Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_001294205.1:WP_053937056.1 Length = 400 Score = 193 bits (491), Expect = 7e-54 Identities = 134/409 (32%), Positives = 204/409 (49%), Gaps = 50/409 (12%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + VWD GK YIDF GGI V +LGHC+P +V A+ Q +L H + N + P LAL Sbjct: 26 GAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNEPALAL 84 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGAT------GKRAIIAFDGGFHGRTL 134 + L V ++ NSGAEA E ALK+AR A+ K +++ FHGRT Sbjct: 85 AKTL---VEHTFAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTF 141 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193 T+++ G+ Y G P + H Y + L S+E ++D A Sbjct: 142 FTVSVGGQ-PKYSDGFGPKPAGIEHFKY----------------NDLASLEALIDDDTAC 184 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 I EP+QGEGG F Q +R CD+ L+I DE+QSG GRTG +A+ G+ PD Sbjct: 185 VIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPD 244 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT-DENLA 312 +L AK + GG P+GA++ +++ L G G TY GNP++ A A +++ +T E L+ Sbjct: 245 ILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRPETLS 304 Query: 313 TWGERQE------QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366 + E QAI +Y P + + G+G + G++ + + Sbjct: 305 GVKAKSERIRAGLQAIADKY---------PVVAEIRGMGLLIGVQLK----AEYAGRSRD 351 Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 V+ AA G+L++ +G ++R L I + ++ GL +E+ A L Sbjct: 352 VLNAAAEEGVLVLAAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398 Lambda K H 0.320 0.137 0.402 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: 420 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: 416 Length of database: 400 Length adjustment: 31 Effective length of query: 385 Effective length of database: 369 Effective search space: 142065 Effective search space used: 142065 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 Sep 24 2021. 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