Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_011383259.1 AMB_RS08365 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000009985.1:WP_011383259.1 Length = 403 Score = 536 bits (1381), Expect = e-157 Identities = 272/405 (67%), Positives = 309/405 (76%), Gaps = 4/405 (0%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G LSHLRVLDLSRVLAGPWAGQ+LAD+GA+VIKVERPG GDDTR WGPPFLKD +G +T Sbjct: 3 GPLSHLRVLDLSRVLAGPWAGQLLADMGAEVIKVERPGEGDDTRGWGPPFLKDGQGGDTG 62 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 EAAY+LSANR K+SVTIDFT+ +GQ LVR LAA+SD+++ENFKVGGLA YGLDY SLKA+ Sbjct: 63 EAAYFLSANRGKRSVTIDFTQAQGQELVRRLAARSDVVLENFKVGGLAKYGLDYASLKAV 122 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 P L+YCSITGFGQ GPYA+RAGYDF+IQG+GGLMSLTG P G P+KVGVALTDI Sbjct: 123 KPDLVYCSITGFGQDGPYAQRAGYDFLIQGMGGLMSLTGEPGGQ----PMKVGVALTDIF 178 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 TG+Y+ AILAALA RD G G ID+ALLDVQVA LANQA NYL G PKRLGNAHPN Sbjct: 179 TGMYAGFAILAALAKRDRTGEGSQIDLALLDVQVAVLANQATNYLVGGATPKRLGNAHPN 238 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 IVPYQ F TADG IL VGNDGQFR+F AG+P+ DPRFATN RV NRA L+PL+ Sbjct: 239 IVPYQAFATADGHIILAVGNDGQFRRFCHTAGRPELGADPRFATNVERVRNRAELVPLLE 298 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 + +A W+ +LE+AGVPCGPINDLA VFADPQV RGL L H LAG + VA+P Sbjct: 299 ALLTSRPSARWIAELEEAGVPCGPINDLANVFADPQVIHRGLRTRLDHPLAGGIDLVANP 358 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 IR APPLLG T EVL LG+ + RE GV+ Sbjct: 359 IRFDGAQALSDRAPPLLGADTAEVLGGWLGMGADEMERLRENGVV 403 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: 649 Number of extensions: 27 Number of successful extensions: 2 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