Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ac3H11_369 CAIB/BAIF family protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_369 Length = 436 Score = 214 bits (545), Expect = 4e-60 Identities = 140/408 (34%), Positives = 209/408 (51%), Gaps = 20/408 (4%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 AL +RV+++ +++AGP+ G+ L + GADVIK+E P GD R W R Sbjct: 44 ALQGVRVIEMGQLIAGPFCGKTLGEFGADVIKIEAPETGDPLRNW--------RLIKGGT 95 Query: 63 AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122 + ++ +RNK+SV +D + EGQ + R+L A++D+L+ENF+ G L +G+ D L A+N Sbjct: 96 SVWWQVQSRNKRSVALDLRQKEGQAIARQLIAEADVLVENFRPGTLEGWGMSPDELHALN 155 Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182 P L+ I+G+GQTGPY G+ + + +GGL LT P G PV+VGV++ D L Sbjct: 156 PGLVILRISGYGQTGPYRDLPGFGVIGEAMGGLRHLTAEP----GRVPVRVGVSIGDTLA 211 Query: 183 GLYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 L+ T +L AL HR GG GQ ID+AL + + + Y G + G+A P Sbjct: 212 ALHGTIGVLTALYHRKVNGGKGQVIDVALHEAVFNVMESLIPEYSAFGAVREAAGSALPG 271 Query: 242 IVPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300 I P +P DG ++L GN D F++ G+ AD P +N RVA + I Sbjct: 272 IAPSNAYPCQDG-WVLVAGNGDSIFKRLMTAIGRQDLADAPDLGSNTGRVARVGEIDTAI 330 Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARG--LAMELPHLLAGKVPQV 358 T ++ + + L A VP G + + DP +AR L E + +VP + Sbjct: 331 GAWTAARSVQQVMETLGAARVPAGKVYTAKDIAEDPHYRARDMLLTQETRDGYSVEVPGI 390 Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 +LS TP R + P LG+ T VL GL + R GV+ Sbjct: 391 VP--KLSGTPGSIRRSAPHLGDDTDAVLAEA-GLTAEQIALLRSKGVI 435 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: 462 Number of extensions: 18 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: 436 Length adjustment: 32 Effective length of query: 374 Effective length of database: 404 Effective search space: 151096 Effective search space used: 151096 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