Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 Length = 406 Score = 540 bits (1392), Expect = e-158 Identities = 263/406 (64%), Positives = 314/406 (77%) Query: 1 MAIEQTAITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCH 60 M++E A+ RA FD+V++P YAPA FIPV+G GSR+WDQ G+E +DFAGGIAV LGH H Sbjct: 1 MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 Query: 61 PALVNALKTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLAR 120 PALV AL Q LWH+SNVFTNEPALRL KL++ATFAER F NSG EANE AFKLAR Sbjct: 61 PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFKLAR 120 Query: 121 HYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVK 180 A R+ K +IIA N+FHGR+LFTV+VGGQ KYSDGFGPK I HVP+NDL A+K Sbjct: 121 RVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180 Query: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFA 240 A + D TCAVV+EPIQGEGGV A +LQG RELC++H ALLVFDEVQ GMGRTG LFA Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDEVQTGMGRTGHLFA 240 Query: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFD 300 Y HYGV PDILTSAK+LGGGFPI+AMLTT ++A G+HG+TYGGNPLACAVAGA D Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVID 300 Query: 301 IINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYA 360 +INTPEVL G+ AK +F L++I ++Y +F+ +RG+GLLIG L +KG+A+D A Sbjct: 301 VINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNA 360 Query: 361 GAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 + G+M+L AGPDV+RFAPSLVVEDADID G+ RF A AK+ A Sbjct: 361 AEQEGLMILQAGPDVVRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406 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: 544 Number of extensions: 17 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 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 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