Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 335 bits (859), Expect = 1e-96 Identities = 174/397 (43%), Positives = 245/397 (61%), Gaps = 8/397 (2%) Query: 12 DFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQA 71 +F+ ++ Y RG G RVWD G+E +DF GIA LGHAHP ++A ++EQ Sbjct: 24 NFNTYVMNTYGRFPIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQI 83 Query: 72 NKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEK 131 +L HVSN++ LA L+ + A++ FFCNSGAEANE A KLAR+ AH++ E Sbjct: 84 KRLHHVSNLYYIPVQGELAQWLIQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIEN 143 Query: 132 YEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSD------ 185 I+ A SFHGRTL T+ GQ KY GF P + G +VPYND+AA+++A+ + Sbjct: 144 PTILTAHASFHGRTLATMTATGQPKYHKGFSPLMPGFYYVPYNDIAAIESAIEELDKDKR 203 Query: 186 KTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYG 245 + A++LE +QGEGG+ P +++Y + RE+C+ LL+ DEVQ GMGRSGK++ Y++ G Sbjct: 204 QVAAIMLEALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYENLG 263 Query: 246 VTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTP 305 + PDI TSAK LGGG PI AML + G+H +T+GGNP ACAVA AV + Sbjct: 264 IEPDIFTSAKGLGGGIPIGAML-CKSHCDVFEPGSHASTFGGNPFACAVALAVCHTLEQE 322 Query: 306 EVLNGVNAKHDKFKTRLEQIGEKY-GLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAERE 364 +L V + D+ + L+ I +KY LF+EVRG GL+ G L+ + DI AA E Sbjct: 323 NLLANVQQRGDELRIELKAIADKYPNLFSEVRGWGLINGLELNATATLTSIDIVKAAMNE 382 Query: 365 GLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAA 401 GL+I+ AGP V+RF P L+V + ++ +D +A A Sbjct: 383 GLLIVPAGPKVLRFVPPLIVTETEVKEAMDLLAKAIA 419 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: 435 Number of extensions: 17 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: 423 Length adjustment: 31 Effective length of query: 375 Effective length of database: 392 Effective search space: 147000 Effective search space used: 147000 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