Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate PP_3001 PP_3001 CAIB/BAIF family protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Putida:PP_3001 Length = 410 Score = 233 bits (593), Expect = 1e-65 Identities = 141/409 (34%), Positives = 212/409 (51%), Gaps = 18/409 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L+ +RV+D S LAGP+ G+ LA LGA+VIKVERPG+GD R + A + ++ Sbjct: 7 LAGIRVVDYSHFLAGPYVGRCLAALGAEVIKVERPGSGDAGR-------QHAFTLDDQQS 59 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 Y+L N KQ V+++ P G+ ++ L +D+ IEN++ G L GL Y L A NP Sbjct: 60 GYFLQLNMGKQGVSVNMKDPRGKAFMQRLTDSADVFIENYRPGALDKLGLGYAELSARNP 119 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +L+YCSI+ +G TGP A RAG+ + + G+M + G P G P + ++L D+ TG Sbjct: 120 RLVYCSISAYGHTGPDAHRAGFGLIAEAKSGIMQMVGVP----GEAPPLLRISLGDMYTG 175 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNA--PKRLGNAHPN 241 +++ AAI AAL R G GQHIDMAL D V+ Y +G P++ G+ P Sbjct: 176 IHAVAAINAALLGRVSSGRGQHIDMALYDTLVSMHEYAVQCYTLSGGTVLPQQTGHDMPT 235 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEV----AGQPQWADDPRFATNKVRVANRAVLI 297 Y F DGD ++ D +++FA + G P + D R+ R A+R ++ Sbjct: 236 STLYGVFRATDGDLVIAAQVDDAWQRFAAMLEANGGPPGFGSDRRYHGLNGRNAHREAIL 295 Query: 298 PLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQ 357 ++R + AE + L+ +P + + +V ADPQ+QAR + +E H G + Sbjct: 296 AVVRDWVGARRVAEILALLDGIDIPSAKVQRIDEVLADPQIQARNMVIEQQHPRYGTLRL 355 Query: 358 VASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 P R S+ P LG+H EV LG + A + GVL Sbjct: 356 ANLPFRFSDCDTTIHQVAPDLGQHNAEVAAG-LGFSPEEITALQADGVL 403 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: 437 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: 410 Length adjustment: 31 Effective length of query: 375 Effective length of database: 379 Effective search space: 142125 Effective search space used: 142125 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