Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= uniprot:A1S8Y2 (425 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 197 bits (501), Expect = 5e-55 Identities = 137/419 (32%), Positives = 206/419 (49%), Gaps = 65/419 (15%) Query: 26 VFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCF------ 79 V R E VWD EG Y+D + +N GH HPK+ A+ +Q K + T Sbjct: 25 VVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSRAFRNDQ 84 Query: 80 MVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAY--------TKRAG 131 + L YE A+ ++++P SG+EAVE+AIK R + +A Sbjct: 85 LALFYEELAALTGS-HKILP---------MNSGAEAVESAIKTVRKWGYEVRGVPENQAE 134 Query: 132 VIAFTSGYHGRTMAALALT------GKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAM 185 +I + +HGRT++ ++ + G P++ G FR V DA Sbjct: 135 IIVCSDNFHGRTISIVSFSTDPDARGGFGPFTPG--------FRT--------VPFGDAA 178 Query: 186 ASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTG 245 A + N A++LEP+QGE G G+++R+R+LC +++I DE+QTG Sbjct: 179 ALEAALTPNTV------AVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTG 232 Query: 246 AGRTGTFFAMEQMGVAADITTFAKSIAGGF-PLSGITGRAEVMDAIGPGGLGGTYGGSPL 304 GRTG A E GV AD+T K+++GGF P+S + +EV+ + PG G T+GG+PL Sbjct: 233 LGRTGKLLAEEHEGVEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPL 292 Query: 305 ACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENG 364 ACA A A + V EE +++ + A G +G + S I E RG G M+A+EL Sbjct: 293 ACAVARAAMRVLVEEGMIDNAAAQGAYFLEQLGAIRSNV--IREARGRGLMLAVELHPEA 350 Query: 365 KPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423 A YC + R RG +L+ T+ + +RI P+ EQ+ L E F+AVL Sbjct: 351 GGARRYCEAL----RARG--VLAKDTHDHTIRIAPPLVITREQVDWAL----EQFDAVL 399 Lambda K H 0.319 0.136 0.391 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: 405 Number of extensions: 23 Number of successful extensions: 6 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: 425 Length of database: 405 Length adjustment: 31 Effective length of query: 394 Effective length of database: 374 Effective search space: 147356 Effective search space used: 147356 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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