Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_061534093.1 CAter10_RS15355 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_001584165.1:WP_061534093.1 Length = 407 Score = 216 bits (549), Expect = 1e-60 Identities = 138/412 (33%), Positives = 215/412 (52%), Gaps = 23/412 (5%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 +L ++V++L ++AGP+A +L GA+VIK+E PG+GD R W R + Sbjct: 11 SLQGVKVIELGTLIAGPYAASLLGQFGAEVIKIESPGDGDPLRKW--------RKLHNGT 62 Query: 63 AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122 + ++ S +RNK+SVT++ +GQ++VR+L +DI+IENF+ G L +GL +D L IN Sbjct: 63 SLWWYSQSRNKKSVTLNLKSAQGQQIVRDLVKDADIVIENFRPGTLEGWGLGWDELSKIN 122 Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182 P LI ++G+GQ GPY R G+ + + +GGL +L G P+ PV+VGV++ D L Sbjct: 123 PNLIMVRVSGYGQDGPYHARPGFAAIAESMGGLRNLAGYPD----RPPVRVGVSIGDTLA 178 Query: 183 GLYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 LY L A+ H GG GQ ID+AL + + + Y G +R G + P Sbjct: 179 SLYGVIGALLAMHHLKANGGKGQFIDIALYEAVFGVMESLIPEYAEFGFVRERTGASFPG 238 Query: 242 IVPYQDFP---TADGD-FILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVL 296 I P +P A+G+ +++ GN D F++ G+ A+DP A N R N ++ Sbjct: 239 ISPSSTYPCRSDANGEHYVIIAGNGDSIFKRLMHAIGRSDLAEDPSLARNDGRAQNNDMI 298 Query: 297 IPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVP 356 I + T + LEQA VP + A + DP +AR + + H+L P Sbjct: 299 DAAIAEWTSQHDLEHVLQVLEQAEVPSSKVYTAADIHQDPHFRARDMIQQ--HVLPDGQP 356 Query: 357 QVASPI--RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 I +LS TP + P LG+HT +V+ +G + + RE GV+ Sbjct: 357 IDLPGIVPKLSVTPGQTNWVGPELGQHT-DVVLASIGRNPEQIALLREQGVV 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: 446 Number of extensions: 23 Number of successful extensions: 5 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 24 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