Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate HSERO_RS18350 HSERO_RS18350 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS18350 Length = 415 Score = 212 bits (540), Expect = 1e-59 Identities = 137/422 (32%), Positives = 216/422 (51%), Gaps = 32/422 (7%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L+ ++VL+L ++AGP+ ++LA+ GADVIKVE PGNGD R W LKD Sbjct: 9 GPLAGIKVLELGTLIAGPFCSRMLAEFGADVIKVEAPGNGDPLRQWR--VLKDGT----- 61 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 + ++ RNK+S+T++ Q + R+LA ++D++IEN++ G L + L Y+ LK + Sbjct: 62 -SLWWSVQARNKKSITLNMKDERAQEIARKLALEADVIIENYRPGVLEKWKLGYEDLKQL 120 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP I ++G+GQTGP G+ + + +GG+ ++G P+ PV++G+++ D + Sbjct: 121 NPATIMVRLSGYGQTGPLRDLPGFGAIGESMGGIRYVSGHPD----RPPVRIGISIGDSI 176 Query: 182 TGLYSTAAILAALAHRDHVGG--------------GQHIDMALLDVQVACLANQAMNYLT 227 L+ + AL HRD GG GQ +D+AL + + + + Sbjct: 177 AALHGVIGAMMALRHRDVTGGRWNGKQGADCVAGQGQMVDVALYEAVFNMMESMVPEFDF 236 Query: 228 TGNAPKRLGNAHPNIVPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATN 286 G +R G A P IVP + T +G I+ GN D F++ G+ A+DP A N Sbjct: 237 AGVVRERTGGALPGIVPSNTYTTGEGMNIVIAGNGDAIFKRLMSAIGREDMANDPGLARN 296 Query: 287 KVRVANRAVLIPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAME 346 RV + I+Q +T + L+ A VP G I + + D Q AR + + Sbjct: 297 DGRVPRTEEIDAAIQQWCSTQTIETALATLQAADVPVGKIYSVKDMMNDAQFLARDMFEQ 356 Query: 347 LPHLLAGKVPQVASPI--RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAG 404 H A P I ++SETP + + P LG H+ E+LQ LG DEA + R+ G Sbjct: 357 --HQFADGTPVKLPGITPKMSETPGQTKWLGPELGAHSDEILQS-LGYDEAHIKMLRDQG 413 Query: 405 VL 406 V+ Sbjct: 414 VV 415 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: 24 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: 415 Length adjustment: 31 Effective length of query: 375 Effective length of database: 384 Effective search space: 144000 Effective search space used: 144000 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