Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_001046645.1:WP_066607952.1 Length = 381 Score = 203 bits (517), Expect = 6e-57 Identities = 130/376 (34%), Positives = 196/376 (52%), Gaps = 3/376 (0%) Query: 16 DQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGG 75 D L + M+RDSA +F+ D++AP E + ++ MGE+GL G T+ E+ GG Sbjct: 5 DFALGDNADMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGG 64 Query: 76 SGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIG 135 GL Y+ + + EV R + S+L + I +G QK KYLPKL SG+ +G Sbjct: 65 LGLGYLEHVVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHVG 124 Query: 136 CFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGD--IRG 193 ++E GSD SM +A K Y L G+K WITN+P AD VV+AK G I Sbjct: 125 SLAMSEAGAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTGEGSKGITT 184 Query: 194 FVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKG-PFTCLNSAR 252 F++EK +G S K+G+R S T E+V D+ VPEENI + G G + L+ R Sbjct: 185 FLIEKDMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYER 244 Query: 253 YGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLG 312 ++ LG +AC T Y +RQQFGRP+ A QL+Q K+ADM + A + Sbjct: 245 TVLAGIQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVA 304 Query: 313 RMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYE 372 R D G + + A+ +A A LGG G + ++ V R++ + ++++ Sbjct: 305 RACDSGKTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGA 364 Query: 373 GTHDVHALILGRAQTG 388 GT+++ +++GR G Sbjct: 365 GTNEIRRMLIGRELIG 380 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: 321 Number of extensions: 17 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: 393 Length of database: 381 Length adjustment: 30 Effective length of query: 363 Effective length of database: 351 Effective search space: 127413 Effective search space used: 127413 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