Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_013009663.1 DACET_RS01590 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000025725.1:WP_013009663.1 Length = 389 Score = 289 bits (739), Expect = 1e-82 Identities = 160/385 (41%), Positives = 213/385 (55%), Gaps = 7/385 (1%) Query: 20 NYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSN 79 NYA V+G G R+ D G DF GI+V LGH+HPA+ ++ QA L H SN Sbjct: 7 NYARYPLSFVKGEGCRLTDDKGEIYFDFGSGISVVNLGHSHPAVTESICTQAGTLIHTSN 66 Query: 80 VFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALN 139 ++ RLA KL +F VFFCNSG EANEAA KLAR + F ++ ++ N Sbjct: 67 LYNIPVQERLADKLSRRSFGGDVFFCNSGMEANEAALKLARIYGNTHFEGKRLRVITLEN 126 Query: 140 SFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAV-SDKTCAVVLEPIQGE 198 SFHGR+ T++ GQ K GF P TH+P ND ALK V A +LE IQGE Sbjct: 127 SFHGRSYMTLSATGQDKIKKGFEPVADFFTHIPANDFDALKREVDKGDVAAFMLELIQGE 186 Query: 199 GGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLG 258 GG+ YL + C +L+ DE+QTG R+G FAY+ +G+ PD++T AK + Sbjct: 187 GGLCALNKKYLAQCADFCRKEGVMLILDEIQTGFCRTGSYFAYEQFGIEPDVITLAKGIA 246 Query: 259 GGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKF 318 G P+ AM+ + AK++ GTHGTT+GGN LACA A AV DV+N L VN K Sbjct: 247 NGVPMGAMIAKPEFAKYMTPGTHGTTFGGNFLACAAALAVFDVMNADGFLEEVNEKGAYM 306 Query: 319 KTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDVIRF 378 K LE I E G V G+G++LG + G+ K+ N A L+++ AG DV+R Sbjct: 307 KEALENIFE--GTDVTVLGMGMMLGAKI----PGRQKEFINKAIENKLLLVPAGHDVVRI 360 Query: 379 APSLVVEDADIDAGLDRFERAAAKL 403 P L + D+DAGL+ + A L Sbjct: 361 YPPLTISQEDLDAGLELISKTATDL 385 Lambda K H 0.320 0.136 0.400 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: 398 Number of extensions: 22 Number of successful extensions: 3 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 Apr 10 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