Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_057509163.1 ABB28_RS13760 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_001431535.1:WP_057509163.1 Length = 426 Score = 139 bits (349), Expect = 2e-37 Identities = 120/381 (31%), Positives = 173/381 (45%), Gaps = 32/381 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P + A + D DG RYID+VG G + +GH +PAV +A++ A + AP Sbjct: 35 PFFVERADGAYLHDVDGNRYIDYVGSWGPMIVGHNHPAVRQAVKKAADSGLSFG---APC 91 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTL 134 + + E L++ VP S + M+ NSG EA +A+++ARGATG+ I+ F+G +HG Sbjct: 92 AAEVTMAETLTRLVP-SCEMVRMV-NSGTEATLSAIRLARGATGRSRIVKFEGCYHG--- 146 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLP-YPSADTGVTCEQALKAMDRLFSV-ELAVEDVA 192 +G K G L V P P+ + +T D ++ E E +A Sbjct: 147 -----HGDSFLVKAGSGMLTLGVPTSPGVPAGLSELTLTLPYNDFDAATALFEAQGEQIA 201 Query: 193 AFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEP 252 I EPV G + + Q LR C G ++I DE+ +GF R A G+ P Sbjct: 202 GLIIEPVVGNANCIPPREGYLQHLRALCTRFGTVLIFDEVMTGF-RVALGGAQAHYGVTP 260 Query: 253 DLLLLAKSIAGGMPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALASLAQMTDE 309 DL K I GGMP+GA G++ELM + G GT SGNP++ AA LA L + Sbjct: 261 DLTTFGKIIGGGMPVGAYGGKRELMQQISPAGPIYQAGTLSGNPVAMAAGLAMLELVQQP 320 Query: 310 NL-ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEF--------ANADGSPA 360 A R + + +G+S T VG M G+ F A A Sbjct: 321 GFHAQLSARAARLCAGLEQAAAEAGVSV---TTTQVGGMFGLFFTDQKVETYAQATACDI 377 Query: 361 PAQLAKVMEAARARGLLLMPS 381 PA + A +G+ L PS Sbjct: 378 PA-FNRFFHAMLEQGVFLAPS 397 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: 469 Number of extensions: 33 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: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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 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