Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate RR42_RS36540 RR42_RS36540 CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS36540 Length = 407 Score = 459 bits (1180), Expect = e-134 Identities = 230/404 (56%), Positives = 279/404 (69%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 AL +RVLDLSR+LAGPW Q LADLGA+VIKVERPG GDDTR+WGPP+L D G + + Sbjct: 4 ALDGVRVLDLSRILAGPWCAQNLADLGAEVIKVERPGVGDDTRSWGPPWLPDGAGNPSRD 63 Query: 63 AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122 A YY ANR K+SVT+D P+GQ +VR+LAAKS I++EN+KVG L YGLDYDSLKAIN Sbjct: 64 ATYYAGANRGKRSVTLDIASPQGQAIVRDLAAKSQIVLENYKVGDLKRYGLDYDSLKAIN 123 Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182 P L+YCSITG+GQ GP A + GYDF+ QG+GGLMS+TG + G GP KVGVA+ D+LT Sbjct: 124 PALVYCSITGYGQEGPSAHKPGYDFIFQGIGGLMSITGERDDLPGGGPQKVGVAVVDMLT 183 Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 G+Y+T A+LAAL H + G GQ IDMALLD VA A + TG P+R GNAH N+ Sbjct: 184 GMYATVAVLAALRHAERTGEGQCIDMALLDAVVAVGATPILAQKVTGKTPQRFGNAHANM 243 Query: 243 VPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 VPY F TADG I+ GNDGQ++ + +P A D RF T R+ NR VL+PL+ Sbjct: 244 VPYHVFATADGYMIVAAGNDGQWQGYCRGVARPDLATDERFTTGTGRIVNRDVLVPLLEA 303 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362 TTA WV LE+ G+PCGPIND AQV DPQV+ R L +++ G P V SP+ Sbjct: 304 HMRTGTTAHWVQALEREGIPCGPINDYAQVLEDPQVRYRELQVDMVRSDGGVCPTVKSPL 363 Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 RLS TPV Y APP LGEHT VL VLG+ + A RE GV+ Sbjct: 364 RLSATPVRYDAAPPRLGEHTESVLGEVLGISAGRIEALREQGVI 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: 580 Number of extensions: 20 Number of successful extensions: 1 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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