Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AZOBR_RS29180 AZOBR_RS29180 CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__azobra:AZOBR_RS29180 Length = 413 Score = 457 bits (1177), Expect = e-133 Identities = 235/406 (57%), Positives = 281/406 (69%), Gaps = 2/406 (0%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 +L+ LRVLDLSRVLAGPWA QIL DLGAD+IK+E P GDDTR+WGPP L+ G+ T + Sbjct: 2 SLAGLRVLDLSRVLAGPWASQILGDLGADIIKIEHPEKGDDTRSWGPPNLRPTPGDRTDD 61 Query: 63 --AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120 +AYYLS NRNK+S+ ID +PEG LVR LA D+++ENFKVGGL+ YGLDY+SLK Sbjct: 62 PPSAYYLSCNRNKRSLAIDIAKPEGAALVRRLARSCDVVLENFKVGGLSRYGLDYESLKR 121 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 NP L+YCSITGFGQTGPYA R GYDF+IQG+ GLMS+TG+PEG G+ P+KVGV ++D+ Sbjct: 122 ENPALVYCSITGFGQTGPYAPRGGYDFLIQGMSGLMSVTGQPEGAPGSEPLKVGVPVSDL 181 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 TGLY+T A+LAAL HRD G GQHID ALLD QVA LANQ MN+L G PKRLGN HP Sbjct: 182 FTGLYATIAVLAALRHRDRAGEGQHIDCALLDTQVAVLANQGMNWLVGGQVPKRLGNGHP 241 Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 N+VPY+ F TADG I+ VGNDGQFR + + D RFA+N R A+RA L + Sbjct: 242 NVVPYRCFATADGHIIVAVGNDGQFRALCRLLNREDLLADERFASNPGRQAHRAELEATL 301 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 + T+A+ + L GVP GPIN + QVF DPQV ARGL L VP V Sbjct: 302 ADSMARWTSADLIEALSGGGVPAGPINRIDQVFDDPQVVARGLVHRLETPGGTPVPIVGF 361 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 P RLS TP YR PP LGE T EVL +L L + R GV+ Sbjct: 362 PARLSRTPACYRRVPPRLGEQTDEVLSDLLDLTGNELEELRAGGVI 407 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: 604 Number of extensions: 21 Number of successful extensions: 2 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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