Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate RR42_RS11190 RR42_RS11190 acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Cup4G11:RR42_RS11190 Length = 540 Score = 415 bits (1066), Expect = e-120 Identities = 234/518 (45%), Positives = 302/518 (58%), Gaps = 9/518 (1%) Query: 10 NQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANVNPPEL 69 NQ L + NLY SD + AV R GAGW+ L G LG ++++ AN + PEL Sbjct: 3 NQVPELKDYNLYTSDPGIRRAVARAGAGWNEGELERQGAVLGAEQTIQHAEDANRHHPEL 62 Query: 70 LRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLHAQVEA 129 + G R+D VRFHPAWH LM + + NL + D R A+ + AA +H+Q+E+ Sbjct: 63 HTHSRIGERIDQVRFHPAWHELMAMARHSGLANLPFA-DTRPSAWASYAASLYMHSQIES 121 Query: 130 GSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGMTEKQG 189 GSLCP MT A P+L + P F + LL+ YD LP KR + +GMGMTEKQG Sbjct: 122 GSLCPTNMTQACIPVLRKE-PGLFAQFGDKLLTQAYDPRDLPIAHKRSINVGMGMTEKQG 180 Query: 190 GSDVMSNTTRAE----RLEDGSYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFFVPRFLP 245 GSDV +NTTRA Y + GHKWFFS P SDAHLVLA T G SCFFVPR+ P Sbjct: 181 GSDVRANTTRAVPGRGEGRGAEYLITGHKWFFSAPMSDAHLVLANTEAGSSCFFVPRWRP 240 Query: 246 DGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTRFDCALG 305 DG +N I ++RLKDK+GNRSN+S EVEF+DA G ++G EG GI IL+M +R +C+L Sbjct: 241 DGSKNPIEIQRLKDKVGNRSNSSSEVEFRDAWGIMVGEEGRGIPTILEMATYSRLNCSLS 300 Query: 306 SHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLARAWDRR 365 S +R+A A+++A R FG PLI+QPLM +L+ MAL+ E L LA A++ Sbjct: 301 SAGFLRQALVQALHYARHRSAFGKPLIRQPLMVRLLADMALEAEAAMLLAMDLATAFEAT 360 Query: 366 ADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMPVNSIWE 425 D W R+ TPA+KF ICKR + EAMEV GG GY E+ + RL+RE PVNSIWE Sbjct: 361 DDPARLAWRRILTPASKFWICKRAVEMTGEAMEVFGGNGYVEDGPMGRLFREAPVNSIWE 420 Query: 426 GSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPAEEL---G 482 GSGN+MCLDVLR + + Y + E V + +V L+ LR P EE Sbjct: 421 GSGNVMCLDVLRAIGRNPHDYLRVLEHMSVVGADEPRIQASVAALRAALRLPEEEQQAEA 480 Query: 483 REITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520 R T +L L ML++A A A+ D G Sbjct: 481 RRTTTRLVLTAQACLMLQHADTATADAFLASRFDPEWG 518 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: 659 Number of extensions: 20 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: 540 Length adjustment: 35 Effective length of query: 506 Effective length of database: 505 Effective search space: 255530 Effective search space used: 255530 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