Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_110207253.1 DNK54_RS12200 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_003194585.1:WP_110207253.1 Length = 385 Score = 339 bits (869), Expect = 9e-98 Identities = 183/389 (47%), Positives = 245/389 (62%), Gaps = 19/389 (4%) Query: 1 MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60 M +L + V D SRVL+GP LADLGADVIKVERPG GDDTR+WGPPFL GE+T Sbjct: 1 MKSLGDILVADFSRVLSGPTVTMFLADLGADVIKVERPGVGDDTRSWGPPFLG---GEST 57 Query: 61 TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120 Y+LS NRNK+SV +D T EG REL A++D+L+ENF+ G + GL Y+ Sbjct: 58 ----YFLSVNRNKRSVALDLTSAEGIAAARELVARADVLVENFRPGTMEKLGLGYEETHR 113 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 +NP L+YCSI+GFG +G A R GYDF++Q +GGLMS+TG PEG P+KVGVAL DI Sbjct: 114 LNPALVYCSISGFG-SGEGADRPGYDFVVQAVGGLMSITGEPEGS----PMKVGVALVDI 168 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 L GL++ +LA+L R G G+H+++ LL ++ LANQ Y G P+RLGN HP Sbjct: 169 LAGLHAAIGVLASLRERQSTGRGRHVEVNLLSSLLSSLANQGSAYALAGVIPQRLGNVHP 228 Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 +I PY+ F T D + G D QF V G + ++DPRF++N+ RV NR+ L+ ++ Sbjct: 229 SITPYELFQTRDKQVAIACGTDRQFEGLCRVLGCGELSEDPRFSSNRDRVGNRSALLEVL 288 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLA---GKVPQ 357 + A T E + L+ AGVP G +ND+A+ FA A L +E +A G +PQ Sbjct: 289 KPAFAAVGTEELLRALDDAGVPAGAVNDIAEAFA----FAERLGLEPLQRVATVEGDLPQ 344 Query: 358 VASPIRLSETPVEYRNAPPLLGEHTLEVL 386 V+SP+R +APP LG+HT E+L Sbjct: 345 VSSPLRFDGVTPRVNSAPPTLGQHTEEIL 373 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: 15 Number of successful extensions: 5 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: 385 Length adjustment: 31 Effective length of query: 375 Effective length of database: 354 Effective search space: 132750 Effective search space used: 132750 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