Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_057508570.1 ABB28_RS10465 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_001431535.1:WP_057508570.1 Length = 398 Score = 226 bits (575), Expect = 1e-63 Identities = 147/404 (36%), Positives = 210/404 (51%), Gaps = 27/404 (6%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L +RV++ ++A P+A ++ A+ GA+VIK+E P GD R W + G+ T Sbjct: 3 GPLHGIRVVEFGTLIAAPFAARLFAEFGAEVIKIESPEGGDPLRKW-----RQLHGD--T 55 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 + L A RNK+SV +D EG R+LAA +D++IENF+ GGL GL +D L A+ Sbjct: 56 SLWWSLQA-RNKKSVALDLKSAEGAEAARQLAASADVVIENFRPGGLEKLGLGWDVLSAM 114 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP L+ I+G+GQ GPY R G+ + + +GG+ T GD P +VG++L D L Sbjct: 115 NPDLVMVRISGYGQDGPYRDRPGFGAIGEAMGGIRYTT----GDPSTPPARVGISLGDSL 170 Query: 182 TGLYST-AAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 L+ A++A L + GGGQ +D++L++ + + + G +R G A P Sbjct: 171 ASLHGVMGALMALLRVKTGQGGGQVVDVSLVESVFNLMESLVPEHAMFGTVRERTGGALP 230 Query: 241 NIVPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299 I P +PTADG F++ GN D FR+ G+ ADD ATN RV A L Sbjct: 231 GISPSNTYPTADGGFVVIAGNSDPIFRRLMRAIGRVDLADDAALATNPGRVLRNAELDAA 290 Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMEL------PHLLAG 353 I T + L+ A VP G I A + ADP +ARG+ +E P L G Sbjct: 291 ITHWTSGLHIDAVLAALDAADVPAGRIYSAADIVADPHYRARGMLLETTLPDGQPITLPG 350 Query: 354 KVPQVASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAV 397 VP +LS TP + P LGEHT +VL LG+ AA+ Sbjct: 351 IVP------KLSATPGQMHWTGPALGEHTDQVL-ATLGMTAAAI 387 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: 456 Number of extensions: 26 Number of successful extensions: 7 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 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