Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_086508284.1 BZY95_RS01740 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_002151265.1:WP_086508284.1 Length = 401 Score = 238 bits (608), Expect = 2e-67 Identities = 152/406 (37%), Positives = 218/406 (53%), Gaps = 18/406 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L+ L+VL+L +++AGP+A ++L + GADVIKVE PG GD R W ++D + Sbjct: 11 LAGLKVLELGQLIAGPFATKLLGEFGADVIKVEPPGTGDPLRKWR--IIEDGT------S 62 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 ++ +R K+S+T+D EGQ +VR LAA++D+L+ENF+ G L +GL Y++L NP Sbjct: 63 LWWHVQSRTKRSITLDLRSEEGQDMVRRLAAEADVLVENFRPGTLEGWGLGYEALAKHNP 122 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 LI ++GFGQ+GPY + G+ + + +GGL LTG+P G V+VGV++ D L+ Sbjct: 123 GLIMVRVSGFGQSGPYRDKPGFGVIGEAMGGLRYLTGQP----GEPSVRVGVSIGDSLSA 178 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 LY+ L AL R G GQ ID+AL + A + + Y TG + G+A P I Sbjct: 179 LYAVIGTLLALQERARSGLGQEIDVALYESVFAMMESLLPEYDATGEVREPSGSALPGIT 238 Query: 244 PYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 P + T GDF+L GN D F++ V G+ A+DP A N R + I Sbjct: 239 PSNAYRTRHGDFVLIAGNGDSIFKRLMGVIGRQDLAEDPELAHNDGRSRRAEEIDAAIEA 298 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMEL--PHLLAGKVPQVAS 360 T + L+ A VPCG A + +DP AR + + P+ KVP V Sbjct: 299 WTCQHDRDAILAALDDARVPCGYPYTAADIASDPHYLAREMIQTITRPNGKPLKVPGVLP 358 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 RLS TP N P LG+HT EVL LG+D R AG++ Sbjct: 359 --RLSATPGRLGNGGPALGQHTDEVLDE-LGIDSETRAKLRAAGII 401 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: 472 Number of extensions: 21 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: 401 Length adjustment: 31 Effective length of query: 375 Effective length of database: 370 Effective search space: 138750 Effective search space used: 138750 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