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 WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_001584165.1:WP_128083232.1 Length = 420 Score = 555 bits (1429), Expect = e-162 Identities = 275/413 (66%), Positives = 327/413 (79%) Query: 7 HQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVE 66 HQR+ +ATPRGVGVMC+F+A A N+ + DVEG +IDFAAGIAVLNTGHRHP LVAA++ Sbjct: 2 HQRKNAATPRGVGVMCDFYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQ 61 Query: 67 QQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTG 126 +QL +FTHTAYQIVPY SYV LAE+INA+ P KT FF+TGAEAVENAVKIARA TG Sbjct: 62 EQLGKFTHTAYQIVPYGSYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAATG 121 Query: 127 RPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAI 186 R VIAFSG FHGRT M MALTGKV PYK+GFGPFP VYHVP+P +LHG+S ++SL A+ Sbjct: 122 RSAVIAFSGAFHGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAAL 181 Query: 187 ERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFAR 246 + LFK+D++ K+VAAII EPVQGEGGF AP + A+R+LCDEHGI+++ DEVQ+GFAR Sbjct: 182 QSLFKADVDPKRVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFAR 241 Query: 247 TGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAA 306 TGKLFA++H PDLMTMAKSLAGGMPLS V G A IMDA APGGLGGTYAGNPLAVA+ Sbjct: 242 TGKLFAVEHSGVIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVAS 301 Query: 307 AHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEP 366 A AVL++I++E L ERAN LG RLK L + VP IA +RGLG+M+AVEF P + +P Sbjct: 302 ALAVLDVIEEEKLVERANVLGGRLKQVLEGLRADVPQIADIRGLGAMVAVEFTQPGSKQP 361 Query: 367 SAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419 A +K+Q AL GLLLL+CG Y N IRFL+PLTI DA D A+ IL A+ Sbjct: 362 DADFTKKVQAEALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAM 414 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: 597 Number of extensions: 27 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: 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 24 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