Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= curated2:Q7N9E5 (403 letters) >FitnessBrowser__MR1:201879 Length = 461 Score = 153 bits (387), Expect = 9e-42 Identities = 125/418 (29%), Positives = 204/418 (48%), Gaps = 44/418 (10%) Query: 18 PIYSPAQFIPVRG----QGSRVWDQHGKEYIDFAGGIAVVALGHCHPTLVDVLKQQGEKL 73 P S + +PV G QG + G++ ID G+ HP ++ ++QQ +L Sbjct: 17 PYTSMTRALPVFGVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMEQQLHQL 76 Query: 74 WHIS-NIFTNEPALILAQKLIDATFAE--RVFFANSGAEANEAAFKLARHYAIARHNPY- 129 H+ T+EPA+ L +KL+ T +VF +SG+ A E A K+A Y + P Sbjct: 77 SHVMFGGITHEPAIELCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLA 136 Query: 130 ----KTKIIAFHQGFHGRTLFTVSV----GGQPKYADGFGPKPA--DIIHVPF------N 173 K +I+ +G+HG T +SV GG K D PF + Sbjct: 137 QKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDAPQTPFGESLHQD 196 Query: 174 DLDAVKAVIDDH---TCAVVLEPV-QGEGGVTAAAPAFIHGVRELCDKHQVLLVFDEVQS 229 DL ++ ++ + AV++EP+ QG GG+ + ++ G+R LCD++ VLL+ DE+ + Sbjct: 197 DLAPMQRILREQHQDIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDEIAT 256 Query: 230 GMGRTGKLFSYMHYDVTPDIITTAKALGNGF-PISAMLTTVNIASVMTPG-----AHGTT 283 G GRTGKLF+Y H D+TPDI+ KAL G+ ++A L T N+A ++ HG T Sbjct: 257 GFGRTGKLFAYEHTDITPDILCLGKALTGGYISLAATLCTDNVAQGISQSPAGVFMHGPT 316 Query: 284 YGGNPLACAVANVAFDIINT---PAVLAGVEKRHNLMVNFLNDINQKYSIFGEIRGKGLL 340 + GNPLACA A + D+IN PA +A +E++ + DI ++ +L Sbjct: 317 FMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAIDI-------PSVKAVRVL 369 Query: 341 IGAELKAPHQGKAKDILQLAAENGLMLLSAGGDVLRFTPSLIISEEEIAQGMERLEQV 398 + HQ LQ + + + +++ P +IS +++Q + ++QV Sbjct: 370 GAVGVLEMHQAVNTAALQQQFVDLGVWVRPFANLIYIMPPYVISSAQLSQLTQAMKQV 427 Lambda K H 0.321 0.138 0.410 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: 472 Number of extensions: 23 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: 403 Length of database: 461 Length adjustment: 32 Effective length of query: 371 Effective length of database: 429 Effective search space: 159159 Effective search space used: 159159 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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