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 BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Koxy:BWI76_RS26375 Length = 421 Score = 651 bits (1679), Expect = 0.0 Identities = 317/419 (75%), Positives = 362/419 (86%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 M ++E +QRR ATPRGVGVMC++F + AENATL D+EGNE IDFAAGIAVLNTGHRHP Sbjct: 1 MKSSELNQRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPK 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 ++AAVEQQLQ FTHTAYQIVPYESYVTLAE+INALAP+ G AKTAFFTTGAEAVENAVKI Sbjct: 61 IIAAVEQQLQAFTHTAYQIVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 ARA+TGRPG+I F GGFHGRT+MTMALTGKVAPYKIGFGPFPGSVYH YP+ HGI+T Sbjct: 121 ARAYTGRPGLITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTA 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 D++ +++R+FK+DI A QVAAI+ EP+QGEGGFNVAP E + A+R LCD HGI++IADEV Sbjct: 181 DAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Q+GFARTGKLFAM HY KPDLMTMAKSLAGG PLSGVVG A +MDAPAPGGLGGTYAGN Sbjct: 241 QTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PLAVAAAHAVL++I++E LC+RA +LG LK L A++S PAIA VRG GSM+AVEFND Sbjct: 301 PLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFND 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419 PQTGEPSA I ++IQQ+A GLLLL+CG YGNVIRFLYPLTIPDAQF A+ IL L Sbjct: 361 PQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419 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: 658 Number of extensions: 17 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: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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