Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_110207232.1 DNK54_RS12090 acyl-CoA dehydrogenase
Query= BRENDA::Q60759 (438 letters) >NCBI__GCF_003194585.1:WP_110207232.1 Length = 384 Score = 379 bits (973), Expect = e-110 Identities = 195/382 (51%), Positives = 261/382 (68%), Gaps = 3/382 (0%) Query: 54 LILEEQLTADEKLIRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTIKGY 113 L L+ LT DE +RDT R +++L+ + + +I +G G+ G ++GY Sbjct: 6 LDLDLLLTPDELAVRDTVRALGRDKLLPDVATWFEEGILPSEIPPLLGSHGLFGMHLQGY 65 Query: 114 GCAGVSSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGEL 173 GCAG+S+V YG+ ELE +DSG RS++SVQ SL M I+ +GSEEQ+Q++LPG+A GE+ Sbjct: 66 GCAGMSAVDYGIACLELEAIDSGLRSLVSVQGSLAMTAIHKFGSEEQKQEWLPGMATGEI 125 Query: 174 LGCFGLTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCEDNCI 233 +GCFGLTEP+HGSDPG M T AR + ++ + L+GTK WITN +A + +VWA+ ++ + Sbjct: 126 VGCFGLTEPDHGSDPGSMRTHARRDGAD--WVLNGTKMWITNGGIAGVAVVWAQTDEG-V 182 Query: 234 RGFILEKGMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVLPNVSSLAGPFGCLNTA 293 RGFI+ G G I+ K SLRAS T +I+D +P + VLP V L GP CLN A Sbjct: 183 RGFIVPAGTPGFRTQNIKHKMSLRASITSELILDDCRLPADAVLPEVKGLRGPLSCLNEA 242 Query: 294 RYGITWGVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADMLTEITLGLHACLQL 353 RYGI WG +GAA C A++YA RIQFG P+A QL QKKLADM E+ G LQ+ Sbjct: 243 RYGIVWGAMGAARACFEAAQEYAGSRIQFGRPIAGFQLTQKKLADMYLELAKGTLLALQI 302 Query: 354 GRLKDQDKATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMNLEAVNTY 413 GRLKD+ KATP+ VS+ K NN +AL IA +AR ILG NGI+ EY VIRHA NLE+V TY Sbjct: 303 GRLKDEGKATPQQVSLGKLNNVREALHIAHEARGILGANGITLEYPVIRHANNLESVYTY 362 Query: 414 EGTHDIHALILGRAITGIQAFT 435 EGT++IH LI+G+A+TGI A++ Sbjct: 363 EGTNEIHTLIVGQALTGIAAYS 384 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: 471 Number of extensions: 17 Number of successful extensions: 3 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: 384 Length adjustment: 31 Effective length of query: 407 Effective length of database: 353 Effective search space: 143671 Effective search space used: 143671 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 24 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