Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_028309837.1 H566_RS0100150 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000482785.1:WP_028309837.1 Length = 452 Score = 152 bits (385), Expect = 2e-41 Identities = 132/428 (30%), Positives = 198/428 (46%), Gaps = 43/428 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ + G A + DG+RY+D V V GH +PA+ EAI QA L H F H Sbjct: 27 PLAIVRGEGAWLHAADGRRYLDAVSSWWVNLHGHAHPAIAEAIAEQARTLPHTMFAGITH 86 Query: 75 GPYLALMEQLSQFVPVSYPLAGML-TNSGAEAAENALKVA-----RGATGKRAIIAFDGG 128 P L +L P PL+ + +++G+ A E ALK+A + +AF+GG Sbjct: 87 EPAARLAAELVARAPA--PLSHVFFSDNGSTAIEVALKIACQYWINQGQKRHRFLAFEGG 144 Query: 129 FHGRTLATL---NLNGKVAPYKQ---RVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182 +HG T + +G AP++ V +P P + P D ++ + RL Sbjct: 145 YHGDTFGAMAAGRSSGFYAPFEDWLFSVDFMPWPQTWIDKPGLD-----DEEAAVLARLD 199 Query: 183 S-VELAVEDVAAFIFEP-VQGEGGFLALDPAFAQALRRFCDER---GILIIIDEIQSGFG 237 + ++ ++AAF+FEP VQG G + A A LR C++ G+ +I DE+ +GFG Sbjct: 200 AWLDRHGHELAAFVFEPLVQGASG---MRMARAPFLRTVCEKVRACGVPVIFDEVMTGFG 256 Query: 238 RTGQRFAFPRLGIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGGL------GGTYS 290 RTG+ FA +G PDLL L K + GG +P+ + + A G+ G T++ Sbjct: 257 RTGRMFAAEHIGFTPDLLCLCKGLTGGFLPMAVTLATPAIHDAFLGDGVDRALLHGHTFT 316 Query: 291 GNPISCAAALASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGI 350 NP+ CAAALASL E+ +R + +R A P + R G + Sbjct: 317 ANPLGCAAALASLRLFDSEDTM---QRIASLEAMQAQRLAALASHPLVSRSRQWGTIAAF 373 Query: 351 EFANADGSPA---PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDI 407 + A + A A + EA ARG+L+ P G A I +L P I L+ Sbjct: 374 DLVPAGAASAGYGSASGRALREAMIARGVLMRPMGDA---IYVLPPYCISVADLDFAYGQ 430 Query: 408 LEQCLAEL 415 L + L EL Sbjct: 431 LREVLDEL 438 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: 516 Number of extensions: 26 Number of successful extensions: 5 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: 452 Length adjustment: 32 Effective length of query: 384 Effective length of database: 420 Effective search space: 161280 Effective search space used: 161280 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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