Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate HSERO_RS23240 HSERO_RS23240 omega amino acid--pyruvate aminotransferase
Query= curated2:O27392 (390 letters) >FitnessBrowser__HerbieS:HSERO_RS23240 Length = 442 Score = 185 bits (469), Expect = 3e-51 Identities = 140/425 (32%), Positives = 207/425 (48%), Gaps = 56/425 (13%) Query: 16 QTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSS 75 + + P +L +G D GN+ +D AG+ +GHAHPK+ A+ L ++ Sbjct: 23 RNFKAAPRMLVSAEGMHYRDDAGNTILDGTAGLWCVPLGHAHPKIVSAVQKSVATLDYAP 82 Query: 76 NIYYTREQV-ELAKLLTAISPH--DRVFFANSGAEANEGAIKLARKF------TGKSEII 126 + ELA+ L A + + VF+ SG+EA + A+K+A + ++ +I Sbjct: 83 SFQLGHPSAFELAERLKAYTGNRFGNVFYTGSGSEAVDTALKIALAYHRAKGNATRTRLI 142 Query: 127 AAENSFHGRTLATVTATG----QKKYSEPFRPLPEGFKHVPYG-------------DIGA 169 E +HG ++ G +K +S P G H+P+ + GA Sbjct: 143 GRERGYHGVGFGGMSVGGIGGNRKTFSTALLP---GVDHLPHTHNLEKNAFTKGEPEYGA 199 Query: 170 -MADAV--------GDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQ 220 +AD + AA+I+EPV G GV+IPP+GYLK ++E+ ++ +LLI DEV Sbjct: 200 HLADELERLVTLHDASNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHGILLIFDEVI 259 Query: 221 TGFGRTGAMFASQLFGVEPDITTVAKAMGGG-YPIGAVLANERVAMAFEPGD------HG 273 TGFGR G FAS F VEPDI T AK + G P+GAV + AF G HG Sbjct: 260 TGFGRLGTPFASDYFDVEPDIFTTAKGLTNGVVPMGAVFVKPEIHDAFMNGPDGIELFHG 319 Query: 274 STFGGNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMI 333 T+ G+P CAA +A++EV E + E A + YF L G V D+R +GL+ Sbjct: 320 YTYSGHPLACAAGLASLEVFQTEGVLENAQAVADYF-QEAAHALRGLPHVIDVRTIGLIA 378 Query: 334 GIEIDGECAGVVDA--------AREMGVLINCTAGKVIRIVPPLVIKKEEIDAAVDVLGH 385 GIE+ G V A A G+LI T G +I + PPL+I K++ID L Sbjct: 379 GIEL-ASIPGRVGARAYDAFVRAFNDGILIRVT-GDIIALSPPLIINKQQIDELFGKLAA 436 Query: 386 VISDL 390 ++ L Sbjct: 437 ILKTL 441 Lambda K H 0.320 0.138 0.404 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: 459 Number of extensions: 21 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: 390 Length of database: 442 Length adjustment: 31 Effective length of query: 359 Effective length of database: 411 Effective search space: 147549 Effective search space used: 147549 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 Aug 03 2021. The underlying query database was built on Aug 03 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