Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 612 bits (1577), Expect = e-180 Identities = 296/420 (70%), Positives = 348/420 (82%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 M N E +QRR ATPRGVGVMC+F+A AENATL DVEG +Y DFA GIAVLNTGHRHP Sbjct: 1 MKNLELNQRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPR 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 ++ AV QL++FTHTAYQIVPYESYV LAE+INAL P+ G KTA FTTGAEAVENAVKI Sbjct: 61 VMQAVIAQLERFTHTAYQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 ARAHTGRPGVIAFSGGFHGRT + MALTGKVAPYK+GFGPFP +YH P+P DLHG+ST+ Sbjct: 121 ARAHTGRPGVIAFSGGFHGRTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTE 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 S+ A+E LFK+DI+ ++VAAII EPVQGEGGF+ AP + + +R LCD+HGI++IADEV Sbjct: 181 QSIQALESLFKTDIDPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Q+GF RTGKLFAM HY PDL+TMAKSLAGGMPLS V G A+IMDAP PGGLGGTYAGN Sbjct: 241 QTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PLAVAAAHAV+ I++E LCERA LG++LK L A ++ P IA +RGLGSM+AVEF+D Sbjct: 301 PLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEFHD 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 P TG+PSA +A+++Q RA+ GL+LLTCG YGN IRFLYPLTIP AQFDAA+ +L L+ Sbjct: 361 PATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVLA 420 Lambda K H 0.319 0.134 0.388 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: 646 Number of extensions: 21 Number of successful extensions: 1 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: 421 Length of database: 424 Length adjustment: 32 Effective length of query: 389 Effective length of database: 392 Effective search space: 152488 Effective search space used: 152488 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 17 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