Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate SMc00675 SMc00675 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Smeli:SMc00675 Length = 975 Score = 315 bits (808), Expect = 3e-90 Identities = 192/482 (39%), Positives = 276/482 (57%), Gaps = 45/482 (9%) Query: 20 AISLLRTDFSTSPSIADAPPHIPPFV--HQ----------PRPYKG-------PSADEVL 60 A+ +R T+P + H P F HQ P P G P A +L Sbjct: 499 ALGFMRVQLCTTPEL-----HPPAFAASHQAGAWCRLCPSPSPILGFDCDAALPDAAGLL 553 Query: 61 QKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAI 120 ++R++ +YY+ P I G ++L+D GR YLD + V GH HP + A+ Sbjct: 554 ERRRRHYARPQKNYYRTPPQIERGWKEHLFDVEGRAYLDMVNNVTLV--GHGHPRLSAAV 611 Query: 121 TEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGS 180 Q LL + + + + A+ +F+E LAA P L V+ VNSGSEAN+LA+ +A ++G+ Sbjct: 612 GRQWSLL-NTNSRFHYAAVTEFSERLAALAPEGLDTVFLVNSGSEANDLAIRLAWAHSGA 670 Query: 181 LEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE------IHHVVNPDPYRGVF-GSDGS 233 MISL AYHG T+ A++T PQ +H VV+P+ YRG F G D + Sbjct: 671 RNMISLLEAYHGW---TVASDAVSTSIADNPQALTTRPDWVHPVVSPNTYRGPFRGEDST 727 Query: 234 L-----YAKDVHDHIEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCI 288 + ++ + D E G GK+AGFI+E + G G + L GYL++VY +VR GVCI Sbjct: 728 VGYVDAVSRKLADLDEKG--GKLAGFISEPVYGNAGGIPLPSGYLEAVYAMVRERSGVCI 785 Query: 289 ADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASK-ILF 347 ADEVQ G+GR G H+WGF+ Q VVPDI+T+AKG+GNG PLGAV+T EIA L + F Sbjct: 786 ADEVQVGYGRLGHHFWGFEQQGVVPDIITVAKGMGNGHPLGAVITRREIADALEKEGYFF 845 Query: 348 NTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMV 407 ++ GG+PV S GL VL+++ + QE+ VG+HL RL+ + R ++G V G GL + Sbjct: 846 SSAGGSPVSSVVGLTVLDILHDDALQENARAVGTHLKSRLEALGDRFPLVGAVHGMGLYL 905 Query: 408 GIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVD 467 G+E V DR+ PA ET+ + ++L +LGI++ G H NV +IKPP+C ++ ADF D Sbjct: 906 GVEFVRDRETLEPATEETAAICDRLLDLGIVMQPTGDHLNVLKIKPPLCLARESADFFAD 965 Query: 468 AL 469 L Sbjct: 966 ML 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: 1103 Number of extensions: 52 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 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