Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate SMc00677 SMc00677 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Smeli:SMc00677 Length = 1017 Score = 335 bits (859), Expect = 4e-96 Identities = 192/430 (44%), Positives = 263/430 (61%), Gaps = 18/430 (4%) Query: 53 GPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHC 112 G +E++++RK+ L P+L Y+KP+ V G+ +L D+ GR YLD F + + GH Sbjct: 583 GRPHEEIIRRRKELLLPNLSISYEKPIKFVRGEGVWLIDDRGRAYLDCFNNVCHI--GHA 640 Query: 113 HPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMM 172 HP ++ A+ Q+ L + T YLH I +AE L A MP L V F NSGSEAN LA+ Sbjct: 641 HPAVVEALARQAGTL-NTNTRYLHDNIVAYAERLTATMPKELAVAAFANSGSEANSLALR 699 Query: 173 MARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE-----IHHVVNPDPYRGV 227 + R +TG + L AYHG + I L+A +K+ G+ +H PD Y Sbjct: 700 LMRAHTGCENAVVLDWAYHGTTQELIDLSA---YKFRRKGGKGQKPHVHVAAVPDSYHAP 756 Query: 228 FG----SDGSLYAKDVHDHIE-YGTSGKVAGF-IAETIQGVGGAVELAPGYLKSVYEIVR 281 G +A++V + I G+ GF +AE+I V G V L GYLK VY +VR Sbjct: 757 AAWPLEEHGKRFAENVAELIAAMRARGEAPGFFLAESIPSVAGQVFLPDGYLKEVYRMVR 816 Query: 282 NAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL 341 AGGVCIADEVQ GFGR GSH+W F+TQ VVPDIVTM K IG+G PL AVVTT EIA+ Sbjct: 817 EAGGVCIADEVQVGFGRVGSHWWAFETQGVVPDIVTMGKPIGDGHPLAAVVTTREIAASF 876 Query: 342 ASKI-LFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDV 400 + + FNTFGGNPV A GLAVL+VI+ E + + ++G+HL+ + +Q+R+++IGDV Sbjct: 877 DNGMEYFNTFGGNPVSCAVGLAVLDVIEGEDLRRNALDIGNHLLTAFRTMQERYEVIGDV 936 Query: 401 RGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKD 460 RG GL +GIELVSDR+ + PA + R+ G+L+G G H NV +++PPM F+K Sbjct: 937 RGLGLFLGIELVSDRRTRAPATEIARAVANGARQRGVLMGTEGPHDNVLKMRPPMIFSKR 996 Query: 461 DADFLVDALD 470 DAD L+ L+ Sbjct: 997 DADHLIAVLE 1006 Lambda K H 0.320 0.138 0.412 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: 1151 Number of extensions: 54 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: 476 Length of database: 1017 Length adjustment: 39 Effective length of query: 437 Effective length of database: 978 Effective search space: 427386 Effective search space used: 427386 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: 54 (25.4 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