Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 169 bits (428), Expect = 2e-46 Identities = 126/404 (31%), Positives = 198/404 (49%), Gaps = 46/404 (11%) Query: 69 LSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKR 128 +S M R ++IV G+ +L+D+ GR YLD AG+AV GH P +V+ + Q Sbjct: 1 MSALMNTYARANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADI 60 Query: 129 LQHPTVLYLNHAIADFSEALASKLPGDLKV--VFFTNSGTEANELALMMAKLYTGCQD-- 184 L H + LY A EALA+KL VFF NSG EA E A+ A+ + G + Sbjct: 61 LWHASNLYRLPA----QEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRP 116 Query: 185 ----IVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKD 240 ++ N +HG AT+ AT Q K ++ A + P+ + G+ Sbjct: 117 ERYRVLTFGNAFHGRTLATISATDQM--KVREGFTPLYDAFDTTPFNDIEGA-------- 166 Query: 241 LQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFAR 300 T A + E IQG GG+ PG+L+ + L I DEVQ+G R Sbjct: 167 -----ARAITPQTAAILVEPIQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGR 221 Query: 301 TGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTA 360 TG+ + E + V PDI+ +AKG+G GFP+GA + T + A +T S+ +T+GGN ++ Sbjct: 222 TGHLFAHELYGVRPDIIAVAKGLGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAV 281 Query: 361 GLAVLNVIEK----EKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDR 416 AVL+ + E ++E AA+V + L E+L L+ ++ +G GLM G+++ Sbjct: 282 ASAVLDAVLAPGFLETVRERAALVDALL-ERL--LRRHSDLFVRAQGHGLMRGLQV---- 334 Query: 417 KLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTK 460 A ++ +++ GV+ G +V R+ PPL ++ Sbjct: 335 ------RASARDVVAHLRDFGVMTVAAG--ADVVRLLPPLTISE 370 Lambda K H 0.320 0.136 0.403 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: 423 Number of extensions: 19 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: 477 Length of database: 392 Length adjustment: 32 Effective length of query: 445 Effective length of database: 360 Effective search space: 160200 Effective search space used: 160200 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