Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3607648 Dshi_1057 L-carnitine dehydratase/bile acid-inducible protein F (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Dino:3607648 Length = 395 Score = 296 bits (758), Expect = 7e-85 Identities = 168/402 (41%), Positives = 233/402 (57%), Gaps = 17/402 (4%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 ALSHL+VLDL+RV AGP ++LAD GADVIK+E P G D A G + Sbjct: 7 ALSHLKVLDLTRVRAGPTCCRVLADFGADVIKIEAP-QGFDPNA----------GMSGAR 55 Query: 63 AAY-YLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 Y L+ +RNK+S+T++ +PEG+ L + +D+++ENF+ G+ YD L A+ Sbjct: 56 HGYDMLNLHRNKRSMTLNLKKPEGRALFLRMVKTADVVVENFRPDVKDRLGIGYDDLAAV 115 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP++I SI+GFGQ GPYA+RAG+D + QG+GGLM +TG P G P++ G A+ D Sbjct: 116 NPRIILASISGFGQDGPYARRAGFDQIAQGMGGLMGVTGMP----GGVPIRAGAAVADSS 171 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 G+++ IL ALA R+ G GQ + +LL+ Q+A + QA YL G+ P GN HP Sbjct: 172 AGIFAATGILVALAEREKSGQGQWVATSLLEAQIALMDFQAARYLVDGDVPPPAGNDHPY 231 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 + P TADG L VG GQ+ F V QP+ A+ P +AT+ R A+R L +R Sbjct: 232 VTPMGVVETADGYLNLGVGGQGQWVAFCNVIDQPELAEHPDYATDTARFAHRGALWDHLR 291 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 +TTA+WV LE GVP GPI + +VFADPQV+ G+A + H + G+ VA+P Sbjct: 292 PVFAQRTTADWVLALEAGGVPAGPIYTMDEVFADPQVRHLGMAAPVHHPVRGETALVATP 351 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREA 403 I++S TP + P G T E+L GL V R A Sbjct: 352 IKMSRTPPSVHASAPDAGAQTDEILAE-YGLSPEEVAQLRAA 392 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: 526 Number of extensions: 24 Number of successful extensions: 3 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: 395 Length adjustment: 31 Effective length of query: 375 Effective length of database: 364 Effective search space: 136500 Effective search space used: 136500 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