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_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 585 bits (1507), Expect = e-171 Identities = 289/419 (68%), Positives = 340/419 (81%), Gaps = 1/419 (0%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 M N + +R+ +ATPRGVGVMCNF+A+ AEN+ L DVEGN YIDFAAGIAVLNTGHRHP Sbjct: 1 MKNADLVRRKDAATPRGVGVMCNFYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPR 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 LV A++ Q+++FTHTAYQIVPY SY+ LAEKINA AP + KTAFFTTGAEAVENA+KI Sbjct: 61 LVQAMQAQMERFTHTAYQIVPYASYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 ARA TGRPGVIAFSGGFHGRT M MALTGKV PYK+GFGPFPG V+H PYP LHG+S Q Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQ 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 DS++A+ +LFK+D++ K+VAAIIFEPVQGEGGFNVAP E V A+R +CDEHGI+++ADEV Sbjct: 181 DSINALHQLFKADVDPKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Q+GF RTGKLFAM+HY PDL TMAKSLAGGMPLS V G A IMDAPAPGGLGGTYAGN Sbjct: 241 QTGFGRTGKLFAMEHYDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PLAVA+A AVL++++ E L ER LGQRL++ L K VP I VRG+G+MIAVEF Sbjct: 301 PLAVASALAVLDVLESEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFRK 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419 G P +++Q RAL +GLLLL+CG YGNV+RFL+PLTIPDA D + IL+ AL Sbjct: 361 AD-GRPDPEFTRQVQDRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAAL 418 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: 653 Number of extensions: 17 Number of successful extensions: 2 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: 420 Length adjustment: 32 Effective length of query: 389 Effective length of database: 388 Effective search space: 150932 Effective search space used: 150932 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