Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 6937588 Sama_1743 acyl-CoA dehydrogenase family protein (RefSeq)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__SB2B:6937588 Length = 578 Score = 112 bits (281), Expect = 2e-29 Identities = 109/376 (28%), Positives = 168/376 (44%), Gaps = 54/376 (14%) Query: 56 FREMGEVGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEF 115 F E G VGL G +YGG G+ + G++ E+ ++ ++ + IN Sbjct: 87 FVEGGWVGLSG---DPEYGGMGMPKML-GVLVDEMGYSACNAFNLYGSLTAGAALAINAH 142 Query: 116 GTEAQKQKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRAR-KVDGGYRLTGSKMWIT-- 172 GTE K YLPKL SGEW G +TEP GSD + TRA + DG Y +TGSK++IT Sbjct: 143 GTEELKSTYLPKLYSGEWAGAMDMTEPQAGSDLRHIRTRAEPQEDGSYLITGSKIFITGG 202 Query: 173 NSPIAD--VFVVWAKDDAG-------------DIRGFVLEKGWQGLSAPAIHGKVGLRAS 217 + + + + +V AK D +G + E G+S +I K+GL+ S Sbjct: 203 DQDLTENVIHLVLAKISGSNTLSLFLVPKIGVDDQGNLTEP--NGVSVGSIEHKMGLKGS 260 Query: 218 ITGEIVMDNV---FVPEENIFPDVRGLKGPFTCLNSARYGISWGALGAAEACWHTARQYT 274 T + D+ + EN +GL FT +N R I LG+A+A A Y Sbjct: 261 ATCVMNFDSARGWLIGREN-----KGLACMFTMMNYERLAIGIQGLGSAQAAVQMASDYA 315 Query: 275 LDRQQ---FGRPLAANQLI-----------QKKLADMQTEITLALQGCLRLGRMKDEGTA 320 +R Q G AA+ ++ + L D + + L L + D+ Sbjct: 316 RERLQGNAVGSTAAADPILVHGDVRRMLLTTRTLTDAGRALAVHTGKQLDLAKFADDDAV 375 Query: 321 AVE-------ITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373 + +T + K + LDI MA+ + GG+G E G+ + + + + YEG Sbjct: 376 KTKAGRYVGLLTPVAKAFLTDRGLDITIMAQQVFGGHGYIRETGIEQLVRDTRIAQIYEG 435 Query: 374 THDVHAL-ILGRAQTG 388 T+ + A+ LGR TG Sbjct: 436 TNGIQAIDFLGRKVTG 451 Lambda K H 0.320 0.137 0.413 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: 537 Number of extensions: 31 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: 393 Length of database: 578 Length adjustment: 33 Effective length of query: 360 Effective length of database: 545 Effective search space: 196200 Effective search space used: 196200 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 (21.8 bits) S2: 51 (24.3 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