Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011157876.1 TX73_RS11845 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000195775.1:WP_011157876.1 Length = 424 Score = 203 bits (516), Expect = 9e-57 Identities = 145/409 (35%), Positives = 205/409 (50%), Gaps = 50/409 (12%) Query: 16 PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 PV+A A S +WD +GK Y+DFAGGIAV GH HPR+V A+ EQ +F HT Sbjct: 23 PVFAERAL------NSEIWDVEGKRYVDFAGGIAVLNTGHCHPRIVAAIREQLDRFTHTC 76 Query: 76 NGYTN-EPVLRLAK---QLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 E +RLA+ QL + ++GAEA E A+K+AR + +SG+ Sbjct: 77 FQVAPYEGYIRLAERLNQLAPINGPLKSILLSTGAEATENAVKIARA------ATGRSGV 130 Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIYNDLDSAKALIDDNTC----- 185 +AF FHGRT F + G+ Y + P P + H + S ++ D C Sbjct: 131 IAFTGGFHGRTAFASAMTGKVIPYKKALGPPLPGVWHVPFPVAGSDVSVEDALRCVQFVF 190 Query: 186 ----------AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGEL 235 A+I+EP+QGEGG A + +RGLR LCD + +LI DEVQTG GRTG++ Sbjct: 191 KADIDASQVAAIIIEPVQGEGGFHQAPPELMRGLRRLCDENGIVLIADEVQTGFGRTGKM 250 Query: 236 YAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEV 295 +A HY V D++ AK+L GG P+ ++ G G TY GNPLACA A Sbjct: 251 FAMEHYDVQADIVCVAKSLAGGLPLSGVIGRAAIMDAAEPGGLGGTYAGNPLACAAA--- 307 Query: 296 FATINTREVLNGVKQRHQWFCERLNAINARYGLFKEI------RGLGLLIGC-VLK---- 344 A ++ E N + + +Q ERL + R+ L + RG G ++ +LK Sbjct: 308 LAVLDVFEEENLIARANQ-IGERLRSAIDRFALSNTLVPTSVARGPGAMVAFDILKQRGS 366 Query: 345 -DEYAGKAKAISNQAAEEGLMILIAG--ANVVRFAPALIISEDEVNSGL 390 + A K ++ A E GL++L G AN +R L S+ V+ GL Sbjct: 367 NEPDAEATKRVTRLAHENGLILLSCGTAANTIRILVPLTASDAIVDEGL 415 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: 443 Number of extensions: 22 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: 424 Length adjustment: 31 Effective length of query: 375 Effective length of database: 393 Effective search space: 147375 Effective search space used: 147375 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