Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AZOBR_RS24675 AZOBR_RS24675 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__azobra:AZOBR_RS24675 Length = 400 Score = 288 bits (738), Expect = 2e-82 Identities = 158/405 (39%), Positives = 229/405 (56%), Gaps = 15/405 (3%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ +RV+DL+ +LAGP++ +L LGA+VIK+ERPG GD TR P + Sbjct: 11 GPLAGVRVVDLTHMLAGPYSTWLLGALGAEVIKIERPGKGDFTRIIAP--------FSEE 62 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 E+ Y+LS NRNK+S+T++ +G+ + +++ A D+L+EN + G + GL Y LKA+ Sbjct: 63 ESIYFLSVNRNKRSLTLNLKEEKGKEIFKKIVATCDVLVENNRAGAMDRLGLGYTDLKAV 122 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+L+Y SI+GFGQ GPY R +D + Q + G+MS+TG P GD P +VG ++ DI Sbjct: 123 NPRLVYASISGFGQDGPYRHRPCFDVVAQAMSGMMSITGEPGGD----PCRVGASIGDIG 178 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 + L++ ILAAL R G G ID+A+LD Q+A + N +L G P+ LG+ HP Sbjct: 179 SSLFAAVGILAALQKRASTGEGSFIDVAMLDCQLALMENAIARFLNAGETPRALGSRHPL 238 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 I P+Q FPTAD + V + Q+ + G DPRF T R AN A L L+R Sbjct: 239 IAPFQAFPTADKPIAICVDTNEQWERMCRAMGLEHLLSDPRFPTGSARNANHAELELLLR 298 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 + + + W+ +E A VP PIN + DPQV R + +E+P + A P Sbjct: 299 EVFLTRGRDAWLDAMEDADVPASPINSVPDALNDPQVIHRKMVVEVPEGSGKRF--AAVP 356 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 I + E P+ + P LGEHT +L LG + AFR V+ Sbjct: 357 ITMPEAPLPAESPAPRLGEHTDAILAD-LGFSPDEIGAFRRDAVV 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: 447 Number of extensions: 22 Number of successful extensions: 4 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