Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__Caulo:CCNA_03233 Length = 467 Score = 134 bits (336), Expect = 7e-36 Identities = 122/425 (28%), Positives = 186/425 (43%), Gaps = 54/425 (12%) Query: 27 IPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVF--TNE 84 I R G + D G ++D G+ +G+ L A EQ +L + + F Sbjct: 39 IVTRADGCYITDGDGHRILDGMAGLWCVNVGYGRKELADAAYEQMLELPYYNTFFKTATP 98 Query: 85 PALRLAHKLVDATFAE--RVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFH 142 P ++LA K+ + VFF +SG+EAN+ F+L R + + ++ N++H Sbjct: 99 PTVKLAAKIAEKMGGHLTHVFFNSSGSEANDTVFRLVRHYWKLKGQPNRTVFISRWNAYH 158 Query: 143 GRTLFTVNVGGQSKYSDGFGPKITGITHV--PY-------NDLAALK----AAVSDK--- 186 G T+ V++GG I G+ HV PY D AA + + DK Sbjct: 159 GSTVAGVSLGGMKHMHVQGDLPIPGVEHVMQPYPFGEGFGEDPAAFRDRAVKEIEDKILE 218 Query: 187 -----TCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAY 241 A + EP+QG GGV+ Y +C + LLV DEV G GR G+ F + Sbjct: 219 VGPENVAAFIGEPVQGAGGVIIPPDGYWPAVEAVCRKYGILLVCDEVICGFGRLGQWFGH 278 Query: 242 QHYGVTPDILTSAKSLGGGF-PIAAMLTTEDLAKHLVVG--------THGTTYGGNPLAC 292 QHYG+ PD++ AK L G+ PI+A+ +A H+V HG TY G+P Sbjct: 279 QHYGIKPDLIAMAKGLSSGYLPISAV----GVADHIVAELREKGGDFIHGFTYSGHPTCA 334 Query: 293 AVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKG 352 AVA I++I +++ + + + L E R LG L+G V KG Sbjct: 335 AVALKNIEIIEREDLITRTREDTGPYLAKALARLNDHPLVGETRSLG-LIGAVEIVREKG 393 Query: 353 -----------KAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAA 401 + + R GLM+ +A D I P L+V A+ID + E++ Sbjct: 394 TNHRFLDKEGEAGPIVRDICIRNGLMV-RAIRDSIVCCPPLIVSHAEIDELVGIIEKS-- 450 Query: 402 KLTQA 406 LT+A Sbjct: 451 -LTEA 454 Lambda K H 0.320 0.136 0.400 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: 473 Number of extensions: 20 Number of successful extensions: 3 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: 406 Length of database: 467 Length adjustment: 32 Effective length of query: 374 Effective length of database: 435 Effective search space: 162690 Effective search space used: 162690 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