Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate YP_001328245.1 Smed_2580 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000017145.1:YP_001328245.1 Length = 975 Score = 305 bits (782), Expect = 4e-87 Identities = 175/429 (40%), Positives = 255/429 (59%), Gaps = 21/429 (4%) Query: 54 PSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCH 113 P A +LQ+R + +YY+ P I G ++L+D GR YLD + V GH H Sbjct: 547 PDAAALLQRRHRHYARPQKNYYRMPPQIERGWKEHLFDLEGRAYLDMVNNVTLV--GHGH 604 Query: 114 PDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMM 173 + A+ Q LL + + + + A+ +F+E LAA P L V+ VNSGSEAN+LA+ + Sbjct: 605 SRLSAAVGRQWSLL-NTNSRFHYAAVAEFSERLAALAPEGLDTVFLVNSGSEANDLALRL 663 Query: 174 ARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE------IHHVVNPDPYRGV 227 A +G+ ++SL AYHG T+ A++T PQ +H VV+P+ YRG Sbjct: 664 AWAASGARNVVSLLEAYHGW---TVASDAVSTSIADNPQALTTRPDWVHPVVSPNTYRGP 720 Query: 228 FGSDGSL------YAKDVHDHIEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVR 281 F +GS ++ + + E G GK+AGFI+E + G G + L PGYL++VY +VR Sbjct: 721 FRGEGSTGDYVDAVSRKLRELDEKG--GKLAGFISEPVYGNAGGIPLPPGYLEAVYALVR 778 Query: 282 NAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL 341 GGVCIADEVQ G+GR G ++WGF+ Q VVPDI+T+AKG+GNG PLGAV+T IA L Sbjct: 779 ARGGVCIADEVQVGYGRLGHYFWGFEQQGVVPDIITVAKGMGNGHPLGAVITRRTIADAL 838 Query: 342 ASK-ILFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDV 400 + F++ GG+PV S GL VL+++ E E+ VG +L RL+ + +R + G V Sbjct: 839 EEEGYFFSSAGGSPVSSVVGLTVLDILHDEALTENARSVGDYLKGRLEALVERFPLAGAV 898 Query: 401 RGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKD 460 G GL +G+E V DR+ PA ET+ + ++L +LG+++ G H NV +IKPP+C ++ Sbjct: 899 HGMGLYLGVEFVRDRETLEPATEETAAICDRLLDLGVIMQPTGDHLNVLKIKPPLCLARE 958 Query: 461 DADFLVDAL 469 ADF D L Sbjct: 959 SADFFADTL 967 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: 1116 Number of extensions: 45 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: 975 Length adjustment: 39 Effective length of query: 437 Effective length of database: 936 Effective search space: 409032 Effective search space used: 409032 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