Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Putida:PP_0214 Length = 425 Score = 193 bits (490), Expect = 1e-53 Identities = 127/389 (32%), Positives = 188/389 (48%), Gaps = 10/389 (2%) Query: 80 PLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH 139 P+ + K + D GR +D GIAV+N GH HP VV V Q+ ++ H L + Sbjct: 25 PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 Query: 140 A-IADFSEALASKLPGDL-KVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAA 197 + E + +PGD K +G+EA E A+ +A+ TG ++A GYHG Sbjct: 85 EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTM 144 Query: 198 ATMGATGQSM---WKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIA 254 T+G TG+ + ++ + AL P G+ D + + IA Sbjct: 145 MTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERI--FKNDAEPRDIA 202 Query: 255 GFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVP 314 I E +QG GG + + + G L IADEVQ+G RTG F+ E V P Sbjct: 203 AIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAP 262 Query: 315 DIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQ 374 D+ T AK I GFPL V E + T+ G+ ++ A LAV+ V E+EKL Sbjct: 263 DLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIEVFEEEKLL 322 Query: 375 ENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMK 434 + + VG L L ++++K+ IIGDVRG G M+ VE V ++ TP A ++ + + Sbjct: 323 DRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVE-VFEKGTHTPNAAAVGQVVAKAR 381 Query: 435 ELGVLIGKGGYFGNVFRITPPLCFTKDDA 463 E G+++ G +GNV RI PL T +DA Sbjct: 382 EKGLILLSCGTYGNVLRILVPL--TAEDA 408 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: 507 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: 425 Length adjustment: 33 Effective length of query: 444 Effective length of database: 392 Effective search space: 174048 Effective search space used: 174048 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