Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= curated2:Q9V1I4 (364 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 212 bits (539), Expect = 2e-59 Identities = 132/376 (35%), Positives = 205/376 (54%), Gaps = 23/376 (6%) Query: 5 RKRLKIVRGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFE 64 R L G+G ++ D GKRYLD + G V LGH++ ++ + +Q KL P F Sbjct: 17 RPELVFTEGKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFY 76 Query: 65 HEEKEEMLEELSRWVNFEYVYMGNSGTEAVEAALKFARLYTGRK------EIIAMTNAFH 118 +E + +L+ F+ V+ NSG EA E A+K AR + GRK EII M ++FH Sbjct: 77 NEPMLRLARQLTDASCFDKVFFANSGAEANEGAIKLARKW-GRKHKNGAFEIITMDHSFH 135 Query: 119 GRTMGALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAVIFEPIQGESGII 178 GRT+ +SA+ K+ + F P VPGF ND+ + ++ I T A++ EP+QGE G+I Sbjct: 136 GRTLATMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLINDKTVAIMLEPVQGEGGVI 195 Query: 179 PAKEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNGVP 237 PA EF++ LR L + L I DEVQ+G R G A E VEPDI+TLGKGIG GVP Sbjct: 196 PASREFMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGGVP 255 Query: 238 VSLTLTNFDV---ERGKHGSTFGGNPLACKAVAVTLRILRKERLVEKASEKFIKVKGKDV 294 ++ L +V E G G T+ GNP+ + + L ++ +K ++ + + Sbjct: 256 LAALLCKAEVASFEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLREQLL 315 Query: 295 VTT--------RGRGLMIGIVLKKPVG-RYVEE---LQNEGYLVHTSGQRVIRLLPPLII 342 T RG GL+ +VL K +G + VEE +Q +G L+++ ++R +P L + Sbjct: 316 ALTSEFGLGGERGEGLLRALVLNKDIGPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNV 375 Query: 343 SKEKMMEVKSAIEGVI 358 + E++ ++ S + ++ Sbjct: 376 TIEEIDQMISMLRTLL 391 Lambda K H 0.318 0.137 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: 319 Number of extensions: 19 Number of successful extensions: 5 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: 364 Length of database: 395 Length adjustment: 30 Effective length of query: 334 Effective length of database: 365 Effective search space: 121910 Effective search space used: 121910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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