Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate SM_b20379 SM_b20379 aminotransferase
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__Smeli:SM_b20379 Length = 461 Score = 159 bits (402), Expect = 2e-43 Identities = 125/419 (29%), Positives = 196/419 (46%), Gaps = 47/419 (11%) Query: 31 GKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETL--WHTSNVFTNEPALR 88 G G V D +GK YI+ G+ LG LVEA Q +T+ +H+ + EP +R Sbjct: 37 GDGIYVVDDEGKRYIEGLAGLFCAGLGFSEQRLVEAATRQLKTMPFYHSFAHKSTEPGIR 96 Query: 89 LGRKLIDATFA--ERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSL 146 L KL+ +V F SG+EAN+TA KL +Y P K KII+ A+HG ++ Sbjct: 97 LAEKLLSIAPVPMSKVFFAGSGSEANDTAIKLIWYYNNALGRPEKKKIISRRKAYHGVTV 156 Query: 147 FTVSVGGQPKYSDGFGPKPADIIHVPF---------------------NDLHAVKAVMDD 185 T S+ G P F A+I+H N+L A+ Sbjct: 157 ATASLTGLPFNHRDFDLPIANILHTDCPHYWRFAETGETEEDFATRMANNLEAIILEEGP 216 Query: 186 HTCAVV-VEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHY 244 T A EP+ GGV + + ++ + ++ LL+ DEV CG GRTG++F Y Sbjct: 217 ETIAAFFAEPVMVSGGVITPPKTYFEKVQAVLRKYDILLIADEVICGFGRTGNMFGSETY 276 Query: 245 GVTPDILTSAKALGGGF-PVSAMLTTQEIASAF-----HVG--SHGSTYGGNPLACAVAG 296 G+ PD+++ AK L + P+SA++ +IA A +G SHG TYGG+P+A AVA Sbjct: 277 GLKPDMISCAKQLSAAYMPISALMINAKIADALVDQSRKIGTFSHGFTYGGHPVAAAVAL 336 Query: 297 AAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARD 356 A I +++ + + F ++ + E + + RG+GL+ G E K K + Sbjct: 337 EALTIYEEIDIVGHVRSVAPAFQDRVRKLGEH-PLIGEARGVGLVAGLEF-VKDKATREN 394 Query: 357 FLYAGAEA----------GVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405 F A A GV+ G D++ P++++++ I + M R A+ +A Sbjct: 395 FPPAWQVANQAGKFATARGVLTRGLG-DMVSLCPAMIIDDEQIDDLMTRMGLALDDTLA 452 Lambda K H 0.322 0.137 0.412 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: 22 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: 405 Length of database: 461 Length adjustment: 32 Effective length of query: 373 Effective length of database: 429 Effective search space: 160017 Effective search space used: 160017 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 (21.9 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