Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate AZOBR_RS19670 AZOBR_RS19670 acyl-CoA dehydrogenase
Query= BRENDA::Q92947 (438 letters) >FitnessBrowser__azobra:AZOBR_RS19670 Length = 400 Score = 578 bits (1489), Expect = e-169 Identities = 281/394 (71%), Positives = 332/394 (84%), Gaps = 2/394 (0%) Query: 41 AKSSRPEFDWQDPLVLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEM 100 A + F W+DPL+L+EQLT DE +IRD R+YCQ++L+PR+ ANR+E+FHREI++EM Sbjct: 8 ASAKLASFAWEDPLLLDEQLTEDERMIRDAARSYCQDKLLPRVTEANRHEIFHREIMNEM 67 Query: 101 GELGVLGPTIKGYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQ 160 GELG LG TI GYGCAGV+ V+YGL+ARE+ERVDSGYRSAMSVQSSLVMHPIYAYGS+ Q Sbjct: 68 GELGFLGSTIDGYGCAGVNYVSYGLVAREVERVDSGYRSAMSVQSSLVMHPIYAYGSDVQ 127 Query: 161 RQKYLPQLAKGELLGCFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMAD 220 R+KYLP+LA GE +GCFGLTEP++GSDP+ M+TRA + Y ++G K WITNSP+AD Sbjct: 128 REKYLPKLATGEWIGCFGLTEPDAGSDPAGMKTRARKVADG--YIVSGAKMWITNSPVAD 185 Query: 221 LFVVWARCEDGCIRGFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGA 280 +FVVWA+ ++G I GF+LEKGM+GLSAP+I+GKFSLRASATG I+MD V VPEEN LP Sbjct: 186 VFVVWAKNDEGKINGFVLEKGMKGLSAPKIEGKFSLRASATGEIVMDEVFVPEENRLPNI 245 Query: 281 SSLGGPFGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADML 340 + GPFGCLN ARYGIAWG +GA+EFC H ARQY +DR QFG PLA NQ+ Q KLA+M Sbjct: 246 EGIVGPFGCLNRARYGIAWGAMGAAEFCFHAARQYQIDRKQFGRPLAANQIPQLKLANMQ 305 Query: 341 TEITLGLHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHV 400 TEI LGL A LQ+GRL D KAAPEM+SL+KRNNCGKAL+IAR ARDM GGNGI+DE+HV Sbjct: 306 TEIALGLQAALQVGRLLDDGKAAPEMISLIKRNNCGKALEIARVARDMHGGNGIADEFHV 365 Query: 401 IRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 434 IRH MNLEAVNTYEGTHDIHALILGRAITGIQAF Sbjct: 366 IRHVMNLEAVNTYEGTHDIHALILGRAITGIQAF 399 Lambda K H 0.319 0.135 0.400 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: 560 Number of extensions: 7 Number of successful extensions: 2 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: 400 Length adjustment: 32 Effective length of query: 406 Effective length of database: 368 Effective search space: 149408 Effective search space used: 149408 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