Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate PP_4780 PP_4780 putative Acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Putida:PP_4780 Length = 550 Score = 407 bits (1046), Expect = e-118 Identities = 223/457 (48%), Positives = 291/457 (63%), Gaps = 10/457 (2%) Query: 4 QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63 +TH V NQP PL+ +NLY D L E R GAGW + + G G ++ G LAN Sbjct: 8 ETHEVTNQPPPLDGANLYRLDLPLQEWSRRFGAGWAESRIDAYGALAG-GPLMQAGFLAN 66 Query: 64 VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123 + PE +D G R+D V FHPA+H LM+ + + +L W E R+GA VARA+ L Sbjct: 67 AHKPEFSSHDRYGHRIDLVEFHPAYHELMRTAVEHGLPSLPWAEP-RAGAHVARASMTYL 125 Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183 H+Q EAG+ CP+TMTFAA P L ++ P + W +L+ YD + K G+ +GM Sbjct: 126 HSQAEAGTGCPLTMTFAAVPAL-RLQPELAEYWLPKILACEYDPRNVGDRHKAGVTLGMA 184 Query: 184 MTEKQGGSDVMSNTTRAERL----EDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239 MTEKQGG+DV +NTTRA + +Y LVGHKWF S P DA L LAQT GLSCF Sbjct: 185 MTEKQGGTDVRANTTRAYPVGAPGPGQAYELVGHKWFCSAPMCDAFLTLAQTEKGLSCFL 244 Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299 +PR PD RN ++RLK+KLGN SNAS EVEF+ A+ W++G EG G+ I++M MTR Sbjct: 245 LPRHRPDDNRNQFYIQRLKNKLGNSSNASSEVEFRGALAWMIGEEGRGVPTIIEMVAMTR 304 Query: 300 FDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLA 359 FDC +GS A+MR+A + A +H R V G L +QPLM++VL+ +AL+ E AL R+ Sbjct: 305 FDCMVGSSALMRQALTQAAHHCAHRKVGGRVLNEQPLMQNVLADLALESEAALALSLRMG 364 Query: 360 RAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMP 419 +A ++ D ++A +ARL T K+ ICKR + EA E LGG GY E+S LPRLYRE P Sbjct: 365 QALEQLDDPQQAHFARLVTAVGKYWICKRAPAMINEAAECLGGAGYVEDSILPRLYREAP 424 Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEV 456 VNS WEGSGN+ CLDVLR L+K+ GV D L FVE+ Sbjct: 425 VNSTWEGSGNVQCLDVLRALSKEPGVLDAL---FVEL 458 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: 725 Number of extensions: 30 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: 550 Length adjustment: 35 Effective length of query: 506 Effective length of database: 515 Effective search space: 260590 Effective search space used: 260590 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 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