Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate GFF2831 PGA1_c28770 taurine--pyruvate aminotransferase Tpa
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Phaeo:GFF2831 Length = 465 Score = 181 bits (458), Expect = 6e-50 Identities = 133/435 (30%), Positives = 214/435 (49%), Gaps = 44/435 (10%) Query: 80 PLNIVDGKMQYLFDESGRRYLDAFAG-IAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLN 138 P IV+GK ++D++G+ +LDA +G + VN G+ ++ + V +Q+ +L + + Sbjct: 36 PRIIVEGKGMRVWDQNGKEWLDAVSGGVWTVNVGYGREEIAKAVYDQLMKLCYFAQSAGS 95 Query: 139 HAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMA-----KLYTGCQDIVAVRN-GY 192 A F+E L K+PG + V++ NSG+EANE A M K Y G + + R+ Y Sbjct: 96 IPGALFAEKLIEKMPG-MSRVYYNNSGSEANEKAFKMVRQIAHKKYGGKKTKILYRDRDY 154 Query: 193 HGNAAATMGATGQSMWKFNVVQNSVHHALNPD--------PYR----GVFGSDGEKY--- 237 HG+ A M A GQ +N + PD YR G+ G+++ Sbjct: 155 HGSTLAAMSAGGQEE------RNMQYGPFAPDFVKVPHCMEYRKHELGLEHLSGKEFGIA 208 Query: 238 -AKDLQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQS 296 A ++++I + E + GG++E GY + K+ L DEV Sbjct: 209 AANQIEEIILREGPDTVGALCLEPVTAGGGVIEAPEGYWPRVQEICKQYDILLHIDEVVC 268 Query: 297 GFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTR------RSYF-- 348 G RTG ++G++ + + PD VTMAKG+ +G+ A + T E + + +YF Sbjct: 269 GVGRTGTWFGYQHYGIQPDFVTMAKGVASGYAAIACLVTTEAVFDMFKDDASDPMNYFRD 328 Query: 349 -NTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLM 407 +TFGG + A L + +IE E L +N +G+ +K L L EKH++IGDVRG+GL Sbjct: 329 ISTFGGCTAGPAAALVNMQIIEDENLLDNCTAMGARMKSNLEALMEKHQVIGDVRGKGLF 388 Query: 408 LGVELVSDRKLKTP-----ATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDD 462 +G ELV+DR K P A A +Q +GV N +P L T +D Sbjct: 389 IGAELVADRDTKEPVDEKLAQAVVAECGNQNVIIGVTNRSIPGKNNTLCFSPALIVTPED 448 Query: 463 ADFLVEAMDYSMSKM 477 D + +A+D +++K+ Sbjct: 449 VDKITDAVDVALTKV 463 Lambda K H 0.320 0.136 0.403 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: 534 Number of extensions: 29 Number of successful extensions: 7 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: 477 Length of database: 465 Length adjustment: 33 Effective length of query: 444 Effective length of database: 432 Effective search space: 191808 Effective search space used: 191808 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