Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_085640964.1 MGEO_RS18005 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_002115805.1:WP_085640964.1 Length = 383 Score = 278 bits (710), Expect = 3e-79 Identities = 153/380 (40%), Positives = 227/380 (59%), Gaps = 16/380 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 LS + +LDL+ VLAGP+ L DLGADVIKVERPG GDDTRA+ PPF A G++ Sbjct: 5 LSGITILDLTHVLAGPFCSMTLCDLGADVIKVERPGTGDDTRAF-PPF---ANGKS---- 56 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AY+ + N K+S+ +D + + L A++D+++EN++ G + G +++L A P Sbjct: 57 AYFAAINHGKKSIALDLKSEADRAIFARLLARADVILENYRPGVMERMGYGWETLHAEYP 116 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LIY +++GFG TGP AKR YD ++Q GG+MS+TG + D PV+VG ++ DI+ G Sbjct: 117 RLIYGAVSGFGHTGPEAKRPAYDMVVQARGGVMSITGEKDRD----PVRVGASIGDIVAG 172 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 ++ +LAAL R+ G G+ +D+++LD Q+A L + TGN P G HP+I Sbjct: 173 MFLCQGVLAALMDRERTGKGRKVDVSMLDSQLAILEHAIAITTVTGNPPAPTGARHPSIA 232 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 P++ F +DG F++ GND F K P +DDPRFATN RV N +L LI Sbjct: 233 PFETFHASDGLFVIAAGNDALFEKLCVALDLP-LSDDPRFATNPARVENARLLKRLIEAV 291 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVA-SPI 362 T+ +T + W+ +L AG+P GPI ++ QV DPQ+ AR + +++ + A +PI Sbjct: 292 TIDRTRSHWIAKLGAAGIPSGPIQNVEQVLRDPQILARNMVVDVLDRNGRPAFKAAGNPI 351 Query: 363 RLS--ETPVEYRNAPPLLGE 380 +LS P AP L G+ Sbjct: 352 KLSGMADPTVRPAAPDLDGD 371 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: 465 Number of extensions: 14 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: 383 Length adjustment: 31 Effective length of query: 375 Effective length of database: 352 Effective search space: 132000 Effective search space used: 132000 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 24 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