Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_012385547.1 BIND_RS13140 aspartate aminotransferase family protein
Query= BRENDA::Q98TS5 (439 letters) >NCBI__GCF_000019845.1:WP_012385547.1 Length = 451 Score = 207 bits (526), Expect = 7e-58 Identities = 138/388 (35%), Positives = 206/388 (53%), Gaps = 37/388 (9%) Query: 67 GVYVWDVEGRRYFDFLSAYSAVNQGHCHPKILDALKSQADKL-TLTSRAFYNDVLGEYEE 125 GV + +G+ DF S Y N GH HP+++ ALK + D+ + +D+ GE E Sbjct: 37 GVELHTSDGKAIIDFNSGYCVHNIGHNHPRLIAALKEELDRSGPAMLQTHVSDLAGELAE 96 Query: 126 YITKIFG--YNKVLPMNTGVEGGETACKLARKWAYTVKGIPKYKAQIIFAAGNFWGRTMS 183 + G + KV ++G EG ET K AR A+T + + I++AA F G T Sbjct: 97 KLCARAGGRFTKVFFASSGSEGVETVIKFAR--AHTER------SGILYAADGFHGLTCG 148 Query: 184 AISSSTDPSSYEGFGPFMPGFKIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVIVPDE 243 A+S +D GFGP +P + + ++D+ ALE L AAF++EPIQGE GV VP Sbjct: 149 ALSLMSDEFWKAGFGPLLPETESVLFDDIEALENKLAAKPFAAFVLEPIQGEGGVRVPAP 208 Query: 244 GYLTGVRQLCTAHNVLFIADEVQTGLARTGKMLAVDHENVRPDLVILGKALSGGVYPVSA 303 YL + LC + LF+ DEVQTG RTG LA H V PD+V+L KA+SGG+ P SA Sbjct: 209 DYLIKAQALCRRYGTLFVLDEVQTGFYRTGDFLAAHHFGVEPDMVVLAKAMSGGLIPCSA 268 Query: 304 VLCDDEVMLTI-----KPGEHGSTYGGNPLGCRVAMASLEVIEEEKLAENANXMGELLRA 358 VL D + +I + H +TY N L R + +L+++E+EKL A +GE LR Sbjct: 269 VLMSDAICNSIYSSLRRAFIHTTTYSENSLAMRAGLTTLDILEDEKLGARAASLGEYLRR 328 Query: 359 ELMKT--PSDIVTAVRGKGLLNAIVIKQSKD----------------CDAWKVCLRL-RD 399 L + ++V VRG GLLNAI ++ + V +RL +D Sbjct: 329 TLTERLGKYEMVAEVRGLGLLNAIEFRKPRSYLLRIPFETFSKIHPAMFGQVVVMRLFKD 388 Query: 400 NGLLAKPTHGDI--IRLAPPLTIKEDEI 425 +G+L++ + +++APPL + +++I Sbjct: 389 HGILSQICGNNFLTLKIAPPLVVSDEQI 416 Lambda K H 0.318 0.136 0.404 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: 448 Number of extensions: 15 Number of successful extensions: 5 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: 439 Length of database: 451 Length adjustment: 32 Effective length of query: 407 Effective length of database: 419 Effective search space: 170533 Effective search space used: 170533 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 (21.7 bits) S2: 51 (24.3 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