Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 191 bits (485), Expect = 4e-53 Identities = 134/374 (35%), Positives = 191/374 (51%), Gaps = 15/374 (4%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHA-IADFSEALA 149 L+D G RY+D AGIAV+N GH HP +V+ + Q++R H + +A + +E + Sbjct: 34 LWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTAYQIVPYASYIELAEKIN 93 Query: 150 SKLPGDL--KVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSM 207 ++ PG K FFT +G EA E A+ +A+ TG ++A G+HG M TG+ + Sbjct: 94 ARAPGAFAKKTAFFT-TGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMALTGKVV 152 Query: 208 -WK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTG-HIAGFICEAIQG 263 +K F V HA P PY G+ G + L L + +A I E +QG Sbjct: 153 PYKVGFGPFPGDVFHA--PYPY-GLHGVSVQDSINALHQLFKADVDPKRVAAIIFEPVQG 209 Query: 264 VGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGI 323 GG ++ A + G L +ADEVQ+GF RTG + E ++V PD+ TMAK + Sbjct: 210 EGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYDVTPDLTTMAKSL 269 Query: 324 GNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSY 383 G PL AV EI T+ GN ++ + LAVL+V+E EKL E A +G Sbjct: 270 AGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLESEKLIERGAALGQR 329 Query: 384 LKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLK-TPATAETLHIMDQMKELGVLIGK 442 L++KL LK + IG+VRG G M+ VE RK P T + D+ E G+L+ Sbjct: 330 LQDKLDGLKSRVPEIGEVRGVGAMIAVEF---RKADGRPDPEFTRQVQDRALERGLLLLS 386 Query: 443 GGYFGNVFRITPPL 456 G +GNV R PL Sbjct: 387 CGVYGNVVRFLFPL 400 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: 519 Number of extensions: 28 Number of successful extensions: 4 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: 420 Length adjustment: 33 Effective length of query: 444 Effective length of database: 387 Effective search space: 171828 Effective search space used: 171828 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