 226/427 (52%), Gaps = 33/427 (7%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYEN 98 ++ R +G + D DG+ D +G+ +NVG+ + +A +Q + +Y+ F++ Sbjct: 39 IVTRADGCYITDGDGHRILDGMAGLWCVNVGYGRKELADAAYEQMLELPYYNT---FFKT 95 Query: 99 A----IILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFY 148 A + LA K+ E G + V + +SG+EAN+ +LV++ R F++ + Sbjct: 96 ATPPTVKLAAKIAEKMGGHLTH-VFFNSSGSEANDTVFRLVRHYWKLKGQPNRTVFISRW 154 Query: 149 HAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVL 208 +A+HG T A +SL K + G P +PGV H+ P P+ +G E+P +R + Sbjct: 155 NAYHGSTVAGVSLGGMKHMHVQGDLP-IPGVEHVMQPYPFGEGFG----EDPAAFRDRAV 209 Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268 IE+ + V P + A EP+QG GG ++PP G++ A++ +YGILL DEV G Sbjct: 210 KEIEDKILE-VGPENVAAFIGEPVQGAGGVIIPPDGYWPAVEAVCRKYGILLVCDEVICG 268 Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV---IHRADITFDKPGR--HATTFG 322 GR G+++ +H+G++PDLI K + G LP++ V H +K G H T+ Sbjct: 269 FGRLGQWFGHQHYGIKPDLIAMAKGLSSGYLPISAVGVADHIVAELREKGGDFIHGFTYS 328 Query: 323 GNPVAIAAGIEVVEIV--KELLPHVQE-VGDYLHKYLEEFKEKYEVIGDARGLGLAQAVE 379 G+P A ++ +EI+ ++L+ +E G YL K L + + ++G+ R LGL AVE Sbjct: 329 GHPTCAAVALKNIEIIEREDLITRTREDTGPYLAKALARLND-HPLVGETRSLGLIGAVE 387 Query: 380 IVKSKETKEKYPELRDR---IVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIF 436 IV+ K T ++ + IV++ R +++ +SI PPLIV+ EID + I Sbjct: 388 IVREKGTNHRFLDKEGEAGPIVRDICIRNGLMVRAIRDSIVCCPPLIVSHAEIDELVGII 447 Query: 437 EEALKAA 443 E++L A Sbjct: 448 EKSLTEA 454 Lambda K H 0.320 0.141 0.418 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: 620 Number of extensions: 44 Number of successful extensions: 7 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: 445 Length of database: 467 Length adjustment: 33 Effective length of query: 412 Effective length of database: 434 Effective search space: 178808 Effective search space used: 178808 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 (21.7 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