Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate WP_041096225.1 SUTH_RS00425 isovaleryl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >NCBI__GCF_000828635.1:WP_041096225.1 Length = 551 Score = 491 bits (1264), Expect = e-143 Identities = 254/509 (49%), Positives = 335/509 (65%), Gaps = 4/509 (0%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH V NQ L N N YL++ L EAV ++GAGW D+L + G + G+AE +E GRLAN Sbjct: 11 THEVLNQAHALENYNAYLNNVPLQEAVAQQGAGWAQDWLIARGAETGSAEWIEHGRLANA 70 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 NPP+L +D G R D+V FHP+WH + L + W D + GA VARAA +++ Sbjct: 71 NPPQLRLFDRYGNRRDEVEFHPSWHECLGWLKRHGCDTGPWA-DPKPGAHVARAAAYVMF 129 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 A++E GSLCP TMT+ A P+L + +P +DW LLS YD +P QK G+LIGMG+ Sbjct: 130 AEIEDGSLCPTTMTYGAVPVL-KHVPEIARDWMPKLLSRDYDKRFIPAAQKTGVLIGMGL 188 Query: 185 TEKQGGSDVMSNTTRAERLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFL 244 TEKQGGSDV +NTTRAER++DGS+R+ GHKWF S P DA LV AQ+ GLSCFFVPR+ Sbjct: 189 TEKQGGSDVRANTTRAERMDDGSWRITGHKWFLSAPMCDAFLVTAQSPKGLSCFFVPRWT 248 Query: 245 PDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRFDCAL 304 PDG+ N +R++R K+K+G+RSNA E EF + GWL+G EG GI +L+MG TR DCA+ Sbjct: 249 PDGRLNELRIQRFKEKMGDRSNAGTEAEFWGSQGWLVGEEGRGIPTVLEMGVYTRLDCAI 308 Query: 305 GSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAWDR 364 GS +MR A S A++H R FG L QPLM + L+ +AL+ E TAL RLARA+D Sbjct: 309 GSTGIMRGALSQAMHHVGLRSAFGKLLRDQPLMINTLADLALETEAATALSMRLARAFDA 368 Query: 365 RADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIW 424 + D E L RL TP AKF ICKR VAEAMEV GG GY +E +PRL+++ P+NSIW Sbjct: 369 QEDESENLLRRLLTPVAKFWICKRCPAMVAEAMEVHGGNGYVDEGPMPRLFKQSPLNSIW 428 Query: 425 EGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKP--AEELG 482 EGSGN+MCLD LR + + D+L+ G++R FD +L+ L P E G Sbjct: 429 EGSGNVMCLDTLRAMGRHPKSVDVLAAEIAPALGKNRAFDAFAAKLKDGLANPQDIETRG 488 Query: 483 REITHQLFLLGCGAQMLKYASPPMAQAWC 511 RE+T + L GA +L++A P+++A+C Sbjct: 489 RELTQGIALAMQGALLLRHAPAPVSEAFC 517 Lambda K H 0.324 0.138 0.428 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: 721 Number of extensions: 36 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: 541 Length of database: 551 Length adjustment: 35 Effective length of query: 506 Effective length of database: 516 Effective search space: 261096 Effective search space used: 261096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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