Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AZOBR_RS27630 AZOBR_RS27630 CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__azobra:AZOBR_RS27630 Length = 397 Score = 310 bits (795), Expect = 4e-89 Identities = 169/404 (41%), Positives = 235/404 (58%), Gaps = 15/404 (3%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 AL H+RVLDL+RV AGP ++LAD GADVIKVE P D P Sbjct: 9 ALEHIRVLDLTRVRAGPTCCRVLADFGADVIKVEAPPGVDRNEGMSGP----------RH 58 Query: 63 AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122 L+ +RNK+S++++ P+G+ L EL +D+++EN++ G+ YD+L+A+N Sbjct: 59 GYDMLNLHRNKRSLSLNLRTPQGRDLFLELVRTADVVVENYRPDVKDRLGIGYDALRAVN 118 Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182 P++I SI+G+GQTGPY +RAG+D + QG+GGLMS+TG P G GPV+ G+A+ D + Sbjct: 119 PRIILASISGYGQTGPYRERAGFDQIAQGMGGLMSVTGLP----GQGPVRAGIAVADSAS 174 Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 GLY+ IL AL+ RD G GQ + +LL+ Q+A + QA YL G P+ GN HP Sbjct: 175 GLYAAIGILVALSERDRSGEGQWVQTSLLESQIALMDFQAARYLVEGEVPQPAGNDHPYS 234 Query: 243 VPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 P TADG + VG DGQ++ F + AD P FAT + R NR L PL+ + Sbjct: 235 TPMGVMATADGHLNIGVGGDGQWQSFCRAIEREDLADAPEFATQEQRFRNRPTLKPLLEE 294 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362 + TA+W+ +LE+ GVP GPI + +VFADPQV G+A+ H G + V P+ Sbjct: 295 VFRTRKTADWLARLEEEGVPAGPIYRMDEVFADPQVGHLGIAVPCEHPARGAMRLVGQPV 354 Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 LS TP P GEHT EVL +GL A V A + G++ Sbjct: 355 GLSRTPARIERPAPDAGEHTAEVL-GAIGLSPADVAALKAQGIV 397 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: 547 Number of extensions: 20 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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