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 N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Dyella79:N515DRAFT_3307 Length = 426 Score = 175 bits (444), Expect = 2e-48 Identities = 122/370 (32%), Positives = 175/370 (47%), Gaps = 30/370 (8%) Query: 3 SNKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVL 53 +N EL QR Q +P GV P F RA+ +WDVEG+ Y+D+ G + Sbjct: 2 TNHELFQRAKQLMPGGVNSPVRAFKSVGGEPFFTARADGAYLWDVEGKRYIDYVGSWGPM 61 Query: 54 NTGHLHPKVVAAVEAQLK---KLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTT 110 GH HP+V AVE +K C + + E + + VP +V + Sbjct: 62 IVGHNHPRVREAVERAVKDGLSFGTPC------PAEITMAETITRLVPS--VDMVRMVNS 113 Query: 111 GSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRAL 170 G+EA +A+++AR AT RS + F G YHG L G + G+ PG V +A Sbjct: 114 GTEATMSAIRLARGATGRSKIVKFEGCYHGHGDSFLVKAGS-GALTFGVPTSPG-VPKAA 171 Query: 171 YPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCD 230 L D +A+ +F A DIA ++IEPV G ++Q LRALC Sbjct: 172 ADLTLTLAYND--LAAAEALFAEHGA--DIAGLIIEPVAGNMNCIPPKDGYLQGLRALCT 227 Query: 231 EHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVA 290 HG +LI DEV +G R A G+ PDL+TF K I GG P+ GR E+M+ +A Sbjct: 228 RHGALLIFDEVMTGF-RVALGGAQAHYGITPDLSTFGKIIGGGMPVGAYGGRRELMEQIA 286 Query: 291 PGG---LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGD 347 P G GT +GNP+A A L +L++ ++ + + L DGL A+A+ Sbjct: 287 PAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYDRLAARTRLLADGLQAVADGEGVPFS 346 Query: 348 VRGLGAMIAI 357 +GAM + Sbjct: 347 TNRVGAMFGL 356 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: 446 Number of extensions: 22 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 09 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