Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_110207576.1 DNK54_RS13740 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_003194585.1:WP_110207576.1 Length = 398 Score = 190 bits (483), Expect = 6e-53 Identities = 127/407 (31%), Positives = 195/407 (47%), Gaps = 17/407 (4%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ LRV++ + A P AG++L D GADVIK+E P GD R W P A G Sbjct: 5 GPLAGLRVIEAGSMYAAPTAGRMLRDFGADVIKIEDPAQGDFARQWQPAHEGTAIG---- 60 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 + N K+SV ID PEG+ L++ L A +D+LIENF+ G + +G+ Y L A Sbjct: 61 ----FARLNSGKRSVGIDMRAPEGRDLLKRLVADADVLIENFRPGRMEKWGMSYAELAAD 116 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 +P L+ ++GFGQTGPY +R G+ + + G L G P A P D + Sbjct: 117 HPGLVMARVSGFGQTGPYRERPGFGTVAETASGYAFLNGWPHTPPTAPP----FGFADSI 172 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 G+ + + AL R G G+ +D+AL + + L + +NY +G +R GNA Sbjct: 173 AGISAAYGVAMALFERGRTGAGREVDVALYEPLMFILGDAVLNYTASGTIMQRHGNASGA 232 Query: 242 IVPYQDFPTADGDFILTVG-NDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 P + ADG ++ G N + + +P D R+ATN R+AN L ++ Sbjct: 233 ASPRGIYEAADGGWLSIAGSNQAIAMRLFDAMERPDLKADERYATNVARMANNESLQAIV 292 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 + E + L++ V +ND + + ADP + R L L + G+ Sbjct: 293 IDWVKQRPRDEVLNILDEYEVVAAAVNDSSDIVADPHFRERTLT-SLTNSALGEALVPGP 351 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRV-LGLDEAAVMAFREAGVL 406 + ++ + P +GEHT E+L + DE A +A AGV+ Sbjct: 352 ILHVNGYDGPRYDGVPAVGEHTTEILTAAGVSTDELARLA--TAGVI 396 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: 414 Number of extensions: 19 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: 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