Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_027722435.1 H589_RS0113085 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000425265.1:WP_027722435.1 Length = 398 Score = 313 bits (802), Expect = 6e-90 Identities = 165/394 (41%), Positives = 247/394 (62%), Gaps = 14/394 (3%) Query: 24 VMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHH 83 + +TYGR+PV++A+ +G RLWD +GK Y+D ++GI+ +GH L++ ++ Q +KL Sbjct: 15 ICNTYGRYPVSVARAKGSRLWDIDGKEYIDLLSGISVVNIGHCREDLVEVMTEQARKLVQ 74 Query: 84 ISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVIL 143 +SNL+Y EQ A+ ++ AD+VFFCNSGAEANEAAIKL R+Y T+ + + I+ Sbjct: 75 VSNLFYQEEQVECAEKLLTTCGADRVFFCNSGAEANEAAIKLARRYMRTIKE-RDAYEII 133 Query: 144 SAKSSFHGRTLATITATGQP-KYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202 + + SFHGRTLAT+TATGQ + F PLP+GF YVP DI AL+ AITD + A Sbjct: 134 TLEGSFHGRTLATLTATGQAGPIKDGFAPLPEGFKYVPTGDIEALKAAITD------KTA 187 Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262 AIM+E +QGEGG++P EY KA+ + EN ILL++DEVQ G+ RTGK+W +++ G+ P Sbjct: 188 AIMIEMVQGEGGIKPLPAEYVKAIENLVAENDILLIVDEVQSGLCRTGKWWAHQHYGVTP 247 Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCAV-FNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321 IFTSAK LA G+P+GAM+ ++ A F PG HA+TFGG + V++ + +E + Sbjct: 248 HIFTSAKALANGLPMGAMLATEAIAKGFTPGSHATTFGGGALVAKVSSKVLDIMTEEKIA 307 Query: 322 ENVNARGEQLRAGLKTLAEKYP-YFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLL 380 + G+ + +K+P + VRG GL+ G+E+ D EV +KG + Sbjct: 308 DRAAEMGDFFITEALKIQKKFPEKINSVRGLGLMLGVELSFD----GSEVFTQLRDKGFI 363 Query: 381 LAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 L K+LR +P L + ++ + L++ L+ Sbjct: 364 LNLTKGKILRLLPALTIDKKDLETFLKTLEELLS 397 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: 396 Number of extensions: 14 Number of successful extensions: 6 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: 398 Length adjustment: 31 Effective length of query: 387 Effective length of database: 367 Effective search space: 142029 Effective search space used: 142029 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 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