Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate WP_090445290.1 BLS63_RS13640 DNA alkylation response protein
Query= SwissProt::P33224 (541 letters) >NCBI__GCF_900100495.1:WP_090445290.1 Length = 549 Score = 405 bits (1040), Expect = e-117 Identities = 236/524 (45%), Positives = 308/524 (58%), Gaps = 10/524 (1%) Query: 4 QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63 +TH VFNQ PL++ NLY D L E R G W + + G G E + G LAN Sbjct: 8 ETHEVFNQVPPLDDVNLYRIDLPLQEWTRRFGGDWAEARIDAYGALAG-GELMAAGFLAN 66 Query: 64 VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123 N P +D G R+D V FHPA+H LM A + + ++ W R GA VARAA L Sbjct: 67 ENKPVFKSHDRFGHRIDLVEFHPAYHQLMSAAIEHGIPSMPWTAP-RPGAQVARAAMSYL 125 Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183 H+Q EAGS CP+TMT+A+ P L ++ P W +LS YD LP QK G IGM Sbjct: 126 HSQAEAGSGCPLTMTYASVPAL-KLQPDIAALWLPKILSREYDPRNLPIEQKNGATIGMA 184 Query: 184 MTEKQGGSDVMSNTTRAERL----EDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239 MTEKQGG+DV +NTTRA + +Y LVGHKWF S P DA L LA T GL+CF Sbjct: 185 MTEKQGGTDVRANTTRAYPVGAPGPGQAYELVGHKWFCSAPMCDAFLTLAYTDRGLTCFL 244 Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299 +PR PDG RN ++RLK+KLGN SNAS EVE++ A+ W++G EG G+ I++M +TR Sbjct: 245 LPRHRPDGTRNQFYIQRLKNKLGNWSNASSEVEYRGALAWMIGEEGRGVPTIIEMVALTR 304 Query: 300 FDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLA 359 FDC +GS A+MR+A + A +H R V G L +QPLM++VL+ +AL+ E AL RL Sbjct: 305 FDCMVGSSALMRQALTQAAHHCAYRQVGGRVLSEQPLMQNVLADLALESEAALALTMRLG 364 Query: 360 RAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMP 419 +A D + +E +ARL T K+ ICKR + EA E +GG GY E+S LPRLYRE P Sbjct: 365 QALDNAHEQQEDKFARLVTAVGKYWICKRAPAMINEAAECMGGAGYVEDSILPRLYREAP 424 Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAE 479 VNS WEGSGN+ CLDVLR L+K+ GV D L + G D ++RLQ R AE Sbjct: 425 VNSTWEGSGNVQCLDVLRALSKEPGVLDALFNELGDGHG-DARLKAHIQRLQADFRDSAE 483 Query: 480 --ELGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGGV 521 R++T + L +L+ + ++ A+ L G V Sbjct: 484 IQYRARQLTEDVALALQAKLLLEAGNATVSDAFIASRLGEGGRV 527 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: 676 Number of extensions: 23 Number of successful extensions: 5 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: 549 Length adjustment: 35 Effective length of query: 506 Effective length of database: 514 Effective search space: 260084 Effective search space used: 260084 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 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