Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized)
to candidate Ga0059261_3674 Ga0059261_3674 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= SwissProt::Q93R93 (395 letters) >FitnessBrowser__Korea:Ga0059261_3674 Length = 415 Score = 166 bits (420), Expect = 1e-45 Identities = 127/395 (32%), Positives = 189/395 (47%), Gaps = 32/395 (8%) Query: 30 LIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMR 89 L+ +GA + A+G ID + + V GHGNP +V A++ QAE L + T Sbjct: 21 LVTHAEGAVLHTADGRRVIDAISSWWVTTHGHGNPRIVAAIRDQAEKLDQLIFAGWTHEP 80 Query: 90 GEFY-RTLTAILPPELNRVFPVNSGTEANEAALKFARAHTG-----RKKFVAAMRGFSGR 143 E R L A++P L+ VF +SG+ + E A+K A H R + + + G Sbjct: 81 AETVARDLVAMMPRPLDHVFFSDSGSTSVEVAIKMALGHFANRGEPRHRIIVMQGSYHGD 140 Query: 144 TMGSLSVTWEPKYREPFLPLVEPVEFIP-------YNDVEALKRAVDEET--AAVILEP- 193 T+G +SV + + PL+ V+ IP Y ++AL++ + AA+I+EP Sbjct: 141 TIGGMSVGARGVFNRSYAPLLFDVDTIPFPEGANEYRALDALEQLCAQSPLPAAMIVEPL 200 Query: 194 VQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLA 253 V G GG++ P LRA REI G L I DE+ TG GRTG A E +VPD+L L+ Sbjct: 201 VLGAGGMKMYPPGVLRAMREICAAHGVLFIADEVMTGWGRTGTLLACEQAAVVPDLLCLS 260 Query: 254 KAL-GGGVPLGVAVMREEVARSMPKGG------HGTTFGGNPLAMAAGVAAIRYLERTRL 306 K L GG +PL V + E+ S H +++ NP+A AA A + + Sbjct: 261 KGLTGGSLPLAVTMATPEIFESHRSKDRSKMFFHSSSYTANPIACAAAAANLAIWREEPV 320 Query: 307 WERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLE-------KEHR 359 ER A L RA+ + K+ +R +G +V +E++ Y++ L +E Sbjct: 321 LERVAHLAHRQRSYSRAL-AGKVNNLRQLGTIVAMEVQAPQGAYLSVLGPRLMSFFRERN 379 Query: 360 VLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394 VL G TV +PP I EDL RV + L Sbjct: 380 VLLRPLGNTVY-VMPPYCISDEDLARVYTVIGEAL 413 Lambda K H 0.319 0.137 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: 377 Number of extensions: 15 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: 395 Length of database: 415 Length adjustment: 31 Effective length of query: 364 Effective length of database: 384 Effective search space: 139776 Effective search space used: 139776 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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