Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ac3H11_198 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_198 Length = 404 Score = 224 bits (571), Expect = 4e-63 Identities = 150/408 (36%), Positives = 212/408 (51%), Gaps = 24/408 (5%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L LRV++ + ++ GP G +LADLGA+VIKVE P +GD TR L A A Sbjct: 15 LEGLRVVEFTHMVMGPTCGMVLADLGAEVIKVE-PVDGDRTR-----HLLGAG------A 62 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 ++ NRNK+S+ +D PEG R+LAA +D++ +NFK G + YGLDY +L INP Sbjct: 63 GFFPMFNRNKKSIALDLRSPEGLAAARKLAASADVVAQNFKPGVMTKYGLDYAALSQINP 122 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LIY + TGF GPY R D ++Q +GGL +TGRP GD P++ G ++ DI+ G Sbjct: 123 RLIYVNHTGF-LPGPYEHRTALDEVVQMMGGLAYMTGRP-GD----PLRAGSSVNDIMGG 176 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 ++ +AAL R G GQ +D AL + V + M Y TG + + + Sbjct: 177 MFGAIGAMAALMQRGITGRGQEVDSALFENNVFLVGQHMMQYAVTGKPAAPMPDRISSWA 236 Query: 244 PYQDFPTAD-GDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 Y F D G L +D Q++ F + G D ATN RV R L+P++R+ Sbjct: 237 VYDVFSVKDGGQIFLAAVSDAQWQTFCDAMGYADLKADTSLATNNDRVRARPTLMPVLRE 296 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARG--LAMELPH-LLAGKVPQVA 359 T E E+ G+P PI ++F DP +QA G + LP AG+ Q+ Sbjct: 297 RLAQHTADELAAVFERHGLPFAPIRRPEELFDDPHLQATGGLADITLPDGERAGQTAQIT 356 Query: 360 -SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 P+RL ++ R PP LG+HT E+LQ LG V A AG + Sbjct: 357 LLPLRLDGQRLDVRCDPPRLGQHTAELLQG-LGYTADEVAALHAAGTI 403 Lambda K H 0.319 0.137 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: 462 Number of extensions: 25 Number of successful extensions: 6 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: 406 Length of database: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 Sep 17 2021. The underlying query database was built on Sep 17 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