Align Gamma-aminobutyrate transaminase 1, mitochondrial; EC 2.6.1.96 (characterized)
to candidate Pf6N2E2_1742 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62)
Query= SwissProt::Q7XN11 (516 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1742 Length = 463 Score = 400 bits (1029), Expect = e-116 Identities = 201/421 (47%), Positives = 273/421 (64%), Gaps = 2/421 (0%) Query: 83 PLVIERSEGSYVYDIDGKKYLDSLAGLWCTALGGSEPRLVKAATEQLHKLPFYHSFWNRT 142 PLVIER G YV D G+ Y++ ++GLWC LG S PRLV+AA Q+ LP+YH+F +R Sbjct: 35 PLVIERGSGIYVTDEHGRDYIEGMSGLWCAGLGFSNPRLVQAAQRQMAVLPYYHTFNHRV 94 Query: 143 TKPSLDLAKELLSMFTAREMGKVFFTNSGSEANDSQVKLVWYYNNALGRPDKKKFIARSK 202 LA+ + S+ E KVFF SGSEANDS VKL W Y+ A G K+K IA K Sbjct: 95 PNVVAQLAERIASLVPF-EKPKVFFACSGSEANDSMVKLAWAYHRARGNDGKRKIIAHQK 153 Query: 203 SYHGSTLISASLSGLPALHQKFDLPAP-FVLHTDCPHYWRFHLPGETEEEFATRLANNLE 261 +HGST++ ASLSGLP +H F LP VLH CPH++R + GE+E +F RL +LE Sbjct: 154 GFHGSTVMGASLSGLPNMHAAFGLPLENSVLHVQCPHFYRHGIEGESEAQFTERLLRDLE 213 Query: 262 ELILKEGPETIAAFIAEPVMGAGGVIPPPKTYFEKVQAIVKKYDILFIADEVITAFGRLG 321 + I EG +TIAAFI+EPVMGAGGVI PP YF VQA++KK+DILF+ADE+I FGR G Sbjct: 214 QRIEAEGADTIAAFISEPVMGAGGVIVPPPGYFVGVQALLKKHDILFLADEIICGFGRTG 273 Query: 322 TMFGSDMYNIKPDLVSMAKALSSAYVPIGAIMVSPEISDVIHSQSNKLGSFAHGFTYSGH 381 FG PD+++ AK+LSS Y PI ++V+ + VI QS +LG F HGFTYSGH Sbjct: 274 RWFGHQTLGFTPDMMACAKSLSSGYQPISCVVVAENVYQVIEEQSQQLGGFGHGFTYSGH 333 Query: 382 PVACAVAIEALKIYQERNIPDHVKQISPRFQEGVKAFAGSPIVGEIRGVGLILGTEFADN 441 PVA AVA+E L +YQE ++P +++ + ++ P++GE+RG+GL+ G E + Sbjct: 334 PVAAAVALETLTLYQEMHLPQRTEELGRLLHQQLEPLLAHPLIGEVRGIGLVAGLELVVD 393 Query: 442 KSPNDPFPAEWGVGAIFGAECQKRGMLVRVAGDNIMMSPPLIMTPDEVEELVSIYGDALK 501 K PFP E +G +++G++VR GD+I ++PP I++ +E+ ELV+ AL Sbjct: 394 KHTRAPFPREIAIGVQVERAAREQGLIVRNMGDSIALAPPFIISAEEIVELVARLTRALD 453 Query: 502 A 502 A Sbjct: 454 A 454 Lambda K H 0.317 0.134 0.396 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: 629 Number of extensions: 27 Number of successful extensions: 3 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: 516 Length of database: 463 Length adjustment: 34 Effective length of query: 482 Effective length of database: 429 Effective search space: 206778 Effective search space used: 206778 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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