Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_013419693.1 RVAN_RS10465 aspartate aminotransferase family protein
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_000166055.1:WP_013419693.1 Length = 453 Score = 172 bits (436), Expect = 2e-47 Identities = 121/395 (30%), Positives = 187/395 (47%), Gaps = 35/395 (8%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVF--TNEPAL 87 +G+G+ ++D +G+ Y+D G+ LGH LV A Q TL + T+EPA+ Sbjct: 39 RGEGATLYDTEGRAYLDGLSGMWNVHLGHGRWELVEAASRQLSTLAFATAYAGATHEPAI 98 Query: 88 RLGRKL--IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145 RL +L I E F SG+EA +T+ + AR + + P KTKIIA ++HG + Sbjct: 99 RLAERLKKIAPAGIESFFFTTSGSEATDTSIRTARWFWRAQGKPAKTKIIAREWSYHGST 158 Query: 146 LFTVSVGGQPKYSDGFGPKPADIIHVPF-------NDLHAVKAVMD--------DHTCAV 190 + S G ++S+GFGP+ +H+P D A +++ + A Sbjct: 159 IGAASATGVDEFSEGFGPRLPGFLHIPSPYPYRFDGDGEAAADLLEAAILREGPETVAAF 218 Query: 191 VVEPIQGEGGVTAATPE-FLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPD 249 + EP+QG GG P+ + + +RE+CD H L + DEV G GRTG FA H+G+ PD Sbjct: 219 IAEPVQGGGGGVIVPPDGYFERIREICDSHDVLFIADEVITGFGRTGKWFALEHWGIAPD 278 Query: 250 ILTSAKALGGGF-PISAMLTTAEIASAFHPGS------HGSTYGGNPLACAVAGAAFDII 302 I+ AK + G+ P+ + +A I HG T +P+ACAVA II Sbjct: 279 IVQFAKGITSGYVPLGGIGISARIKDVLDGAESDRRWWHGFTASAHPVACAVALETLRII 338 Query: 303 NTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRAR------- 355 + ++E + + L++ + ++RG+GLL G EL + RAR Sbjct: 339 DEERLVERAAGQGGALLGRLREALGWHPHVGEVRGLGLLAGVELVADRRTRARFAPEFRI 398 Query: 356 -DFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADI 389 L A A + D + AP L D D+ Sbjct: 399 ASKLRAELLARGLYTRIVNDTICLAPPLTTTDTDL 433 Lambda K H 0.322 0.138 0.415 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: 487 Number of extensions: 25 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: 406 Length of database: 453 Length adjustment: 32 Effective length of query: 374 Effective length of database: 421 Effective search space: 157454 Effective search space used: 157454 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 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