Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012741023.1 EUBREC_RS00440 acetylornithine/succinylornithine family transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000020605.1:WP_012741023.1 Length = 404 Score = 284 bits (727), Expect = 3e-81 Identities = 161/400 (40%), Positives = 230/400 (57%), Gaps = 18/400 (4%) Query: 22 QYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKL 81 +Y++ TY RF EG L+D G YLDF AGIA G +P ++ AV Q+ + Sbjct: 19 KYMIETYERFDFIAETAEGMYLYDENGTPYLDFYAGIAVNNAGSRNPKVVAAVKDQVDDI 78 Query: 82 HHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPV 141 H N Y Q LA+ + + DK+F+ NSG EANEA IK+ RKY + + Sbjct: 79 MHTFNYPYTIPQALLAEKVCKTIGMDKIFYQNSGTEANEAMIKMARKYG--IEKYGPNRY 136 Query: 142 -ILSAKSSFHGRTLATITATGQPKY--QKHFDPLPDGFAYVPYNDIRALEEAITDIDEGN 198 I++AK FHGRT ++ATGQP Q F P+ GF+Y PYND++A ++A T+ Sbjct: 137 HIVTAKDGFHGRTFGAMSATGQPGNGCQVGFGPMTYGFSYAPYNDLKAFKDACTE----- 191 Query: 199 RRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENL 258 AIM+E +QGEGGV P E+ K +R CDE G+LL++DEVQ G RTG Y N Sbjct: 192 -NTIAIMIEPVQGEGGVHPATPEFMKGLREFCDEKGMLLLIDEVQTGWCRTGAVMSYMNY 250 Query: 259 GIEPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQ 317 GI+PDI + AKGL GG+PIGA+ + + F+ G H +TFGG+P CAAALA V L Sbjct: 251 GIKPDIVSMAKGLGGGMPIGAICATEEVSKAFSAGSHGTTFGGHPVCCAAALAEVNELLD 310 Query: 318 ENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEK 377 +L N G+ A L EK P+ +VR GL+ G+E D ++ ++V ++ Sbjct: 311 RDLAGNAKKVGDYFAAKL----EKLPHVKEVRHQGLLVGVEF--DDTISGVDVKHGCFDR 364 Query: 378 GLLLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLAAMA 417 +L+ G ++R VPPLIVS E ++A ++ +T+ +++ Sbjct: 365 HMLITAIGSHIIRMVPPLIVSEEECDKAFDIIKETVESLS 404 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: 467 Number of extensions: 23 Number of successful extensions: 7 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: 404 Length adjustment: 31 Effective length of query: 387 Effective length of database: 373 Effective search space: 144351 Effective search space used: 144351 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 13 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