Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_061535420.1 CAter10_RS16755 acetylornithine transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001584165.1:WP_061535420.1 Length = 400 Score = 175 bits (444), Expect = 2e-48 Identities = 131/400 (32%), Positives = 195/400 (48%), Gaps = 41/400 (10%) Query: 37 DVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQK 96 D G+ YLD+ G AV GH + A+ AQ KK+ + P +EL ++ Sbjct: 32 DHTGKRYLDYLQGWAVNALGHSPQCIQDALVAQSKKIINPS-PAFYNAPSIELANLLTAN 90 Query: 97 VPGDFAKKTLLVTTGSEAVENAVKIAR---------AATKRSGTIAFSGAYHGRTHYTLA 147 D + +G+EA E A+K+AR A R I F+ ++HGRT T++ Sbjct: 91 SCFD---RVFFTNSGAEANEGAIKLARKWGKKNPNKAGQNRFEIITFNHSFHGRTLATMS 147 Query: 148 LTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEP 207 +GK + +PG +P +E + +AS+ + + A+++EP Sbjct: 148 ASGKPGWDTIFAPQVPG------FPK-----AELNDLASVENLINDKTV-----AVMLEP 191 Query: 208 VQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFA 267 VQGE G ++ FMQ LR L +HGI+LI DEVQSG GRTG LFA + G+ PD+ T Sbjct: 192 VQGESGVIPATREFMQALRELTKKHGILLIVDEVQSGMGRTGELFAYQLSGIEPDIMTLG 251 Query: 268 KSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDL 327 K I GG PLA + R E+ G GGTY GNP+ + V+K + LQ D Sbjct: 252 KGIGGGVPLAALLAREEIA-VFEAGDQGGTYNGNPLMTAVGVAVIKTLLEPGFLQSVKDK 310 Query: 328 GQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGLI- 386 G L LL + KH G+ RG G + A++L +D + +IV ARD + Sbjct: 311 GAYLSSELLKLTAKHGLEGE-RGEGLLRALKLGKD---------IGPQIVDIARDLNPVG 360 Query: 387 LLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEAKQ 426 LL P N+LR + L + A+I Q + ++S + ++ Sbjct: 361 LLLNSPRPNLLRFMPSLNVTTAEIDQMIAMLSDVLTQLEK 400 Lambda K H 0.320 0.137 0.401 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: 425 Number of extensions: 25 Number of successful extensions: 5 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: 426 Length of database: 400 Length adjustment: 31 Effective length of query: 395 Effective length of database: 369 Effective search space: 145755 Effective search space used: 145755 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 24 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