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_043918626.1 jaqu_RS08900 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000877395.1:WP_043918626.1 Length = 394 Score = 191 bits (486), Expect = 3e-53 Identities = 132/388 (34%), Positives = 190/388 (48%), Gaps = 39/388 (10%) Query: 36 WDVE--GREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIM 93 W VE GR YLD GIAV GH HP + A+ AQ +L HT YE + E+ Sbjct: 23 WLVERGGRRYLDLGAGIAVNVLGHAHPALTEALTAQAGQLWHTSN---LYE-IPQQQELA 78 Query: 94 NQKVPGDFAKKTLLVTTGSEAVENAVKIARA--ATK---RSGTIAFSGAYHGRTHYTLAL 148 + V FA +G+EA E AVK+AR +TK R+ +AF+G++HGR+ +A Sbjct: 79 ERLVEATFADTVFFTNSGTEACELAVKMARKYWSTKGEDRATIVAFTGSFHGRSSAGIAA 138 Query: 149 TGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPV 208 G L+PG V+ + DA A + + +DIAA+++EP+ Sbjct: 139 AGSKKMTDGFGPLLPGFVHVPF--------GDHDAFAEVMK-------RDDIAAVILEPI 183 Query: 209 QGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAK 268 QGEGG ++ LR +CD G ++I DEVQ G GRTG LFA E GV PD+ AK Sbjct: 184 QGEGGIVPVPDQCLKGLRDVCDRTGALMILDEVQCGMGRTGKLFAHEWAGVTPDIMMVAK 243 Query: 269 SIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQKANDLG 328 I GGFPL + ++ G G TY GNP+AC V++V E L + Sbjct: 244 GIGGGFPLGALLATEHAAAGMSAGTHGSTYGGNPLACAVGNAVMEVVADEAFLAEVRRKA 303 Query: 329 QKLKDGLLAIAEKHPEIGD-VRGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGLIL 387 L+ GL + HP++ + VRG G M+ ++ +++A ARD +++ Sbjct: 304 GLLRQGLEGLVASHPDVFEVVRGSGLMLGLKC----------RVPVGDVIAAARDAEVLI 353 Query: 388 LSCGPYYNVLRILVPLTIEDAQIRQGLE 415 + R+L L I D IR+ L+ Sbjct: 354 VPAAD--ETARLLPALNIGDDDIREALD 379 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: 491 Number of extensions: 32 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: 426 Length of database: 394 Length adjustment: 31 Effective length of query: 395 Effective length of database: 363 Effective search space: 143385 Effective search space used: 143385 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