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_012537706.1 AFE_RS15145 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000021485.1:WP_012537706.1 Length = 430 Score = 164 bits (416), Expect = 4e-45 Identities = 120/336 (35%), Positives = 167/336 (49%), Gaps = 34/336 (10%) Query: 17 RGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKK---- 72 RGVG PIF D AE WDVEG+ YLD+ G + GH HP+V+AAV AQ+ K Sbjct: 28 RGVGG-DPIFIDHAEGPFFWDVEGKRYLDYVGSWGPMIHGHGHPEVLAAVHAQVNKGLGF 86 Query: 73 LSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTI 132 + T +V E+ E++ VPG + + ++G+EAV A+++AR T R I Sbjct: 87 GAPTAIEV-------EMAELVCALVPG--IESVRMTSSGTEAVMTAIRLARGYTGRDRII 137 Query: 133 AFSGAYHGRTHYTLALTGK-----VNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASI 187 F G YHG + L G P SAG +P V + P + + A+ + Sbjct: 138 KFEGNYHGHSDSLLVKAGSGALTLGQPSSAG---VPREVSQNTLVLPYNDL---PAVVEM 191 Query: 188 HRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGR 247 F D+A I++EPV G G P F++ LRA+CD++G +LI DEV +G R Sbjct: 192 MAQF-----GFDVATIIVEPVAGNMGCVPPEPGFLEGLRAVCDQYGCVLIFDEVMTGF-R 245 Query: 248 TGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGG---LGGTYAGNPIA 304 A GV PDLTT K I GG P+ V G E+M+ +AP G GT +GNP+A Sbjct: 246 VALGGAQALYGVRPDLTTLGKIIGGGLPVGAVGGPREIMEYLAPTGPVYQAGTLSGNPVA 305 Query: 305 CVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAE 340 A L L++ ++ L +GL AE Sbjct: 306 MAAGLATLRLLTVPGFHERLAAQTAVLCEGLAERAE 341 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: 481 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: 430 Length adjustment: 32 Effective length of query: 394 Effective length of database: 398 Effective search space: 156812 Effective search space used: 156812 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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