Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900105005.1:WP_090271605.1 Length = 417 Score = 239 bits (610), Expect = 1e-67 Identities = 142/391 (36%), Positives = 206/391 (52%), Gaps = 8/391 (2%) Query: 30 DGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLSQFVP 89 DGK Y+DF GIGV + GHC+P VV A + Q +L H + H P L L E+L +P Sbjct: 28 DGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQPMLDLAERLVGKMP 87 Query: 90 VSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQR 149 +N+G+EA E AL++AR AT + +I F+GGFHGRT+ ++ + Sbjct: 88 DGIDSVAF-SNAGSEAVEMALRLARHATRRANVIVFNGGFHGRTMGAASMTTSGTKVRNA 146 Query: 150 VGELPGPVYHLPYP-SADTGVTCEQA----LKAMDRLFSVELAVEDVAAFIFEPVQGEGG 204 + V P+P S G + E+A L +D + + A ED AA + EPVQGE G Sbjct: 147 YHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQTAPEDTAAMVIEPVQGEFG 206 Query: 205 FLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAGG 264 + + AF Q L C + GIL++ DEIQ+GFGR+G+ ++ GI PD+++ AK +A G Sbjct: 207 YYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQHFGITPDIVITAKGLASG 266 Query: 265 MPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAIVS 324 PL A+ + LMA G GGTY N +SCAAALA+L M +ENL + Q + Sbjct: 267 FPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVMDNENLVANAAARGQQLWD 326 Query: 325 RYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMPSGKA 384 + + P + L G G M G+E A + P A + A+ GLLL+ G Sbjct: 327 HLQILRQQ--YPQLADLRGKGLMLGLEIAQSPDKPLADLAASLTTASEEEGLLLLRCGTD 384 Query: 385 RHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 IIR L PL + +++ + + LA + Sbjct: 385 SQIIRWLPPLVVSEAEVDDAVQRFTRVLARV 415 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: 408 Number of extensions: 28 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: 417 Length adjustment: 31 Effective length of query: 385 Effective length of database: 386 Effective search space: 148610 Effective search space used: 148610 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