Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AZOBR_RS19675 AZOBR_RS19675 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__azobra:AZOBR_RS19675 Length = 400 Score = 557 bits (1436), Expect = e-163 Identities = 273/405 (67%), Positives = 321/405 (79%), Gaps = 7/405 (1%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G LSH+RVL+LSRVLAGPWA Q LADLGADVIKVERPG GDDTRAWGPP+ + Sbjct: 3 GPLSHVRVLELSRVLAGPWAAQTLADLGADVIKVERPGAGDDTRAWGPPWAGE------- 55 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 E+AY+LS NR K+S+TIDF RPEGQ LVR+LAA++D++IENFKVGGL YGLDYDSLKAI Sbjct: 56 ESAYFLSTNRGKRSITIDFERPEGQELVRKLAAQADVVIENFKVGGLVKYGLDYDSLKAI 115 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP L+YCSITGFGQ GPYAKRAGYDFMIQG+GGLMS+TG+P+ + G GPVKVGVA+TD+ Sbjct: 116 NPGLVYCSITGFGQDGPYAKRAGYDFMIQGMGGLMSITGQPDTEAGGGPVKVGVAVTDVF 175 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 TGLY+T +L ALAHRD G GQ +++ALLDVQVA LANQAMNYL G AP+RLGNAHPN Sbjct: 176 TGLYATIGVLGALAHRDRTGEGQWVNLALLDVQVAVLANQAMNYLVGGKAPQRLGNAHPN 235 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 IVPYQ F T DG IL VGNDGQF KF +VAG+P+ A DPR+ATN RVANR L+P++ Sbjct: 236 IVPYQAFATLDGHIILAVGNDGQFAKFCQVAGRPELAQDPRYATNPARVANRKELVPILE 295 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 +T+ +W+ LE GVPCGPIND++QVFADP VQAR + +LPH AG VP VASP Sbjct: 296 LLLEQRTSRDWLAALEAVGVPCGPINDVSQVFADPHVQARHIHQDLPHPTAGTVPTVASP 355 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 IR S TP+E+ APP LG+HT VL+ LGL A + A RE GV+ Sbjct: 356 IRYSATPIEHTAAPPTLGQHTDAVLEEALGLCAADIAALREKGVV 400 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: 631 Number of extensions: 29 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: 400 Length adjustment: 31 Effective length of query: 375 Effective length of database: 369 Effective search space: 138375 Effective search space used: 138375 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