Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Pf1N1B4_1815 L-carnitine dehydratase/bile acid-inducible protein F
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1815 Length = 406 Score = 764 bits (1972), Expect = 0.0 Identities = 380/406 (93%), Positives = 392/406 (96%) Query: 1 MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60 MGALSHLRVLDLSRVLAGPWAGQILADLGA+VIKVERPGNGDDTRAWGPPFLKDA GENT Sbjct: 1 MGALSHLRVLDLSRVLAGPWAGQILADLGAEVIKVERPGNGDDTRAWGPPFLKDAYGENT 60 Query: 61 TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120 +EAAYYLSANRNKQSVTIDFTRPEGQ+LVRELAAKSDILIENFKVGGLAAYGLDY+SLKA Sbjct: 61 SEAAYYLSANRNKQSVTIDFTRPEGQQLVRELAAKSDILIENFKVGGLAAYGLDYESLKA 120 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 INP+LIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI Sbjct: 121 INPKLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 LTGLYST AILAALAHRD GGGQHIDMALLDVQVACLANQAMNYLTTG APKRLGNAHP Sbjct: 181 LTGLYSTVAILAALAHRDQGGGGQHIDMALLDVQVACLANQAMNYLTTGVAPKRLGNAHP 240 Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 NIVPYQDFPTADGDFILTVGNDGQFRKFA+VAGQPQWADDPRFATNK+RVANRAVLIPLI Sbjct: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAQVAGQPQWADDPRFATNKLRVANRAVLIPLI 300 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 RQATVFKTTAEWV QLEQAGVPCGPINDLAQ+FADPQVQARGLA+ELPH LAG VPQVAS Sbjct: 301 RQATVFKTTAEWVAQLEQAGVPCGPINDLAQMFADPQVQARGLAIELPHALAGMVPQVAS 360 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 PIRLSETPVEYR+APPLLGEHTLEVLQRVLGLD V F+ +GVL Sbjct: 361 PIRLSETPVEYRSAPPLLGEHTLEVLQRVLGLDAGVVAGFKASGVL 406 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: 731 Number of extensions: 13 Number of successful extensions: 1 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 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 17 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