Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 172 bits (437), Expect = 2e-47 Identities = 138/426 (32%), Positives = 208/426 (48%), Gaps = 35/426 (8%) Query: 82 VEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGD 141 V G YL D +G+RYLD G GH +++ A+ EQ L A T +L + Sbjct: 17 VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAE 76 Query: 142 -FAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY------TGSLEMISLRNAYHGGS 194 A+ L ++ PG+L VYFV+ GSEA E A+ +AR Y T +I+ R +YHG Sbjct: 77 ALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHG-- 134 Query: 195 SNTIGLTAL--NTWKYPLPQGEIHHVVNPDP-YRGVFGSDGSL---YAKDVHDHIEYGT- 247 NT+G A N W+ + + + P Y V DG Y + V + +E Sbjct: 135 -NTLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEIL 193 Query: 248 ---SGKVAGFIAETIQGV-GGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHY 303 V F+AE + G GAV GY K + EI G + I DEV G GRTG H Sbjct: 194 RLGPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTG-HL 252 Query: 304 WGFQTQDVVPDIVTMAKGIGNGL-PLGAVVTTPEIASVLASKILF----NTFGGNPVCSA 358 + + V PDI+ +AKG+G G P+GA++ + +I + F +T+ G+PV +A Sbjct: 253 FACEADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATA 312 Query: 359 GGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDK 418 GLAV+ + + AE+G L L +H +GD+RGRGL GIELV+DR+ K Sbjct: 313 AGLAVVRALLDRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRESK 372 Query: 419 TPAKAETSV---LFEQLRELGILV-----GKGGLHGNVFRIKPPMCFTKDDADFLVDALD 470 TP + L + E G++ + G +G+ + PP ++D + D L+ Sbjct: 373 TPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKLE 432 Query: 471 YSISRL 476 ++ ++ Sbjct: 433 VALDQV 438 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: 533 Number of extensions: 30 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: 440 Length adjustment: 33 Effective length of query: 443 Effective length of database: 407 Effective search space: 180301 Effective search space used: 180301 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