Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 493 bits (1270), Expect = e-144 Identities = 231/399 (57%), Positives = 303/399 (75%) Query: 8 ITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNAL 67 +TR TFDEV++P+++PA F+P +G GSR+WD QG++Y+DFAGGIAVTALGH HP L+N L Sbjct: 6 VTRQTFDEVMVPVFSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVL 65 Query: 68 KTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRH 127 QG LWHI N +TNEP LRL ++L + TFA+R F NSG EANE A KLAR A RH Sbjct: 66 HEQGGKLWHIGNGYTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRH 125 Query: 128 SPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHT 187 K +II+F +FHGR+ FTVSVGGQPKYS+GFGP PA I H+P+ND+ AVK + T Sbjct: 126 GADKYEIISFTQSFHGRTFFTVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQT 185 Query: 188 CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVT 247 CAV+VEPIQGEGGV A P FL+ LRE CDQH ALL+FDEVQ G+GR+G +AY GVT Sbjct: 186 CAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVT 245 Query: 248 PDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEV 307 PDILT+AKALG GFPI AMLTT E+A+ F G HG+TYGGNPL A+A ++++ P++ Sbjct: 246 PDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKL 305 Query: 308 LEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVM 367 LEG++++ + HL K+++++ +F+++RG GLLIGAEL +KGRA+DF+ A + GV+ Sbjct: 306 LEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVI 365 Query: 368 VLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406 +L AGPDV+RF PSL++ D++EG +R A A+ +VGA Sbjct: 366 MLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIESIVGA 404 Lambda K H 0.322 0.138 0.415 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: 573 Number of extensions: 21 Number of successful extensions: 1 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: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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