Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 197 bits (501), Expect = 5e-55 Identities = 135/406 (33%), Positives = 206/406 (50%), Gaps = 44/406 (10%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + VWD G Y+DF GGI V LGHC+PA+V A++ Q +L H + N + P LAL Sbjct: 30 GEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWHLS-NTMTNEPALAL 88 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134 +L V ++ NSGAEA E ALK+AR K +IAFD FHGRT Sbjct: 89 ATKL---VEATFADRVYFANSGAEANEAALKLARRYAIEKFGEHKVEVIAFDKAFHGRTF 145 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193 T+++ G+ A Y G P + HLP+ + + ++E AV D A Sbjct: 146 FTVSVGGQAA-YSDGFGPKPAAITHLPF----------------NDIAALEAAVSDNTCA 188 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 + EP+QGEGG + DP F +A+RR D+ L+I DE+Q+G GRTG +A+ I PD Sbjct: 189 IMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPD 248 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313 +L AK++ GG P+ A++ ++ + L G G TY GNP++CA A + + + Sbjct: 249 ILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLD 308 Query: 314 WGERQEQ----AIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369 + +EQ + E++ S G+ +GA+ +FA + + Sbjct: 309 GVKHREQLFRDGLAQINEKYHV--FSEIRGKGLLLGAVLNEQFA--------GRSRDFLN 358 Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 A+ A GLL + +G +++R L I + EGL E+ +A++ Sbjct: 359 ASVAEGLLTLMAG--ANVVRFTPSLVIPEADIVEGLARFERAVAKV 402 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: 432 Number of extensions: 24 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: 404 Length adjustment: 31 Effective length of query: 385 Effective length of database: 373 Effective search space: 143605 Effective search space used: 143605 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 17 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