GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas fluorescens FW300-N2C3

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate AO356_20400 AO356_20400 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20400
          Length = 714

 Score =  391 bits (1005), Expect = e-113
 Identities = 273/726 (37%), Positives = 378/726 (52%), Gaps = 35/726 (4%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61
           MT+A       D I V+T+D+PG+  NT+ A +   + A + +L+  K+ + GV+  SAK
Sbjct: 1   MTAAIRYETGQDRIVVLTLDMPGQSANTMNARYREAMAACVTRLKAEKDAIAGVIITSAK 60

Query: 62  PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118
              F AG D+N +       EA+A       L A++ AL      V+AAI+GA LGGG E
Sbjct: 61  -QTFFAGGDLNELVKVGKP-EAKAFYDMVLLLKAQLRALETLGKPVVAAINGAALGGGWE 118

Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178
           + LACH RV  + P   LGLPEV LGLLPG GG  R+ RL+G+  AL  +L GK++ A+Q
Sbjct: 119 ICLACHHRVALEQPSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVSAQQ 178

Query: 179 ALKLGLVDDVVPHSILLEAAVELAKKERPSS-RPLPVRERILAG------PLGRALLFKM 231
           AL+ GL+D++      L A         PS  +P   +   L G       +G+ L   +
Sbjct: 179 ALQAGLIDELAKDREELLAKSRAWILANPSVVQPWDAKGYRLPGGTPSDPKVGQMLA--I 236

Query: 232 VGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSIFF 290
                 +KTQG  PA E+IL     G      + +  E R F EL     ++ L  +++F
Sbjct: 237 APSILRNKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVAKNLIGTLWF 296

Query: 291 ASTDVKKDPGSDAPPAPL--NSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHA 348
              ++K         AP     VG+LG G+MG GIAYV+A  AGI V +KD++       
Sbjct: 297 QLNEIKAGGSRPQGVAPYLTKKVGVLGAGMMGAGIAYVSAV-AGIAVVLKDVDLTAAEKG 355

Query: 349 LKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVA 408
              S   L+ KV R  L A +R+  LA I  T +    A  DLIIEAVFE+  LK  + A
Sbjct: 356 KARSAALLDKKVARGQLTAEQREATLARIQATDNNADLAGCDLIIEAVFEDRALKASVSA 415

Query: 409 EVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQ 468
             +      T+ ASNTS+LPI  +A     P + IGLHFFSPVEKMPLVEII  A TS  
Sbjct: 416 AAQAVAGDDTVIASNTSTLPITGLAMAVPDPTKFIGLHFFSPVEKMPLVEIIKGARTSDA 475

Query: 469 TIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGF 528
           T+A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+    K G 
Sbjct: 476 TLARGFDFVLQINKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIETEARKAGM 535

Query: 529 PVGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRG 582
           PVGP+ + DEV +   + I       L A        PA  V+  +LN+  R G+  G G
Sbjct: 536 PVGPLAISDEVSLSLMSHIRAQTAKDLHAEGKTPIEHPAFAVIDLLLNEYKRPGKAAGAG 595

Query: 583 FYLYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVRCVDEQVI 639
           FY Y   G+K        ++P + +   Q  G+IS   + +R + +   E VRCV+E V+
Sbjct: 596 FYEYPANGQK-------YLWPQLKSRFEQADGQISPQDIRDRLLFIQALETVRCVEEGVL 648

Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMG 699
            S  D +IG++FGIGF  + GG  ++I+  G  + V   Q LA QYG RF+P   L+E  
Sbjct: 649 TSTADANIGSIFGIGFAAWTGGALQFINQYGLQDFVDRSQYLAEQYGERFSPPALLLEKA 708

Query: 700 ARGESF 705
           AR E F
Sbjct: 709 ARHELF 714


Lambda     K      H
   0.319    0.137    0.393 

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: 988
Number of extensions: 37
Number of successful extensions: 7
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: 714
Length of database: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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