Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__WCS417:GFF1577 Length = 389 Score = 287 bits (734), Expect = 4e-82 Identities = 159/377 (42%), Positives = 222/377 (58%), Gaps = 9/377 (2%) Query: 14 MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73 +M Y P A RG G+RLWDQQG+EY+D G+AV +GH+HPRLV A++EQAG H Sbjct: 6 LMTTYQPLALSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLH 65 Query: 74 TGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVA 133 T N Y+ + RLA++L + DR FF NSGAEANE ALKLAR + + G E +V Sbjct: 66 TSNLYSIDWQQRLAQRLTQLSGLDRAFFNNSGAEANETALKLARLHGWKK-GIEAPLVVV 124 Query: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKAL---IDDNTCAVIVE 190 +NAFHGRTL T++A P+ F LP + DL + +A+ AV++E Sbjct: 125 MENAFHGRTLGTLAASDGPSVRLGFQQLPGDFLKVRFGDLAALEAITKAFGPRITAVLLE 184 Query: 191 PMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLST 250 P+QGE GV+PA + +L+ LR+ C L++ DE+QTG+GRTG +A+ H G+ PD+++ Sbjct: 185 PIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPDVMTL 244 Query: 251 AKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQ 310 AK LG G PIGA LA A + T G+HG+T+GGNPLAC V V I + +L Q Sbjct: 245 AKGLGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQNAAQ 304 Query: 311 RHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEE-GLMILIAG 369 + + RL + IRG GL+IG E A + ++ +AA+E GL+I + Sbjct: 305 QGERLLARLRVELNEHAQVVAIRGQGLMIGI----ELASPCRDLAQRAAQEHGLLINVTR 360 Query: 370 ANVVRFAPALIISEDEV 386 ++R P L + EV Sbjct: 361 GKIIRLLPPLTLDTQEV 377 Lambda K H 0.321 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: 377 Number of extensions: 10 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: 406 Length of database: 389 Length adjustment: 31 Effective length of query: 375 Effective length of database: 358 Effective search space: 134250 Effective search space used: 134250 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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