Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 254 bits (649), Expect = 3e-72 Identities = 144/381 (37%), Positives = 205/381 (53%), Gaps = 6/381 (1%) Query: 20 NYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSN 79 NY P + RGEG VWD G +D + + GH HP +++A+ +QA ++ S Sbjct: 19 NYKPLDVVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSR 78 Query: 80 VFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYG--PQKYEIIAA 137 F N+ +L T + ++ NSGAEA E+A K R++ +V G + EII Sbjct: 79 AFRNDQLALFYEELAALTGSHKILPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVC 138 Query: 138 SNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQG 197 S++FHGRT+ V+ P GFGP G VP+ D AL+AA++ T AV+LEPIQG Sbjct: 139 SDNFHGRTISIVSFSTDPDARGGFGPFTPGFRTVPFGDAAALEAALTPNTVAVLLEPIQG 198 Query: 198 EGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSL 257 E GV+ YL R LC E N +++ DE+Q+G+GR G+L A H GV D+ K+L Sbjct: 199 EAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVEADVTLIGKAL 258 Query: 258 GGGF-PIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHE 316 GGF P+ A+L+ E+ L G HG+T+GGNPLA AVA AA+ V+ ++D A+ Sbjct: 259 SGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLVEEGMIDNAAAQGA 318 Query: 317 RFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVV 376 F +L I + E RG GL++ L E G AR A V+ + Sbjct: 319 YFLEQLGAI--RSNVIREARGRGLMLAVELHPE-AGGARRYCEALRARGVLAKDTHDHTI 375 Query: 377 RFAPSLVIDDAEIDEGLERFE 397 R AP LVI ++D LE+F+ Sbjct: 376 RIAPPLVITREQVDWALEQFD 396 Lambda K H 0.318 0.135 0.394 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: 374 Number of extensions: 21 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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