Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Pedo557:CA265_RS15205 Length = 378 Score = 214 bits (546), Expect = 3e-60 Identities = 134/390 (34%), Positives = 211/390 (54%), Gaps = 30/390 (7%) Query: 26 VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH--TGNGYTNEPV 83 VR +G ++D Q K++ID GI V+ +GH HP +VKA+ EQA + H Y P Sbjct: 5 VRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQTPQ 64 Query: 84 LRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141 + AK L D +F NSG EA E A+KLA++Y + + G +A KNA+HG Sbjct: 65 VNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRY------TGRKGFIACKNAYHGS 118 Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPA 201 T S YS + P P + +N+L + + ++ AV +EP+QGE G+ + Sbjct: 119 TQGAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEKITNE-IAAVFIEPIQGEAGIRVS 177 Query: 202 DADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIG 261 D +++ LR C LLIFDE+Q+G GR+G+++A+ HY V PD+L AK +GGG PIG Sbjct: 178 DLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGGMPIG 237 Query: 262 ALLASERCASVMT---VGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFCER 318 A ++S SV++ + H TT+GG+P+ CA T+ +++ V+++ Q F + Sbjct: 238 AFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQLFKQL 297 Query: 319 LNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMI--LIAGANVVRFA 376 L ++ KEIRG GL++ ++ E K I + +G++ + +N +R A Sbjct: 298 L-----QHPAIKEIRGKGLML--AVEFENFEINKKIIDACILDGVLSDWFLHCSNSMRIA 350 Query: 377 PALIISEDEVNSGLDRFELACKRFLAGVSS 406 P LII+++E+ AC L V+S Sbjct: 351 PPLIITKEEIAE-------ACTIILKNVNS 373 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: 386 Number of extensions: 22 Number of successful extensions: 6 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: 378 Length adjustment: 31 Effective length of query: 375 Effective length of database: 347 Effective search space: 130125 Effective search space used: 130125 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