Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Echvi_1686 Echvi_1686 Predicted acyl-CoA transferases/carnitine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Cola:Echvi_1686 Length = 387 Score = 168 bits (425), Expect = 3e-46 Identities = 118/382 (30%), Positives = 188/382 (49%), Gaps = 19/382 (4%) Query: 9 VLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEAAYYLS 68 VL+ + L+GP AG LADLGA VIK+E PG GD R +K+ EN ++ + + Sbjct: 19 VLEFCQYLSGPSAGLRLADLGARVIKIENPGKGDLCRILP---IKNRWVEN--DSLLFHT 73 Query: 69 ANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINPQLIYC 128 NRNK+S T + ++ L K+D+L+ NF+ G + GL Y+++KA+N L+Y Sbjct: 74 INRNKESYTANLKSEHELAEIKRLIGKADVLMHNFRPGVMEKLGLGYEAVKALNAGLVYA 133 Query: 129 SITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTGLYSTA 188 I+G+G GP+A++ G D ++Q + GLM + G++ GP+ G+A+ D+L G + Sbjct: 134 EISGYGAEGPWARKPGQDLLLQAMSGLMFAS----GNQKDGPMPFGLAIGDMLCGAQAVQ 189 Query: 189 AILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKR--LGNAHPNI-VPY 245 ILAAL HR G G I ++LL+ + Y +G P R + +AHP + PY Sbjct: 190 GILAALVHRKRTGKGSRISLSLLESLLDMQFEVLTTYFASGKRPLRSAVNSAHPLLGAPY 249 Query: 246 QDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQATV 305 + T D + + R+ A G+ + D T+ R A + VL ++ A Sbjct: 250 GIYATKDSHLAIAMIPIAPLRE-ALGCGELERFDQSMVFTH--RDAIKQVLADFLKSA-- 304 Query: 306 FKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIRLS 365 TT W+ +L + G+ + D Q+ A + L + + PIR+ Sbjct: 305 --TTDHWLAKLREKGLWAMDVKDWKQLKATQGYRQSNLEQIIKLTNGQSIKTNRCPIRID 362 Query: 366 ETPVEYRNAPPLLGEHTLEVLQ 387 + P LGEHT + Q Sbjct: 363 GEVLLSDRPAPTLGEHTASIKQ 384 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: 396 Number of extensions: 18 Number of successful extensions: 4 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: 387 Length adjustment: 31 Effective length of query: 375 Effective length of database: 356 Effective search space: 133500 Effective search space used: 133500 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