Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate WP_015798369.1 AFER_RS04845 aspartate aminotransferase family protein
Query= reanno::Btheta:353284 (373 letters) >NCBI__GCF_000023265.1:WP_015798369.1 Length = 431 Score = 213 bits (543), Expect = 6e-60 Identities = 144/400 (36%), Positives = 208/400 (52%), Gaps = 43/400 (10%) Query: 12 INIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKL 71 I + +G+GC VWD +G YLD +GG S+GH P V IS+Q A + S +N+ Sbjct: 23 IELDRGEGCWVWDAHGERYLDCFGGILTTSVGHNVPEIVSAISDQAARVIHSSTLYLNRP 82 Query: 72 QQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRTSLAV 131 ++AERL K SG D +F SG EAN+ AL LA+ G +V + ++HGR+ + Sbjct: 83 MIELAERLAKASGIPDAKVFFTTSGTEANDAALLLATAALGSNQVFALRNSYHGRSFTEI 142 Query: 132 EATNN----PTIIAPIN-----------------NNGHVTYLPLNDIEAMKQELAKGDVC 170 T N PT +P++ ++ + D+E G V Sbjct: 143 AVTGNRTWSPTSYSPLSVSWLQGGSRLRGPLAGLSDAEYVARGVADLEDALLTTTAGRVA 202 Query: 171 AVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGK-FFAHQYNHIQ 229 A+I E IQGVGG +P + EL +V G + I DE+Q+G+GR+G+ F+ ++ + I Sbjct: 203 ALIAEPIQGVGGFCLPPDGYFGELWRVTQREGILWISDEVQTGFGRTGEHFWGYEAHGIT 262 Query: 230 PDIITVAKGIGNGFPMAGVLISPMFKPVYGQLGT----TFGGNHLACSAALAVMDVIEQD 285 PD+IT AKG+GNG +AGV+ V LGT TFGG+ + +A +A D I Sbjct: 263 PDLITFAKGVGNGMSLAGVIGR---AEVMDALGTNSISTFGGSPITAAAGVATFDYIIDH 319 Query: 286 NLVENAKAVGDYLLEEL----KKFPQIKEVRGRGLMIGLEF-----EEPIKELRSRLI-- 334 +L+ NA+A G L E L + P I EVRG+GLM G+E EP EL +R + Sbjct: 320 DLMANARARGAELREGLDAIARSTPAIGEVRGKGLMQGVELVWPGTVEPAPELATRALEA 379 Query: 335 -YDEHVFTGASGT--NVLRLLPPLCLSMEEADEFLARFKR 371 E V G G NVLR+ PP+ +S E+ + L F+R Sbjct: 380 ARREGVLIGKGGLHGNVLRIAPPMTISAEQIEHALEAFRR 419 Lambda K H 0.320 0.139 0.403 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: 354 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: 373 Length of database: 431 Length adjustment: 31 Effective length of query: 342 Effective length of database: 400 Effective search space: 136800 Effective search space used: 136800 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