Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate SMa2400 SMa2400 diaminobutyrate--2-oxoglutarate aminotransferase
Query= BRENDA::B1XNF8 (418 letters) >FitnessBrowser__Smeli:SMa2400 Length = 470 Score = 214 bits (546), Expect = 3e-60 Identities = 143/423 (33%), Positives = 224/423 (52%), Gaps = 55/423 (13%) Query: 30 RFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK---LHHISN 86 RFPVA+ GC + D +G+SYLD +AG T LGH HP +I+ + + LH + Sbjct: 48 RFPVALKSASGCIVTDVDGRSYLDCLAGAGTLALGHNHPEVIETLQQVLGSGLPLHTLDL 107 Query: 87 LYYIPEQ------GALAQWIVEHSCADKVFFCN-SGAEANEAAIKLVRKYAHTVSDFLEQ 139 + ++ G L + + + K+ FC+ SG +A EAAIKL + Sbjct: 108 TTPVKDRFVSDIFGTLPAGLRDEA---KIQFCSPSGTDAVEAAIKLAKTATGRTD----- 159 Query: 140 PVILSAKSSFHGRTLATITATGQ--PKYQ-------KHFDPLPDGFAY-VPY----NDIR 185 ++S + ++HG + +++ G PK HF P P +AY P+ N+ Sbjct: 160 --LVSFRGAYHGMSQGSLSLMGSLGPKASVGQLVPGAHFFPYP--YAYRCPFGRGGNETA 215 Query: 186 AL-----EEAITDIDEGNRRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLD 240 L E A+ D + G R AA++LEA+QGEGGV P VE+ +AVRR+ + GI L++D Sbjct: 216 TLAAEYFERALRDPEGGINRPAAVILEAVQGEGGVIPAPVEWLRAVRRVTRDLGIPLIVD 275 Query: 241 EVQVGVGRTGKYWGYENLGIEPDIFTSAKGLAGGIPIGAMMCKDSCAVFNPGEHASTFGG 300 EVQ GVGRTG ++ ++ GI PD+ +K + GG+P+ ++ ++ ++ PG HA TF G Sbjct: 276 EVQSGVGRTGSFYAFQKAGIIPDVVVLSKAIGGGLPLAVVIYREDLDLWKPGAHAGTFRG 335 Query: 301 NPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIK 360 N + AA +E +E+E L+E G +LRA L+ +A + PY +VRG GL+ G+E+ Sbjct: 336 NQLAMAAGSKTLEIIERERLVERAAIAGRRLRANLERIAAQTPYIGEVRGEGLMLGVEVV 395 Query: 361 ADLELTSI--------EVVKAAMEK----GLLLAPAG--PKVLRFVPPLIVSAAEINEAI 406 L E+ + + G++L G VLR +PPL++S AEI++ Sbjct: 396 DPEGLPDALGHPPHGQEIARMIQHEMFRAGIILETGGRFGSVLRLLPPLVISDAEIDQVS 455 Query: 407 ALL 409 L Sbjct: 456 GAL 458 Lambda K H 0.319 0.136 0.406 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: 451 Number of extensions: 18 Number of successful extensions: 4 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: 418 Length of database: 470 Length adjustment: 32 Effective length of query: 386 Effective length of database: 438 Effective search space: 169068 Effective search space used: 169068 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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