Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_06133 H281DRAFT_06133 hypothetical protein
Query= BRENDA::Q60759 (438 letters) >FitnessBrowser__Burk376:H281DRAFT_06133 Length = 377 Score = 167 bits (423), Expect = 5e-46 Identities = 122/382 (31%), Positives = 184/382 (48%), Gaps = 22/382 (5%) Query: 60 LTADEKLIRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTIKG-YGCAGV 118 LT + ++IR++ R + ERL ++N F + E+GELG LG ++ +G AG+ Sbjct: 3 LTQEHEMIRESIRTFAAERLAPHASDWDKNHTFPAAALKELGELGALGMVVEEKWGGAGL 62 Query: 119 SSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGELLGCFG 178 ++ L E+ D +++SVQ+SL YGSE+Q++++L LA+G+ LGCF Sbjct: 63 DYMSLVLALEEIAAGDGATSTIVSVQNSLACGITSKYGSEKQKEQWLRPLAQGQKLGCFC 122 Query: 179 LTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCEDNC----IR 234 LTEP+ GSD + T AR + + L+G K +IT AD+ IV+A + + I Sbjct: 123 LTEPHTGSDASALRTTARRD--GDEWVLNGVKQFITTGKYADVAIVFAVTDKSADKKGIS 180 Query: 235 GFILEKGMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVLPNVSSLAGPFGC----- 289 F++ G R+E K AS T II + V ++S++ G G Sbjct: 181 CFLIPTATPGYVVARLEEKMGQHASDTAQIIFEDCRV-------HLSAMMGQEGDGYRIA 233 Query: 290 ---LNTARYGITWGVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADMLTEITLG 346 L R GI +G A A +YA +R FG L +Q V +LADM T+I Sbjct: 234 LSNLEAGRIGIAAQAVGMARAAFEAAVKYAKERETFGKLLIEHQAVTFRLADMATQIEAA 293 Query: 347 LHACLQLGRLKDQDKATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMN 406 + LKD KA SM K A + A I GG G ++ V R + Sbjct: 294 RMMVWRAATLKDAGKACLTEASMAKMFASEMAEKVCSDAIQIHGGCGYVSDFPVERIYRD 353 Query: 407 LEAVNTYEGTHDIHALILGRAI 428 + YEG +DI +++GRAI Sbjct: 354 VRVCQIYEGANDIQRMVIGRAI 375 Lambda K H 0.320 0.136 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: 320 Number of extensions: 9 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: 438 Length of database: 377 Length adjustment: 31 Effective length of query: 407 Effective length of database: 346 Effective search space: 140822 Effective search space used: 140822 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: 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