Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_001592305.1:WP_068170823.1 Length = 428 Score = 213 bits (543), Expect = 7e-60 Identities = 139/400 (34%), Positives = 199/400 (49%), Gaps = 34/400 (8%) Query: 29 EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTGNGYTNEPV---LR 85 + + LWD +G+ +IDFAGGIAV GH HP++ A+ Q +F H+ Y P + Sbjct: 37 KNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQRFTHSC--YQVVPYAEYVS 94 Query: 86 LAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRT 142 LA+++ + + F ++GAEA E A+K+AR + +SG++AF AFHGR+ Sbjct: 95 LAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARS------STGRSGVIAFGGAFHGRS 148 Query: 143 LFTVSAGGQ-PAYSQDFAPLPPQIQHAIYN----DLDSAKALID---------DNTCAVI 188 LF VS G+ Y F P PP+I H + LD K +D A++ Sbjct: 149 LFAVSLTGKVQPYKAGFGPFPPEIYHVPFPAEGASLDETKRAMDHVFKCDIEPSRVAAIV 208 Query: 189 VEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLL 248 EP+QGEGG P D + LR LCD H LLI DEVQTG RTG ++A HYGV+PDL+ Sbjct: 209 FEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQTGFARTGRMFAMEHYGVSPDLM 268 Query: 249 STAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGV 308 + AK++ GG + A+ G G TY GNPLA A + V + ++ Sbjct: 269 TMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPLAIAASHAVLDVMAEEKLPERA 328 Query: 309 KQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEY----AGKAKAISNQAAEEGLM 364 ++ L A A+Y E+RGLG ++ C D A K + A + GL+ Sbjct: 329 QRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVDAAGAPDADTTKQVQAAALKRGLL 388 Query: 365 ILIAG--ANVVRFAPALIISEDEVNSGLDRFELACKRFLA 402 +L G NV+R+ L I + L + A LA Sbjct: 389 LLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAETLA 428 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: 465 Number of extensions: 21 Number of successful extensions: 5 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: 428 Length adjustment: 31 Effective length of query: 375 Effective length of database: 397 Effective search space: 148875 Effective search space used: 148875 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 09 2024. 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