Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_013835162.1 THICY_RS03115 diaminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000214825.1:WP_013835162.1 Length = 428 Score = 209 bits (531), Expect = 2e-58 Identities = 135/422 (31%), Positives = 221/422 (52%), Gaps = 33/422 (7%) Query: 20 FDQYVMHTYG---RFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSA 76 F+QY + G FP + D EGK Y+DF G + GH HP + QA+ Sbjct: 6 FEQYESNVRGYIRSFPAVFDTATSATIVDVEGKRYIDFFGGAGSLNYGHNHPLINQALIT 65 Query: 77 QIQKLHHISNLYYIPEQG------ALAQWIVEHSCAD-KVFFCN-SGAEANEAAIKLVRK 128 IQ+ + I+N A I++ D K+ F +GA E A+KL RK Sbjct: 66 YIQR-NGITNALDKATVAKHDFISAFQSIILKPRKMDYKIQFVGPTGANGVETALKLARK 124 Query: 129 YAHTVSDFLEQPVILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYND----- 183 ++ +++ +++HG +L + TG Y + +P +PY++ Sbjct: 125 MK-------KRSNVIAFTNAYHGHSLGALAVTGNEFYHGDYYDVPRNVNKMPYDNYFDHD 177 Query: 184 ---IRALEEAITDIDEGNRRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLD 240 + L + D G AA+++E++QGEGG+ V + + + +C E ILL++D Sbjct: 178 MDSVDMLRHYLGDGSSGYELPAAVIVESIQGEGGINVASVGWLQKLSALCKEMDILLIMD 237 Query: 241 EVQVGVGRTGKYWGYENLGIEPDIFTSAKGLAGGIPIGAMMCKDSCAVFNPGEHASTFGG 300 E+QVG GRTG Y+ +E GI PDI T +K + G+P+ ++ K S V++PGEH TF G Sbjct: 238 EIQVGNGRTGDYFSFERAGIMPDIITLSKSIGTGMPMSIVLMKPSVDVWSPGEHTGTFRG 297 Query: 301 NPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYP-YFSDVRGWGLINGMEI 359 N ++ A A +E ++ ++ A+G+Q+ A K ++P + +DVRG G+I G+E Sbjct: 298 NSYAFIAGAAALELWRNDDFSRSIRAKGKQVEAAFKDFQARFPGWITDVRGLGMIWGLE- 356 Query: 360 KADLELTSIEVVKAAMEKGLLLAPAG--PKVLRFVPPLIVSAAEINEAIALL-DQTLAAM 416 + +E EV K A ++GL++ AG +VL+F+ PL++S E+NE +L D LAA+ Sbjct: 357 -SLVEGFCNEVSKQAFQRGLMMETAGASDQVLKFLGPLVISETELNEGFEILTDAILAAV 415 Query: 417 AL 418 A+ Sbjct: 416 AV 417 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: 408 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 428 Length adjustment: 32 Effective length of query: 386 Effective length of database: 396 Effective search space: 152856 Effective search space used: 152856 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