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 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::P50457 (421 letters) >MicrobesOnline__882:208688 Length = 423 Score = 141 bits (355), Expect = 4e-38 Identities = 123/402 (30%), Positives = 179/402 (44%), Gaps = 28/402 (6%) Query: 25 FAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYES 84 F A + L V+G +IDF + GH HP++ AAV + + T P E Sbjct: 36 FIARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYG---APCED 92 Query: 85 YVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144 V LA K+ P G +G EA +A+++AR +TGR ++ F G +HG Sbjct: 93 EVVLAAKVVDALP--GVDMVRMVNSGTEATMSALRLARGYTGRTKLVKFVGCYHGHADPF 150 Query: 145 MALTGK-VAPYKIGFGP-FPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAI 202 +A G VA I P P S ++ + L A++ LF + K +AAI Sbjct: 151 LASAGSGVATLSIPGTPGVPESTVRDTL------LAPYNDLAAVKDLFA--LHGKDIAAI 202 Query: 203 IFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDL 262 I E V G G + +R LCD+HG ++I DEV +GF R A + PDL Sbjct: 203 IVEAVAGNMGLVPPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDL 261 Query: 263 MTMAKSLAGGMPLSGVVGNANIMDAPAPGG---LGGTYAGNPLAVAAAHAVLNIIDKESL 319 T+ K + GG+P+ G IM AP G GT +GNPLA+AA A L+++ + Sbjct: 262 TTLGKIIGGGLPVGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSRSDY 321 Query: 320 CERANQLGQRLKNTLIDAK-ESVPAIAAVRGLGSMIAVEF-NDPQTGEPSA-----AIAQ 372 ++ +K K + VP + L SM V F NDP T SA A+ Sbjct: 322 AGLEARVAAFVKELEAILKGKGVP--VRINTLASMFTVFFTNDPVTDFASAKTADGALYT 379 Query: 373 KIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKI 414 ++ AQG+ L ++ F + A DAA K+ Sbjct: 380 SFYKQMRAQGIYLAPSPFEAAMVSFAHTDDDLAAMLDAARKV 421 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: 440 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: 421 Length of database: 423 Length adjustment: 32 Effective length of query: 389 Effective length of database: 391 Effective search space: 152099 Effective search space used: 152099 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