Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__PV4:5208066 Length = 405 Score = 528 bits (1360), Expect = e-154 Identities = 251/397 (63%), Positives = 313/397 (78%) Query: 8 ITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNAL 67 +TRA FDEV++P YAP+ IPV+G+GSR+WDQ+G E+VDFAGGIAV LGHCHPALV AL Sbjct: 7 LTRAQFDEVMVPNYAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGAL 66 Query: 68 KTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRH 127 K QGE +WH++NV TNEPAL L KL+EATFAE+V F NSG EANE A KLAR YA + Sbjct: 67 KEQGEKIWHLANVMTNEPALALATKLVEATFAEKVYFANSGAEANEAALKLARRYALDKF 126 Query: 128 SPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHT 187 K +IIAF AFHGR+ FTVSVGGQ YSDGFGPKP I H+PFND+ A++A + D T Sbjct: 127 GAEKDQIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALEAEVSDKT 186 Query: 188 CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVT 247 CA+++EP+QGEGG+ A PEFL+ +R L D+H AL++FDEVQ G+GR G+L+AYM VT Sbjct: 187 CAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVT 246 Query: 248 PDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEV 307 PDILT+AKALGGGFPI+AMLTT EIAS G+HGSTYGGNPLACA+ A D++NTPEV Sbjct: 247 PDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEV 306 Query: 308 LEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVM 367 L+G++ + Q D L +I+++Y VF+++RG GLL+GA L QY+GR++DFL AG G+M Sbjct: 307 LDGVKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVAGTSEGLM 366 Query: 368 VLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVV 404 L AGP+V+RF PSLV+ +ADI EG+ RF AVAKVV Sbjct: 367 CLIAGPNVIRFTPSLVIPEADIAEGLARFERAVAKVV 403 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: 528 Number of extensions: 11 Number of successful extensions: 1 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: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 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: 50 (23.9 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