Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 8502295 DvMF_3003 putative transcriptional regulator, GntR family (RefSeq)
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Miya:8502295 Length = 394 Score = 305 bits (781), Expect = 1e-87 Identities = 169/384 (44%), Positives = 238/384 (61%), Gaps = 13/384 (3%) Query: 17 IQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGY 76 + S IRE+LK+T +P I+SFAGGLP P FP + A AAA +L E G ALQY+ TEG+ Sbjct: 10 VPRSYIREILKVTAQPDIISFAGGLPHPASFPVDAVASAAASVLEEAGPEALQYTTTEGF 69 Query: 77 APLRAFVAE-----WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQA 131 PLR ++A+ I V P+++LITTGSQQALDLV K +D G V++E P Y+GAIQ Sbjct: 70 PPLRQWIADRYKRQGINVSPDDILITTGSQQALDLVAKACIDRGGRVVMERPGYLGAIQC 129 Query: 132 FRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQM 191 F + GP F+TVP G D DAL + + Y +PSFQNP+G R+ + ++ Sbjct: 130 FSVFGPDFVTVPLTPRGVDTDALRKA--ATGAQVFYAVPSFQNPSGITYDEQTRREVAEI 187 Query: 192 VMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVA 251 + E G ++VED+ Y EL F LP + + P V+ LGSFSKV+SPGLR+ + A Sbjct: 188 MAETGCLMVEDNPYGELRFMGQHLPPVRAYMQA---PSVL-LGSFSKVVSPGLRLGWVCA 243 Query: 252 HPEALQKLVQAKQGADLHTPMLNQMLVHE-LLKEGFSERLERVRRVYREKAQAMLHALDR 310 E L ++ AKQ +DLHTP Q ++H L+ + + +R Y + AM+ A+ R Sbjct: 244 PQEVLNPMITAKQASDLHTPGFTQRILHRYLMDNDVDKHIASIRARYGAQRDAMVQAIRR 303 Query: 311 EVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLS 370 P++V T P+GGMF+W LP+G+SAE LF +A+E VAFVPG PF+ + ++T RL+ Sbjct: 304 HFPEDVACTEPEGGMFLWCTLPEGISAEALFHKAIERKVAFVPGRPFYVD-ETDDTFRLN 362 Query: 371 YATLDREGIAEGVRRLGRALKGLL 394 ++ E I EG+ RLG+ L+ L Sbjct: 363 FSNSSPELIEEGIARLGQCLREYL 386 Lambda K H 0.320 0.139 0.403 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: 479 Number of extensions: 25 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: 397 Length of database: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 09 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