Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF1502 PGA1_c15210 putative CoA-transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Phaeo:GFF1502 Length = 391 Score = 264 bits (674), Expect = 4e-75 Identities = 148/385 (38%), Positives = 226/385 (58%), Gaps = 15/385 (3%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 LS + VLDL+ VLAGP+A L DLGA VIKVERPG+GDDTRA+ PPF KD ++ Sbjct: 5 LSDIVVLDLTHVLAGPYASMTLRDLGARVIKVERPGHGDDTRAF-PPF-KDG------DS 56 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AY+ + N K+S+ +D E + + +L ++D+++ENF+ G + G +++L A P Sbjct: 57 AYFSTINHGKESIALDLRAEEDRGIFEQLLTQADVILENFRPGVMERLGYGWEALHARFP 116 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +L+Y +++GFG TGP R YD ++Q GG+MS+TG + + PV+VG ++ DI G Sbjct: 117 KLVYGAVSGFGHTGPDRLRPAYDMVVQARGGVMSITGERDRE----PVRVGASIGDIAAG 172 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 ++ +LAAL GQ +D+A+LD Q+A L + TG AP+ G HP+I Sbjct: 173 MFLCQGVLAALYAVRGGAPGQKVDIAMLDSQLALLEHAVAITSVTGEAPRPSGARHPSIT 232 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 P++ F +DG F++ GND F P A D RFA+N+ R N +L LI Sbjct: 233 PFETFHASDGLFVIAAGNDTLFATLCTALDLP-LATDARFASNQARCENARLLKRLIEAV 291 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMEL-PHLLAGKVPQVASPI 362 T+ + + W+ +L++AGVP GPI +A+V DPQ+ AR + +++ + +P+ Sbjct: 292 TLDQPASHWIDRLQRAGVPTGPIQSVAEVMRDPQILARNMLVDVCDQEGTPRFKAAGNPV 351 Query: 363 RLSETPVEYRNAP-PLLGEHTLEVL 386 +LS P E P P+L EH ++L Sbjct: 352 KLSALPDETTRPPAPMLDEHRAQIL 376 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: 473 Number of extensions: 30 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: 391 Length adjustment: 31 Effective length of query: 375 Effective length of database: 360 Effective search space: 135000 Effective search space used: 135000 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