Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF2609 Psest_2660 Predicted acyl-CoA transferases/carnitine dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__psRCH2:GFF2609 Length = 400 Score = 241 bits (615), Expect = 3e-68 Identities = 152/406 (37%), Positives = 222/406 (54%), Gaps = 19/406 (4%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L L+V+++ +++AGP+A ++L + GADVIK+E P GD R W LKD + Sbjct: 11 LQGLKVIEMGQLIAGPFASKLLGEFGADVIKIEPPKVGDPLRKWRK--LKDGT------S 62 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 ++ +RNK+SVT+D EGQ +VR+L A++DIL+ENF+ G L +GL +D L +NP Sbjct: 63 LWWHVQSRNKRSVTLDLKAAEGQAIVRQLVAEADILVENFRPGTLEEWGLGWDELSKLNP 122 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LI I+G+GQTGPY G+ + + +GGL L+G P G PV+VGV++ D L+ Sbjct: 123 RLIMLRISGYGQTGPYRDLPGFGVIGEAMGGLRHLSGYP----GQPPVRVGVSIGDSLSS 178 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 LY +L AL R+ G GQ ID+AL + A + + Y G + G+A P I Sbjct: 179 LYGVIGVLLALQERNRSGQGQEIDVALYESVFAMMESLVPEYDAFGYVREPAGSALPGIT 238 Query: 244 PYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 P +P DG ++L GN D +++ + G+ ADDPRFA N R + ++ I + Sbjct: 239 PSNSYPCNDGAYVLIAGNGDSIYKRLMTLMGRQDLADDPRFAHNDGRAQHAELIDAAIGE 298 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAG--KVPQVAS 360 T+ E + L+ A VP G A + DP AR + +E AG KVP V Sbjct: 299 WTIQHGRDEVIEALKGARVPAGYPYTAADIVKDPHYLARQM-IEQVQTFAGPLKVPGVLP 357 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 +LS TP P LGEHT +VL LGL + RE G++ Sbjct: 358 --KLSRTPGRIGEGGPQLGEHTDDVLAG-LGLTDEQRQGLRERGII 400 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: 494 Number of extensions: 22 Number of successful extensions: 6 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: 400 Length adjustment: 31 Effective length of query: 375 Effective length of database: 369 Effective search space: 138375 Effective search space used: 138375 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