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 CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 181 bits (460), Expect = 3e-50 Identities = 140/403 (34%), Positives = 189/403 (46%), Gaps = 44/403 (10%) Query: 27 QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTA--YQIVPYES 84 + A L EG EY+D AGIA GH HP LV ++ Q ++ H + Y+I E Sbjct: 26 ERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYRIPEQEE 85 Query: 85 YVTLAEKINALAPVSGQAKTAFFT-TGAEAVENAVKIARAH---TGRP---GVIAFSGGF 137 LA+ + A + A FFT +G EAVE A+K AR + G+P + F G F Sbjct: 86 ---LADALCA----NSFADVVFFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGSF 138 Query: 138 HGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAK 197 HGRTY + +G + Y GFGP +P S L T DAI K+ I + Sbjct: 139 HGRTYAAVNASGNPS-YVDGFGP------RLPGYSQL----TFGDHDAI----KAAIASP 183 Query: 198 QVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD-HY 256 AAII EPVQGEGG P + + +R+LCDEHG+++I DEVQ G RTGKLFA + Sbjct: 184 TTAAIIVEPVQGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMGRTGKLFAYEWAE 243 Query: 257 ADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK 316 +P +M +AK+L GG P+ + G T+ GNPLA+A A L II Sbjct: 244 GGEPHIMAVAKALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAMAVGKAALEIIKS 303 Query: 317 ESLCERANQLGQRLKNTLIDAKESVP-AIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQ 375 + + L K+ P I VRG G +I V+ I Sbjct: 304 PETLDNVKTVSGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKL-----------IPNNRD 352 Query: 376 QRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDA 418 LA+ LL G N +R L PL + + A+ L+ A Sbjct: 353 FMVLARDEKLLIAGGGDNCVRLLPPLNLTIEEASEAIAKLEKA 395 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: 411 Number of extensions: 19 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: 405 Length adjustment: 31 Effective length of query: 390 Effective length of database: 374 Effective search space: 145860 Effective search space used: 145860 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