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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources