Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AO353_02795 AO353_02795 carnitine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__pseudo3_N2E3:AO353_02795 Length = 393 Score = 201 bits (512), Expect = 2e-56 Identities = 142/408 (34%), Positives = 206/408 (50%), Gaps = 21/408 (5%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ L+VLD S +L GP+A +LAD+GA+V+++E P D R P + T+ Sbjct: 3 GPLASLKVLDFSTLLPGPFASLLLADMGAEVLRIESPTRMDLVRVLPP------HDQGTS 56 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 + YL NRNK+S+ +D +P +V++L DIL+E F+ G + GL Y++LKAI Sbjct: 57 ASHAYL--NRNKRSLALDLKQPAALEVVKQLLQDHDILLEQFRPGVMERLGLGYEALKAI 114 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+LIY SITG+GQTGPY RAG+D L G+ S TG E +GP+ +GV + DI Sbjct: 115 NPRLIYVSITGYGQTGPYKDRAGHDINYLSLAGVSSYTGH----EDSGPLPLGVQVADIA 170 Query: 182 TG-LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 G L+ +LAA+ R+H G GQH+D+++ D + A YL G P R Sbjct: 171 GGSLHGVIGLLAAVIAREHSGQGQHLDVSMTDCAFSLNAMAGAGYLACGVTPGREDQMLN 230 Query: 241 NIVPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299 Y + T DG ++ + F ++ GQP+ A V + + L Sbjct: 231 GGSFYDYYRTRDGRWMSVGSLEPDFMQQLCTALGQPELA-----VLGLSPVPEQQKALKL 285 Query: 300 IRQATVFK-TTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQV 358 Q K AE T P+ LA+ PQ++AR L ++P Q+ Sbjct: 286 AFQIEFEKHDFAELCTLFAGLDACVEPVLSLAEAVEHPQLKARDLVTQVPRGDGTAQAQM 345 Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 A P++ SE E R+ LGEHT +VL LG + A R A V+ Sbjct: 346 ACPLKFSEGLPEPRHIGAALGEHTDQVLGE-LGYSAERIEALRRARVV 392 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: 415 Number of extensions: 18 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: 393 Length adjustment: 31 Effective length of query: 375 Effective length of database: 362 Effective search space: 135750 Effective search space used: 135750 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