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_012468162.1 GLOV_RS00310 acetylornithine transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000020385.1:WP_012468162.1 Length = 397 Score = 171 bits (434), Expect = 3e-47 Identities = 126/407 (30%), Positives = 198/407 (48%), Gaps = 46/407 (11%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAY 83 PI + + D G+ YLDF G AV GH + A+ Q +L Sbjct: 18 PIVMVAGQGSWLTDSNGKRYLDFIQGWAVNCLGHAPAVITQALSQQAAQLISPS-PAFYN 76 Query: 84 EPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAY----- 138 +P + L +++ ++ +G+EA E A+K+AR + G++ GAY Sbjct: 77 QPAIRLADLLTAN---SCFERVFFANSGAEANEGAIKLAR----KWGSLHKQGAYEIITM 129 Query: 139 ----HGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194 HGRT T++ +GK + +PG + G+++ +A+ + Sbjct: 130 VNGFHGRTLATMSASGKPHWQGLFEPKVPGFIKV--------GLNDLEAVTA-------- 173 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 A E AI++EPVQGE G +S F+Q LR L D+H ++LI DEVQ+G GR G+LFA Sbjct: 174 AISERTVAIMLEPVQGEAGVIPASQLFLQGLRQLADQHQLLLIFDEVQTGMGRLGSLFAY 233 Query: 255 EQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKV 314 +Q GV PD+ + K I GG PLA + + E + PG GGTY GNP+ VL+ Sbjct: 234 QQAGVEPDIMSLGKGIGGGVPLAALLAK-EAVCCFEPGDQGGTYNGNPLMAAVGCAVLEA 292 Query: 315 FEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTA 374 Q L++ + G +L +GL ++ +H +G+VRG G + A+ L N DA Sbjct: 293 MLQPGFLEQVRERGVQLANGLRKLSTRH-GLGEVRGSGLLQALAL----PANNGDA---- 343 Query: 375 EIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCF 421 + AR+ GLI+ + P + LR + L + ++ L ++ Q F Sbjct: 344 -VTEAARELGLIINAARP--DTLRFMPALNVSADEVDTCLRLLDQVF 387 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: 402 Number of extensions: 19 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: 397 Length adjustment: 31 Effective length of query: 395 Effective length of database: 366 Effective search space: 144570 Effective search space used: 144570 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