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_092993143.1 BLP65_RS04710 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_900102855.1:WP_092993143.1 Length = 425 Score = 279 bits (714), Expect = 1e-79 Identities = 161/421 (38%), Positives = 233/421 (55%), Gaps = 16/421 (3%) Query: 18 GVGQIHPIF-------ADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQL 70 G G + P+ A R E ++D G YLDF GI V +TGH HPKVV A + Q+ Sbjct: 8 GAGHLSPLLKQSSDITAVRGEGVWLYDDSGERYLDFTSGIGVTSTGHCHPKVVEAAQRQV 67 Query: 71 KKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSG 130 L H + ++ ++P +EL + +K+P D + G+EA+E A++++R AT R Sbjct: 68 ANLIHGQYAIVRHQPLVELAGRLGEKMP-DPISAFFFASAGTEAIEAAMRLSRHATGRPN 126 Query: 131 TIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYP-CPLHGISEDDA----IA 185 IAF G +HGRT +L++T AG+ M G V A +P +G ED A + Sbjct: 127 FIAFQGGFHGRTMGSLSMTSSSVGLRAGLQPMMGGVVYAPFPDTDRYGWEEDAAADFCLR 186 Query: 186 SIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGA 245 + + + P + AA+ IEP+QGE G+ +S FMQ LR CD+HGI+L+ DEVQ+G Sbjct: 187 ELDHVLATVSTPRETAAMFIEPIQGEAGYIPASARFMQGLRERCDQHGILLVMDEVQAGF 246 Query: 246 GRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIAC 305 GRTG + + GV PD+ AK +A GFPL+ +M+ PG GGTY GN +AC Sbjct: 247 GRTGKFWGHQHFGVEPDVVVTAKGLASGFPLSAFGTSPSLMEQGWPGSQGGTYGGNAVAC 306 Query: 306 VAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDH 365 AAL + V E+E L++ A + G L L + ++PEIG VRG G M+ + DGD Sbjct: 307 AAALATMDVMEEEGLVENAAEQGTHLLARLEQLRNQYPEIGVVRGRGLMLGTGIV-DGD- 364 Query: 366 NKPDAKLTAEIVARARDKGLILLSCGPY-YNVLRILVPLTIEDAQIRQGLEIISQCFDEA 424 KPD + A IV A + L+L+ CG Y V+R L PL ++ +QI Q ++ Q A Sbjct: 365 GKPDGERAARIVKEAERRNLLLIRCGAYGGQVIRWLPPLIVQHSQIDQAIDTFEQALSAA 424 Query: 425 K 425 + Sbjct: 425 R 425 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: 452 Number of extensions: 18 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: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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