Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 485 bits (1248), Expect = e-141 Identities = 236/399 (59%), Positives = 297/399 (74%), Gaps = 1/399 (0%) Query: 8 ITRATFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEAL 67 ++R FDEV++P YAP IPV+G+GSR+WDQ+G+E+ID GGIAVT LGH HP LV AL Sbjct: 6 VSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGAL 65 Query: 68 KSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRH 127 Q E +WH SNV TNEPALRL + L D TFAERV F NSG EANE AFKLAR YA H Sbjct: 66 HDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHH 125 Query: 128 SPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMD-DH 186 K +II+F N+FHGR+LFTVSVGGQPKY +GF P P I H FNDL +VK ++ + Sbjct: 126 GKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEK 185 Query: 187 TCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGV 246 TCA+VVEPIQGEGGV FL+GLRDLCDE+ ALLVFDEVQ G+GR+G +AY YGV Sbjct: 186 TCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGV 245 Query: 247 TPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPE 306 PDIL+SAK LGGGFPV+AMLTT ++A++ VG+HGSTYGGN LACAVA D ++ PE Sbjct: 246 VPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPE 305 Query: 307 VLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGV 366 +L+G+ + + + + I E++ +F+++RG GLL+G L K++G+A+DFL AG E GV Sbjct: 306 ILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGV 365 Query: 367 MVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405 MVL AGA+V+R APSL++ E DI ++RF AV K+ A Sbjct: 366 MVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404 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: 513 Number of extensions: 17 Number of successful extensions: 2 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: 404 Length adjustment: 31 Effective length of query: 374 Effective length of database: 373 Effective search space: 139502 Effective search space used: 139502 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