Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate GFF3397 HP15_3339 acyl-CoA dehydrogenase domain protein
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Marino:GFF3397 Length = 566 Score = 447 bits (1149), Expect = e-130 Identities = 240/523 (45%), Positives = 321/523 (61%), Gaps = 8/523 (1%) Query: 5 THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64 TH VFNQP L N NL+ D AL EA REGAG ++ L + G G A++++LG AN Sbjct: 23 THEVFNQPPALENYNLFEQDIALQEAALREGAGKAAEDLKAFGALAGAAQTIDLGFRANA 82 Query: 65 NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124 N P +D G R+D+V FHPA+H LM+ N +H+ W + GA VARAA++ +H Sbjct: 83 NKPVFNTHDRFGHRIDEVDFHPAYHELMRIAFDNGLHSSPWSHPGQ-GAHVARAAKYYMH 141 Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184 +QVEA CP+TMTFAA P + + P DW +L+D YD LP QK + IGM M Sbjct: 142 SQVEAAHCCPVTMTFAAIPSIRKQ-PELAADWEARILADSYDPRNLPDSQKSSVTIGMAM 200 Query: 185 TEKQGGSDVMSNTTRAERLEDG----SYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFV 240 TEKQGGSDV +N+TRA + G +Y LVGHKWF S P DA LVLAQT GLSCF + Sbjct: 201 TEKQGGSDVRANSTRAYPIGAGGPGQAYELVGHKWFVSAPMCDAFLVLAQTQSGLSCFLM 260 Query: 241 PRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRF 300 PR+ PDG +N +++RLK+K+GN +NAS E E + A+ W++G EG G+ I++M MTRF Sbjct: 261 PRWRPDGTKNPWQVQRLKNKMGNVANASSEAELRGALAWMVGEEGRGVPTIIEMVAMTRF 320 Query: 301 DCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLAR 360 DC +GS A MR+A + A +H R FG LI QPLM++VL+ +AL+ E A R+AR Sbjct: 321 DCMIGSSAGMRQAIAQASHHCRHRSAFGARLIDQPLMQNVLADLALESEAALAYTMRIAR 380 Query: 361 AWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPV 420 A D + E L ARL TP K+ ICKR EAME +GG G E+ +PRL+RE PV Sbjct: 381 ALDNQDKEHERLLARLATPVGKYWICKRTPNHAYEAMECIGGSGVMEDCIMPRLFRESPV 440 Query: 421 NSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLR--KPA 478 N+IWEGSGN+ CLD LR L K+ D E KG DR FD+ + +LQ Sbjct: 441 NAIWEGSGNVQCLDTLRALQKEPETLDAFFNEAAEAKGADRRFDQFLAQLQHDFADISDF 500 Query: 479 EELGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGV 521 + R + ++ L G+ +L+++ +A A+C L+ GG+ Sbjct: 501 QYRARNLVDRMALALQGSLLLRHSDAAVADAFCASRLEASGGM 543 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: 681 Number of extensions: 28 Number of successful extensions: 6 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: 566 Length adjustment: 36 Effective length of query: 505 Effective length of database: 530 Effective search space: 267650 Effective search space used: 267650 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: 53 (25.0 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