Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012503231.1 CPAR_RS10185 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q8ZV07 (383 letters) >NCBI__GCF_000020505.1:WP_012503231.1 Length = 424 Score = 129 bits (325), Expect = 1e-34 Identities = 120/400 (30%), Positives = 192/400 (48%), Gaps = 37/400 (9%) Query: 11 YGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLNFAT 70 Y ++ G M + D G++ ID ++ G+ +P + A +Q+E + V T Sbjct: 24 YPVKSASGVMIELED--GRQLIDGMSSWWAAIHGYNHPVLNRAATEQLERMSHVMFGGLT 81 Query: 71 --PARERFIEEFSKLLPPKFGVVFLQNTGTEAVEVAIKIAKKVTR------KPTIVAFTN 122 PA E + LLP VF ++G+ +VEVAIK+A + R K ++ + Sbjct: 82 HEPAIE-LGKILISLLPDPLDSVFFCDSGSVSVEVAIKMALQYWRAAGKPDKKRLLTVRS 140 Query: 123 SFHGRTMGSLSIT-----WNEKYKKAF-EPLY---PHVRFGKFNVPHEVDKLI------G 167 +HG T ++S+ + + A E L+ P FG+ ++++ Sbjct: 141 GYHGDTFMAMSVCDPVTGMHSLFSGAVPEQLFVESPSCGFGEPWREEAIEEMRQALEDHA 200 Query: 168 EDTCCVVVEPI-QGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQK 226 + V++EPI QG GG+ +P +L+ LRE G LLIFDE+ TGFGRTG ++A ++ Sbjct: 201 DTIAAVIIEPIVQGAGGMRFYSPVYLQRLRELCTEHGVLLIFDEIATGFGRTGKLFAMER 260 Query: 227 YGVEPDIFTAGKPVAGG-LPIGLAVAREDFGDVFEPGE-----HGSTFAGNAVVMAAAAA 280 GV PDI GK + GG + + +A D G+ HG TF N + A A A Sbjct: 261 AGVTPDIVCLGKALTGGYMTLAATIATGHVADTISGGDPGLFMHGPTFMANPLACAVAVA 320 Query: 281 ASRLLREEDVPGRAERIGAELAKALGDTGSRLAVR-VKGMGLMLGLELRVKAD--QFIQP 337 + RLL D +RI +LA+ L AVR V+ +G + +EL D + Sbjct: 321 SLRLLLSGDWRATVQRIERQLAEGLAPCVKLSAVRDVRVLGAIGVVELYHPVDMASIQKR 380 Query: 338 LLERGVMALTAGVNTLRFLPPYMISKEDVEVVHAAVTEVL 377 +E GV G + +PP++IS+ ++ + +AV EVL Sbjct: 381 FVEYGVWVRPFG-RLVYLMPPFIISEAELVRLTSAVCEVL 419 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: 388 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 424 Length adjustment: 31 Effective length of query: 352 Effective length of database: 393 Effective search space: 138336 Effective search space used: 138336 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