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_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000204645.1:WP_013518270.1 Length = 398 Score = 207 bits (526), Expect = 6e-58 Identities = 134/410 (32%), Positives = 210/410 (51%), Gaps = 40/410 (9%) Query: 7 LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66 L++ S + G++ PI +R + RVWDV G++YLD GGIAV GH HP++V A+ Sbjct: 4 LIEAASPHVMNTYGRV-PIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPAL 62 Query: 67 EAQLKKLSHTC--FQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124 + Q+ KL HT + V E EL ++ + TG EA E A+KIAR Sbjct: 63 QEQIAKLIHTSNYYHVPGQE---ELARLLTGRAR---MTNAFFCNTGLEANECAIKIARK 116 Query: 125 -----ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGIS 179 ++ + + A+HGR+ T+ TG + L+ G + A P + + Sbjct: 117 YGVDKGIEKPEIVVYDHAFHGRSIATMTATGNPKVRNGFGPLLEGFIRVA--PNDIEALQ 174 Query: 180 EDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIAD 239 E + P ++ A+++EP+QGEGG + ++Q++R LCD +G +L+ D Sbjct: 175 E-----------ATEGNP-NVVAVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLD 222 Query: 240 EVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYA 299 EVQ+G GRTG FA + G+ PD+ T AK + G P+ V + + PG G T+ Sbjct: 223 EVQAGMGRTGKWFAHQWAGIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFG 282 Query: 300 GNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIEL 359 GNP+A A +E +++ E+E LLQ A D+G LK GL P + +VRG G +I +EL Sbjct: 283 GNPLAMRAGVETIRIMEEEGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVEL 342 Query: 360 FEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQ 409 ++P ++ RA GL+L V+R++ LT+ A+ Sbjct: 343 ------DRP----CGVLIDRAAQAGLLLSVTAD--RVIRLVPALTLTRAE 380 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: 444 Number of extensions: 21 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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 Apr 09 2024. 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