Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate YP_001328243.1 Smed_2578 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000017145.1:YP_001328243.1 Length = 1018 Score = 329 bits (844), Expect = 2e-94 Identities = 188/429 (43%), Positives = 259/429 (60%), Gaps = 18/429 (4%) Query: 53 GPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHC 112 G + +E+++ RK L +L Y+KP+ V G+ +L D+ GR YLD F + + GH Sbjct: 584 GRTHEEIVRLRKDLLLSNLSISYEKPIKFVRGEGVWLIDDRGRAYLDCFNNVCHI--GHA 641 Query: 113 HPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMM 172 HP ++ AI Q+ L + T YLH I +AE L + +P L + F NSGSEAN LA+ Sbjct: 642 HPAVVEAIARQAATL-NTNTRYLHDNIVAYAERLTSTLPKELAIAAFANSGSEANSLALR 700 Query: 173 MARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPL-----PQGEIHHVVNPDPYRGV 227 + R +TG + L AYHG + I L+A +K+ P+ +H PD Y Sbjct: 701 LMRAHTGRENALVLDWAYHGTTQELIDLSA---YKFRRKGGRGPKSHVHVAAVPDSYHAP 757 Query: 228 FG----SDGSLYAKDVHDHIE-YGTSGKVAGF-IAETIQGVGGAVELAPGYLKSVYEIVR 281 G +A+D+ + I G+ GF +AE+I V G V L GYLK VY +VR Sbjct: 758 ADWPAEEHGKRFAEDIAELIAAMRARGEAPGFFLAESIPSVAGQVFLPDGYLKEVYRMVR 817 Query: 282 NAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL 341 +AGGVCIADEVQ GFGR GSH+W F+TQ VVPD+VTM K IG G PL AVVTT EIA+ Sbjct: 818 DAGGVCIADEVQVGFGRVGSHWWAFETQGVVPDVVTMGKPIGAGHPLAAVVTTREIAASF 877 Query: 342 ASKI-LFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDV 400 + + FNTFGGNPV A GLAVL+VI+ E + + E+G++L+ + +Q+R+++IGD+ Sbjct: 878 DNGMEYFNTFGGNPVSCAAGLAVLDVIEGEDLRRNALEIGNYLLAAFRSMQERYEVIGDI 937 Query: 401 RGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKD 460 RG GL +GIELVSDR K PA + R+ G+L+G G H NV +++PPM F+K Sbjct: 938 RGLGLFLGIELVSDRSTKAPATEIARAVSNGARQRGVLMGTEGPHDNVLKMRPPMIFSKR 997 Query: 461 DADFLVDAL 469 DAD L+ L Sbjct: 998 DADHLIAVL 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: 1099 Number of extensions: 55 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: 1018 Length adjustment: 39 Effective length of query: 437 Effective length of database: 979 Effective search space: 427823 Effective search space used: 427823 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 10 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