Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate HSERO_RS14050 HSERO_RS14050 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS14050 Length = 399 Score = 197 bits (502), Expect = 3e-55 Identities = 133/409 (32%), Positives = 213/409 (52%), Gaps = 23/409 (5%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L + V+ L +A P+ + LADLGA VIK+ERPG GD R + D+R + Sbjct: 8 LEGITVISLEHAIAAPFCTRQLADLGARVIKIERPGVGDFARGY------DSRVNGLS-- 59 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 ++++ NR+K+S+T++ EG+R++ +L ++D+L++N G A GL +L A +P Sbjct: 60 SHFVWTNRSKESLTLNLKDEEGRRIIDQLLQQADVLVQNLAPGAAAGLGLSAQALHARHP 119 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LI C I+G+G+ GPY + YD +IQ G +S+TG P+ VK G ++ DI G Sbjct: 120 RLIVCDISGYGEDGPYRDKKAYDLLIQSEAGFLSVTGTPD-----DVVKAGCSIADIAAG 174 Query: 184 LYSTAAILAALAHR---DHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240 +Y+ + ILAAL R G G HID+++L+ ++ +AP R G H Sbjct: 175 MYAYSNILAALIKRGREGREGRGSHIDLSMLESLAEWMSFPLYYAYQGASAPLRSGAEHA 234 Query: 241 NIVPYQDFPTADGDFI-LTVGNDGQFRKFAE-VAGQPQWADDPRFATNKVRVANRAVLIP 298 I PY F DG + L + N+ +++ F E V A D RF++N R +R VL Sbjct: 235 TIYPYGPFSAGDGKTVMLGLQNEREWKVFCEQVLQDAALASDARFSSNARRHEHRDVLRQ 294 Query: 299 LIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQV 358 LI + + +L++A + +N + +++ PQ+ AR E+ GKV + Sbjct: 295 LILDVFAGLSAEQVAARLDEAQIANARVNTMQELWQHPQLAARQRWTEVA-TPVGKVAAL 353 Query: 359 ASPIRLSETPVEYR-NAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 P + +YR A P LG+HT +L LG + + A RE G + Sbjct: 354 LPP--GANDSYDYRMEAIPALGQHTESILS-ALGYEAGQIAALRERGAV 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: 408 Number of extensions: 16 Number of successful extensions: 4 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