Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate CCNA_03677 CCNA_03677 CoA-transferase family III protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Caulo:CCNA_03677 Length = 403 Score = 261 bits (668), Expect = 2e-74 Identities = 149/406 (36%), Positives = 223/406 (54%), Gaps = 12/406 (2%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L LRV+++ ++AGP+ GQ+L D GA+VIK+E P GD R WG R + Sbjct: 8 GPLQGLRVIEMGSLIAGPFCGQVLGDFGAEVIKLEDPKVGDPMRQWG-------RSKPKG 60 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 + ++ RNK+SVT+D G+ + R L AK+D+++ENF+ G L +G+ Y++L Sbjct: 61 LSPWWPVIGRNKKSVTVDLRSEAGRDIARALIAKADVVVENFRPGTLEKWGMGYEALAKT 120 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP L+ ++GFGQTGPYA RAGY + + +GGL +TG P+ P + G+++ D L Sbjct: 121 NPGLVMARVSGFGQTGPYASRAGYALVGEAMGGLRHITGEPD----RPPARAGISIGDSL 176 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 +GL + ++ AL R G GQ +D A+ + + + N Y TG +R G P Sbjct: 177 SGLNAALGVMMALHARQRTGKGQVVDTAIYESVLTVMENLVTEYDLTGYVRERSGAVLPG 236 Query: 242 IVPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 I P +PT G+ +L N D FR+ E+ G+P ADDPR+ + R A++A L I Sbjct: 237 IAPSNVYPTRSGELVLIGANQDTLFRRLCELMGRPDLADDPRYRDHAARGAHQAELDARI 296 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 T + + + +LE AG+ G I + DPQ AR + +PH + G++ + Sbjct: 297 AAWTADQDIEDLLPKLEGAGLATGRIYRAPDMLTDPQYAARESIVTVPHPVFGEIKMQNA 356 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 RL+ETP R P LGEHT VL V G+ A+ R+AGVL Sbjct: 357 FPRLTETPGGVRWPGPTLGEHTDAVLADVAGMSAEAIEGLRKAGVL 402 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: 486 Number of extensions: 30 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: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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