Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3609887 Dshi_3269 L-carnitine dehydratase/bile acid-inducible protein F (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Dino:3609887 Length = 368 Score = 415 bits (1066), Expect = e-120 Identities = 225/378 (59%), Positives = 259/378 (68%), Gaps = 14/378 (3%) Query: 1 MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60 M L L+V++L+R+LAGPW GQ LADLGA+VIKVE P GDDTR WGPPF+ + Sbjct: 1 MTPLEGLKVVELARILAGPWIGQALADLGAEVIKVEAP-QGDDTRTWGPPFITR---DGD 56 Query: 61 TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120 AAY+ +ANR K+SV DF GQ VR+L A +DILIENFKVGGLA YGLDY +L A Sbjct: 57 RSAAYFYAANRGKRSVVADFRTEAGQAKVRDLVADADILIENFKVGGLAKYGLDYAALAA 116 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 INP+LIYCS+TGFGQ GPYA RAGYDFMIQG+ GLMS+TG P+ A P KVGVA+TDI Sbjct: 117 INPRLIYCSVTGFGQDGPYAHRAGYDFMIQGMSGLMSITGEPD----AAPQKVGVAVTDI 172 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 +TGLY T ILAA+ R G GQH+DMALLD A LANQAMN L TG AP RLGNAHP Sbjct: 173 VTGLYGTIGILAAVEQRHRTGRGQHLDMALLDCATALLANQAMNQLATGTAPTRLGNAHP 232 Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 NIVPYQ F ADG IL VGNDGQF E+ P A DPRFATN RV NR L L+ Sbjct: 233 NIVPYQVFEAADGHMILAVGNDGQFASLCEILDLPGTASDPRFATNAGRVENRDALTELL 292 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 + A+ ++ LE AGVP GPIN + QVFADPQVQARGL + + VP V Sbjct: 293 SLRLRGWSVAQLLSALEAAGVPAGPINTIDQVFADPQVQARGLQVSVE-----GVPGVRG 347 Query: 361 PIRLSETPVEY-RNAPPL 377 P R S+ + R AP L Sbjct: 348 PWRFSDAELSLDRTAPKL 365 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: 494 Number of extensions: 21 Number of successful extensions: 4 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: 368 Length adjustment: 30 Effective length of query: 376 Effective length of database: 338 Effective search space: 127088 Effective search space used: 127088 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