Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF2665 HP15_2609 acyl-CoA transferase/carnitine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Marino:GFF2665 Length = 398 Score = 260 bits (664), Expect = 6e-74 Identities = 143/391 (36%), Positives = 222/391 (56%), Gaps = 9/391 (2%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L +R++DL+ +L+GP+AG +LAD+GA+ IKVE P G+ TR+ KD R Sbjct: 5 LEGVRIIDLTHMLSGPYAGMLLADMGAESIKVE-PLKGEGTRSL---LAKDPRNSYNGHG 60 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AY+++ NRNK+SV ID G + +L +DI+++NF G A +D++ L +NP Sbjct: 61 AYFITLNRNKKSVCIDLKSEAGLQTFYDLVKDADIVLDNFSAGVPAKLKIDHEHLSRVNP 120 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 ++I CS+TGFGQ GP KR +D ++QG+GG MS+TG + P + G+ + D+ G Sbjct: 121 RIITCSVTGFGQAGPNFKRPAFDQVVQGIGGGMSITGH----DAEHPARAGIPIGDLGGG 176 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 +++ +LAAL R G GQH+D+++LD Q++ L A Y +G+ P +GN H V Sbjct: 177 MFAVMGVLAALHSRAVNGYGQHVDISMLDCQISMLNYMATMYFLSGDNPSPIGNGHFVHV 236 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 PY F T++G I+ V D + E+ G + DP + T R A++ + ++ Sbjct: 237 PYDAFRTSNGFVIIAVIFDSFWDNLVELLGIDE-LRDPAYKTQPGRFADKHKINGILTDL 295 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363 TT WV L A +PC P+N + +DPQV R + +++P G V +PI+ Sbjct: 296 LKTNTTEHWVELLSSARIPCAPVNKFSDALSDPQVLFRNMVVDIPQFDGGTVKAPGNPIK 355 Query: 364 LSETPVEYRNAPPLLGEHTLEVLQRVLGLDE 394 LS + APPLLG+HT +VL+ + DE Sbjct: 356 LSVDSSDSYTAPPLLGQHTEDVLKSLGYSDE 386 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: 449 Number of extensions: 22 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: 398 Length adjustment: 31 Effective length of query: 375 Effective length of database: 367 Effective search space: 137625 Effective search space used: 137625 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