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 PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Length = 413 Score = 209 bits (531), Expect = 2e-58 Identities = 132/385 (34%), Positives = 195/385 (50%), Gaps = 32/385 (8%) Query: 34 LKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAEKIN 93 L D G EY+D AG+AV N GH HP +VAA+ +Q HT+ + + LA+K+ Sbjct: 47 LWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLHTS-NLYSIDWQQRLAQKLT 105 Query: 94 ALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPG-----VIAFSGGFHGRTYMTMALT 148 LA G + F +GAEA E A+KIAR H G V+ FHGRT T++ + Sbjct: 106 QLA---GMDRAFFNNSGAEANETALKIARLHGWHKGIEQPLVVVMENAFHGRTLGTLSAS 162 Query: 149 GKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIFEPVQ 208 A ++GF PG VP+ DL +LD +++ F S ++ A++ EP+Q Sbjct: 163 DGPA-VRLGFNKLPGDFVKVPF-GDL------GALDKVQQAFGS-----RIVAVLMEPIQ 209 Query: 209 GEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMTMAKS 268 GE G +AP ++A+R LC+ +++ DE+Q+G RTG+ FA H PD+MT+AK Sbjct: 210 GESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 269 Query: 269 LAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERANQLGQ 328 L G+P+ + + PG G T+ GNPLA VL+I++++ L E A G Sbjct: 270 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARLQGA 329 Query: 329 RLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQGLLLLTC 388 RL L P ++ +RG G MI +E P I A GLL+ Sbjct: 330 RLLERLRTELAGNPNVSQIRGQGLMIGIELKQP--------IRDLSLIAARDHGLLINV- 380 Query: 389 GAYGNVIRFLYPLTIPDAQFDAAMK 413 GN IR L PLT+ + + + ++ Sbjct: 381 -TRGNTIRLLPPLTLDEREVEMIVR 404 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: 414 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: 413 Length adjustment: 31 Effective length of query: 390 Effective length of database: 382 Effective search space: 148980 Effective search space used: 148980 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