Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_009562813.1 AFE_RS01930 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000021485.1:WP_009562813.1 Length = 388 Score = 183 bits (464), Expect = 1e-50 Identities = 129/406 (31%), Positives = 200/406 (49%), Gaps = 32/406 (7%) Query: 69 PSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQ 128 P + Y + P+ G+ +LYD GRRYLDA AGI GH HP + A+ Q+ L Sbjct: 2 PLMSTYARLPVAFARGEGVWLYDTEGRRYLDALAGIAVCGLGHSHPAVTRALQTQAGQLL 61 Query: 129 HATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY-----TGSLEM 183 H + +Y A ++ L A + +F NSG+EANE A+ +ARL+ ++ Sbjct: 62 HTSNLYRIPAQEKLSDTLCAV--SGMDAAFFCNSGAEANEAAIKIARLHGHGKGIAEPQI 119 Query: 184 ISLRNAYHGGSSNTIGLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHI 243 + NA+HG + T LTA T + + +G + P R +G ++ A + Sbjct: 120 LVFSNAFHGRTLAT--LTA--TGNFRIQEG--FSPLLPGFVRAPYGDLSTVRA------L 167 Query: 244 EYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHY 303 G + +AE +QG GG G+L + E+ G + + DEVQTG GRTG+ + Sbjct: 168 VQANPG-ICAILAEPLQGEGGVRPAPEGFLTGLREVCDAHGLLLMLDEVQTGIGRTGAFF 226 Query: 304 WGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAV 363 Q + PD++++AKG+GNG+P+GA++ A++ TFGG P+ A AV Sbjct: 227 AYQQIPGLRPDVLSLAKGLGNGVPIGAMLAGQSTAALFGPGKHGTTFGGGPLVCAAAQAV 286 Query: 364 LNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKA 423 L+ + +E H +G+ L QRL+ H + ++RG GLMVGIEL Sbjct: 287 LDTMQQEDLPAHAGRMGALLRQRLQKRLGGHPEVLEIRGMGLMVGIELAH---------- 336 Query: 424 ETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDAL 469 + L E+ E G+L+ V R+ PP+ + + D LV L Sbjct: 337 KPERLVERALEAGLLINVTA--EKVIRLLPPLILQEAEIDLLVAGL 380 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: 443 Number of extensions: 19 Number of successful extensions: 3 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: 388 Length adjustment: 32 Effective length of query: 444 Effective length of database: 356 Effective search space: 158064 Effective search space used: 158064 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 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