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_011840643.1 RSPH17029_RS04315 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P50457 (421 letters) >NCBI__GCF_000015985.1:WP_011840643.1 Length = 425 Score = 511 bits (1315), Expect = e-149 Identities = 247/420 (58%), Positives = 316/420 (75%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 M N + +RR A RGVG+ +A A NA + D+EG YIDFAAGIAV+NTGH HP Sbjct: 1 MLNADVSRRRTEAVSRGVGMQTQIYADRALNAEIWDIEGRRYIDFAAGIAVVNTGHCHPK 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 ++AAV +Q+ +FTHT +Q++PYE+Y+ LAE++NA AP KT F TTGAE+VENA+KI Sbjct: 61 VMAAVAEQMGRFTHTCHQVLPYENYIRLAERLNAAAPGDFAKKTVFVTTGAESVENAIKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 AR HTGR V+AF GGFHGRT+MTM+LTGKV PYK GFG VYHVP+P LHGIST+ Sbjct: 121 ARIHTGRSAVVAFGGGFHGRTFMTMSLTGKVEPYKKGFGTMMPEVYHVPFPQALHGISTE 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 +++ A+ RLFK+D++ +VAAIIFEPVQGEGGF AP +LV AIR+LCD HGIVMIADEV Sbjct: 181 EAMAALARLFKADLDPGRVAAIIFEPVQGEGGFYPAPPDLVRAIRQLCDAHGIVMIADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Q+GFARTG LFAM Y PDL+TMAK L GG+P++ V G A IMDA PGGLGGTY GN Sbjct: 241 QTGFARTGTLFAMHGYDVAPDLVTMAKGLGGGLPIAAVTGRAEIMDAAHPGGLGGTYGGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PL +AAAHAVL++I++E+LC RA +LG RLK L + + + P IA +RG G M+ EF D Sbjct: 301 PLGIAAAHAVLDVIEEENLCARATELGSRLKQKLAEIRATAPEIADIRGPGFMVGAEFAD 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 P + P A ++++ AL +GL+LLTCG +GNVIRFL P+TIP+ F A++IL+ +++ Sbjct: 361 PGSKAPDAGFTNRVREEALKRGLILLTCGVHGNVIRFLAPITIPEPHFAEALEILEASVA 420 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: 592 Number of extensions: 23 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: 425 Length adjustment: 32 Effective length of query: 389 Effective length of database: 393 Effective search space: 152877 Effective search space used: 152877 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 Apr 10 2024. 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