Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_011383897.1 AMB_RS07510 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000009985.1:WP_011383897.1 Length = 401 Score = 532 bits (1370), Expect = e-156 Identities = 262/405 (64%), Positives = 315/405 (77%), Gaps = 6/405 (1%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 GALSHLR+LDLSRVLAGPWAGQ+LAD+GA+V+K+E+PG GDDTRAWGPPFL G Sbjct: 3 GALSHLRILDLSRVLAGPWAGQLLADMGAEVLKIEKPGEGDDTRAWGPPFLDADEGRG-- 60 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 E+AYYLSANR K SVTIDFT+P+GQ LVR L A+ D+++ENFKVGGLA YGLDYDSLKAI Sbjct: 61 ESAYYLSANRGKHSVTIDFTQPQGQALVRRLVAQCDVVLENFKVGGLAKYGLDYDSLKAI 120 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 P L+YCSITGFGQ GPYA+RAGYDF++QG+GGLMSLTG P+G+ P+KVGVALTDI Sbjct: 121 KPDLVYCSITGFGQDGPYAQRAGYDFLVQGMGGLMSLTGTPDGE----PMKVGVALTDIF 176 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 TG+Y+ A+LAALAHRD G GQHID+ALLDVQVA LANQA NYL G PKRLGN+HPN Sbjct: 177 TGMYAGFAVLAALAHRDRTGEGQHIDLALLDVQVAVLANQATNYLVGGVIPKRLGNSHPN 236 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 IVPYQ F TA+G IL +GND QFR+F EVAG P+ DP +ATN RV +RA+L+P++ Sbjct: 237 IVPYQAFATAEGHIILAIGNDAQFRRFCEVAGHPELGTDPLYATNADRVRHRAILVPVLV 296 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 + W+ +LE+AGVPCGPIN L +VFADPQV+ RG+A+ + H + VA+P Sbjct: 297 EIMTEHDADYWIAELEKAGVPCGPINSLDRVFADPQVKHRGMAVAMEHPQREDLRLVANP 356 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 I LS+TPV Y PPLLG T +VL R+LGLDE R +GV+ Sbjct: 357 IHLSKTPVTYDRPPPLLGADTDDVLARLLGLDEGERAELRSSGVI 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: 614 Number of extensions: 22 Number of successful extensions: 3 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 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