Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Pf1N1B4_3018 L-carnitine dehydratase/bile acid-inducible protein F (EC 2.8.3.16)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3018 Length = 399 Score = 212 bits (539), Expect = 2e-59 Identities = 137/407 (33%), Positives = 216/407 (53%), Gaps = 19/407 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 LS L+V++L ++AGP+A +I + GA+VIK+E P GD R W + T Sbjct: 8 LSGLKVIELGTLIAGPFASRICGEFGAEVIKIESPDGGDPLRKWRKLY-------EGTSL 60 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 +++ A RNK+S+T++ P+G ++++L +++DILIENF+ G L GL ++ L A+NP Sbjct: 61 WWFVQA-RNKKSLTLNLKHPDGLAILKQLLSEADILIENFRPGVLEKLGLGWEVLHALNP 119 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +L+ ++GFGQTGP + G+ + + +GGL +T G E PV+ G+++ D + Sbjct: 120 KLVMVRLSGFGQTGPMKDQPGFGAVGESMGGLRYIT----GFEDRPPVRTGISIGDSIAA 175 Query: 184 LYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 L+ L AL HR+ GG GQ +D+AL + A + + + G +R GN P I Sbjct: 176 LWGVIGALMALRHREVNGGLGQVVDVALYEAIFAMMESMVPEFDVFGFIRERTGNIMPGI 235 Query: 243 VPYQDFPTADGDFI-LTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 P +ADG + + D F++F + G+ A+DP A+N R + R + +I Sbjct: 236 TPSSIHTSADGKHVQIGANGDAIFKRFMLIIGREDLANDPVLASNDGRDSRRDEIYGVID 295 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAME--LPHLLAGKVPQVA 359 + + QL QA VP I +F+DPQ AR + ++ LP K+P + Sbjct: 296 RWVNSLPLDAVIEQLNQADVPASRIFSAEDMFSDPQYLAREMFLQAKLPDGKDFKMPGIV 355 Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 +LSETP P LGEH +VL LG D A + RE G + Sbjct: 356 P--KLSETPGSSEWVGPQLGEHNAQVLHD-LGYDPAQIARLREDGAI 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: 439 Number of extensions: 26 Number of successful extensions: 7 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: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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