Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate HSERO_RS00035 HSERO_RS00035 4-aminobutyrate aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__HerbieS:HSERO_RS00035 Length = 442 Score = 278 bits (711), Expect = 3e-79 Identities = 173/424 (40%), Positives = 234/424 (55%), Gaps = 14/424 (3%) Query: 54 TGPSADVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGH 113 T P+ ++ +R+ + YR P++ V +L D+ G YLDA+ + V GH Sbjct: 21 TAPATRALIERRRNTFGDGVPLFYRDPVHFVSASGVWLRDQDGLEYLDAYNNVPSV--GH 78 Query: 114 CHPDVVEPVINQIKRLQHPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELAL 173 CHP VVE V Q L T YL+ + ++E L LP +L V FT+SGTE+ +LA+ Sbjct: 79 CHPRVVEAVSKQAATLNTHT-RYLSDVVTSYAERLLGTLPRELSKVLFTSSGTESVDLAM 137 Query: 174 MMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSD 233 +A+LYTG + R YHG++ A T + + +V PD YR Sbjct: 138 RLARLYTGGSGFIVTRFAYHGHSTAVAEIT-PAFGPGVPIGINVRLVDAPDGYRQD-APV 195 Query: 234 GEKYAKD----LQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLF 289 G K+A+D + D+ ++G AG I + + G+ PG+L A TVKKAGG+F Sbjct: 196 GIKFAQDVAAAIADMERHGI--RFAGLILDTVCSSDGLFVDPPGFLKDAIATVKKAGGVF 253 Query: 290 IADEVQSGFARTGN-FWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRS-Y 347 IADEVQ GF RTG WGFE H +VPDIV M K +GNG P+ A VT +I T RS Y Sbjct: 254 IADEVQPGFGRTGEGMWGFERHRIVPDIVVMGKPMGNGMPIAATVTRADIMQAFTERSGY 313 Query: 348 FNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLM 407 FNTFGGN+V A AVL+VIE E L NA G+ LK L QLK +H+ IGDVR GL Sbjct: 314 FNTFGGNTVCCAAASAVLDVIESEGLINNAKETGASLKLGLEQLKGQHQCIGDVRAIGLY 373 Query: 408 LGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLV 467 VE V KT T LH+++ +++ +LI G GN+ +I PPL F++ D LV Sbjct: 374 AAVEFVLP-DTKTADTDMALHVVNTLRQKRILISTCGPAGNILKIRPPLQFSRQHCDLLV 432 Query: 468 EAMD 471 A+D Sbjct: 433 TAID 436 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: 540 Number of extensions: 27 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: 442 Length adjustment: 33 Effective length of query: 444 Effective length of database: 409 Effective search space: 181596 Effective search space used: 181596 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