Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase
Query= BRENDA::A0A3B6KM96 (472 letters) >FitnessBrowser__Cup4G11:RR42_RS16955 Length = 395 Score = 210 bits (534), Expect = 8e-59 Identities = 128/385 (33%), Positives = 209/385 (54%), Gaps = 12/385 (3%) Query: 59 MVFSKGEGSHILDPEGNKYIDFLSAYSAVNQGHCHPKVLRALIEQAERLTLSSRAFYNDK 118 +VF++G+GS + D G +Y+DF+ ++ GH + ++ AL++Q+++L S AFYN+ Sbjct: 20 LVFTEGKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFYNEP 79 Query: 119 FPVFAQYLTSMFGYDMMLPMNTGAEGVETAIKLARKWGYEKKNIPKNEALIVSCCGCFHG 178 A+ LT +D + N+GAE E AIKLARKWG + KN I++ FHG Sbjct: 80 MLRLARQLTDASCFDKVFFANSGAEANEGAIKLARKWGRKHKN---GAFEIITMDHSFHG 136 Query: 179 RTLGVISMSCDNDATRGFGPLVPGHLKVDFGDIDGLEKIFKEHGDRICGFLFEPIQGEAG 238 RTL +S S F P VPG K D D+ +EK+ D+ + EP+QGE G Sbjct: 137 RTLATMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLI---NDKTVAIMLEPVQGEGG 193 Query: 239 VIIPPDGYLKAVRDLCSRHNILMIDDEIQTGIARTGKMLACDWEGVRPDMVILGKALGAG 298 VI +++ +R L +H +L I DE+QTG R G M A + GV PD++ LGK +G G Sbjct: 194 VIPASREFMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGG 253 Query: 299 VVPVSAVLADKDIMLCIKPGEHGSTFGGNPLASAVAIASLKVVKDEGLVERAAELGQEFR 358 VP++A+L ++ + G+ G T+ GNP+ +AV A + + G ++ + G R Sbjct: 254 -VPLAALLCKAEV-ASFEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLR 311 Query: 359 DQLRKVQQKFPDIIREIRGRGLLNAVDLSSKALYPASAYDICIKLKERGILAKPTHDTII 418 +QL + +F + RG GLL A+ L +K + P + ++ +G+L ++ Sbjct: 312 EQLLALTSEFG--LGGERGEGLLRALVL-NKDIGP-QLVEEARDMQPQGLLLNSPRPNLL 367 Query: 419 RLAPPISISPEELTEASKALSDVLE 443 R P ++++ EE+ + L +L+ Sbjct: 368 RFMPALNVTIEEIDQMISMLRTLLK 392 Lambda K H 0.321 0.138 0.410 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: 428 Number of extensions: 22 Number of successful extensions: 6 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: 472 Length of database: 395 Length adjustment: 32 Effective length of query: 440 Effective length of database: 363 Effective search space: 159720 Effective search space used: 159720 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 Apr 09 2024.
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