Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate H281DRAFT_03364 H281DRAFT_03364 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_03364 Length = 407 Score = 264 bits (675), Expect = 3e-75 Identities = 148/405 (36%), Positives = 222/405 (54%), Gaps = 14/405 (3%) Query: 1 MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60 +G LS R+LDL+ + AGP +LADLGADV+KVE P GD +R G F++ Sbjct: 6 VGPLSGYRILDLTVMTAGPVGTVLLADLGADVVKVEEPMAGDLSRKLGNQFVQG------ 59 Query: 61 TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120 E+ +LS NRNK+S+ +D P+G+ +A ++D+++ENF+ G + G+ Y ++KA Sbjct: 60 -ESVQFLSQNRNKRSIRLDLKSPKGRDAFLRMAEQADVVVENFRPGTVDRLGIGYAAVKA 118 Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180 NP+++Y S++ FGQ+GPYA D ++Q + GLM +T G+ G PV++G L D Sbjct: 119 RNPKIVYASVSAFGQSGPYAAWPANDPIVQAVAGLMDMT----GEAGGNPVRLGAPLPDF 174 Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 I AAL HR+ G GQ ID +LL + + L +G AP+RLG+ HP Sbjct: 175 GAAALLAFGISAALLHRERHGEGQRIDTSLLSAALFSTIPRDGETLRSGKAPERLGSGHP 234 Query: 241 NIVPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299 +VPY+++ +DG + +F + G+ + D RF N R ANR L + Sbjct: 235 TMVPYRNYQGSDGRYFFAACFTEKFWQNLCRALGREELLSDERFIGNTARTANRHALDVI 294 Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDL-AQVFADPQVQARGLAMELPHLLAGKVPQV 358 + + + T WV L A VPC + D + DPQ+ +E+ H +AG+V + Sbjct: 295 LEEQFLLHTAEYWVAHLSAADVPCAIVQDYHTALTQDPQISHNHAVVEIEHPVAGRVTNI 354 Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRV-LGLDEAAVMAFRE 402 ASP+ +PV YR PP LG+HT EVL G +E A + RE Sbjct: 355 ASPVNFHGSPVAYRRPPPTLGQHTAEVLAEYGFGEEEIAALEGRE 399 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: 474 Number of extensions: 20 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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