Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 241 bits (615), Expect = 3e-68 Identities = 145/413 (35%), Positives = 222/413 (53%), Gaps = 12/413 (2%) Query: 58 EVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDIL 117 ++L++R + +GP++ +Y PL+IV G+ +L+D GRRYLD + + V GHCHP ++ Sbjct: 3 DLLKRRARLMGPNVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNNVPHV--GHCHPRVV 60 Query: 118 NAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY 177 +AI Q+++L + T YLH + D+ E L M L V +GSEA ++A+ MAR Sbjct: 61 DAIARQARVL-NTHTRYLHEGVLDYIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAA 119 Query: 178 TGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAK 237 TG +I+ N YHG NT + L+T + P+ H + P P G G+ + Sbjct: 120 TGKTGLIATDNTYHG---NTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVA 176 Query: 238 DVHDHIEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFG 297 +E G VA I I G L G+L+ +R GG+ I+DEVQ GFG Sbjct: 177 RAAAELETAGHG-VAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFG 235 Query: 298 RTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKI-LFNTFGGNPVC 356 R G +WG+Q + PD+VT+ K +GNG P+ VV EI FNTFGG+PV Sbjct: 236 RLGDVFWGYQALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVA 295 Query: 357 SAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRK 416 +A +AVL+V++ E E+ VG + ++RL+ + RH I VRG GL ++LV Sbjct: 296 AAAAMAVLDVLEDEGLVENAKRVGRYTLERLQAL--RHPAIDGVRGYGLAFALDLVD--T 351 Query: 417 DKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDAL 469 D P A + + E+ + +L+ + G ++ +I+PP+ F + D L D L Sbjct: 352 DGAPNTALAAAVTEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRLGDVL 404 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: 463 Number of extensions: 26 Number of successful extensions: 6 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: 413 Length adjustment: 32 Effective length of query: 444 Effective length of database: 381 Effective search space: 169164 Effective search space used: 169164 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