Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_029134000.1 A3GO_RS0114455 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000428045.1:WP_029134000.1 Length = 367 Score = 148 bits (374), Expect = 2e-40 Identities = 111/347 (31%), Positives = 162/347 (46%), Gaps = 32/347 (9%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L+ RVLDLS+ + GP+A ++L+DLGADVIKVE P G P +N T + Sbjct: 7 LAGYRVLDLSQYIPGPFATRMLSDLGADVIKVEPPR--------GDPMRNFMLSDNATPS 58 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 A Y NR K+ V +D G+ + L ++D+L+E+F+ G + G D L+ +NP Sbjct: 59 ALYRHLNRGKRVVRLDLKSDAGKTELSRLLKQADVLLESFRPGVMERLGFDRTRLELLNP 118 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 QLI+C+++GFGQ GPY AG+D G +S TG + P+ + L D Sbjct: 119 QLIHCALSGFGQNGPYRDHAGHDLTYCAASGALSATGTL-----SQPMIIFPPLADHAGA 173 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 + + AI +AL R G G ID++L D + A YL A + G ++ Sbjct: 174 MQAVTAIQSALLGRVKSGKGAFIDISLFD------SAMAWQYLGLSEAKENAGLQREQLL 227 Query: 244 ------PYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVL 296 Y + TAD F+ + +F R F E + W PR N + A L Sbjct: 228 LNGGAACYNIYETADNQFLALAPLEAKFWRAFCEAVDRHAWI--PRQLENMPQTA----L 281 Query: 297 IPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGL 343 I +R+ + + W L I L Q PQV+ARGL Sbjct: 282 IQELRELFLSQPLEHWQHLLGDVDCCFETIPTLDQAKNHPQVEARGL 328 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: 381 Number of extensions: 21 Number of successful extensions: 3 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: 367 Length adjustment: 30 Effective length of query: 376 Effective length of database: 337 Effective search space: 126712 Effective search space used: 126712 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