Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012675040.1 SULAZ_RS07245 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000021545.1:WP_012675040.1 Length = 453 Score = 124 bits (310), Expect = 7e-33 Identities = 113/415 (27%), Positives = 185/415 (44%), Gaps = 57/415 (13%) Query: 7 YYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEI-WAVP 65 Y E + + +G Y++D G +Y+D + GH +PK+ +A+ QV +I Sbjct: 24 YREEDNVIVERGEGNYIYDIFGNKYLDGVASLWCNVHGHNHPKLNKAICDQVSKISHFTT 83 Query: 66 LNFATPARERFIEEFSKLLPPKFGVVFLQNTGTEAVEVAIKIA------KKVTRKPTIVA 119 L + ++ ++ P VF G+EA+E+AIKIA K K + Sbjct: 84 LGASNVPAILLAKKLVEITPKNLNKVFYSEDGSEAMEIAIKIAYHYWHNKGYKEKTKFIT 143 Query: 120 FTNSFHGRTMGSLSI----TWNEKYKKAFEPLY----PHVRFGKF-----NVPHEVDKLI 166 + ++HG T+GS+S+ ++EKYK +Y P+++ + + +E K + Sbjct: 144 LSEAYHGDTIGSVSVGGINIFHEKYKPLLFDVYKLPSPYLKALEIAGREKALEYETTKKL 203 Query: 167 GED------------TCCVVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTG 214 E+ V+ +QG G+ P +LK + + L+I DEV TG Sbjct: 204 VEEVEEFVFKHHQTIAGFVLEAGVQGAAGILPFPKGYLKEVERICREYNVLMIVDEVATG 263 Query: 215 FGRTGAVWAFQKYGVEPDIFTAGKPVAGG-LPIGLAVAREDFGDVF--EPGE-----HGS 266 FGRTG ++A K GV PDI GK + GG LP+ + ++ + F E GE HG Sbjct: 264 FGRTGEMFACIKEGVNPDIMALGKGITGGYLPLAATLTTDEVFEAFLGEFGEAKHFYHGH 323 Query: 267 TFAGNAVVMAAAAAASRLLREEDVPGRAERIGAELAKALGD-TGSRLAVRVKGMGLMLGL 325 T+ GN + A A L EE + L K L + + V+ GLM G+ Sbjct: 324 TYTGNPIACNVALANIDLFEEEKTLENVRKNIDILEKRLLEFLELNHVIDVRNYGLMAGV 383 Query: 326 ELRVKADQFIQP--------------LLERGVMALTAGVNTLRFLPPYMISKEDV 366 EL +K + QP +L+RG+ G + + +PP I +E++ Sbjct: 384 EL-IKDKKTKQPYPYGERTGFKVAKAMLKRGIWVRPLG-DVMVIMPPLSIKEEEL 436 Lambda K H 0.320 0.138 0.408 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: 446 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 453 Length adjustment: 31 Effective length of query: 352 Effective length of database: 422 Effective search space: 148544 Effective search space used: 148544 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