GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_6000 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6000
          Length = 714

 Score =  382 bits (981), Expect = e-110
 Identities = 268/725 (36%), Positives = 373/725 (51%), Gaps = 33/725 (4%)

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

Query: 62  PDNFIAGADINMIGNCKTAQ-EAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGL 117
              F AG D+N +   K  + EA+A       L A++  L      V+AAI+GA LGGG 
Sbjct: 61  -HTFFAGGDLNEL--IKVGKPEAKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGW 117

Query: 118 ELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAK 177
           E+ LACH RV  D P   LGLPEV LGLLPG GG  R+ RL+G+  AL  +L GK++ A+
Sbjct: 118 EICLACHHRVALDLPSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVNAQ 177

Query: 178 QALKLGLVDDVVPHSILLEAAVELAKKERPSS-RPLPVRERILAGPLGR----ALLFKMV 232
           QAL  GL+D++      L A         PS  +P   +   L G        A +  + 
Sbjct: 178 QALLAGLIDELAKDRNELLAKSRAWILANPSVIQPWDAKGYRLPGGTPSDPKVAQMLAIA 237

Query: 233 GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAS 292
                +KTQG  PA E+IL     G      + +  E R F EL     ++ L   F+  
Sbjct: 238 PSILRNKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVAKNLIGTFWFQ 297

Query: 293 TDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL 349
            +  K  GS      P     VG+LG G+MG GIAYV+A  AGI V +KD++        
Sbjct: 298 LNEIKAGGSRPQGLAPYLTKKVGVLGAGMMGAGIAYVSAV-AGIAVVLKDVDLAAAEKGK 356

Query: 350 KYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAE 409
             S   L+ K+ R  L A +R+  LA I  T      A  DL+IEAVFE+  +K  + A 
Sbjct: 357 ARSAALLDKKIARGQLTAEQREATLARIHPTDSNADLAGCDLVIEAVFEDRAVKASVSAA 416

Query: 410 VEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQT 469
            +       + ASNTS+LPI  +A     P + IGLHFFSPVEKMPLVEII  A TS +T
Sbjct: 417 AQAVVGDDAVIASNTSTLPITGLAMAVPDPTKFIGLHFFSPVEKMPLVEIIKGARTSDET 476

Query: 470 IATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFP 529
           +A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+    K G P
Sbjct: 477 LARGFDFVLQINKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIETEARKAGMP 536

Query: 530 VGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRGF 583
           VGP+ + DEV +   + I       L A        PA  V+  +LN+  R G+  G GF
Sbjct: 537 VGPLAVSDEVSLSLMSHIRAQTAKDLHAEGKMPIEHPAFAVIDLLLNEYKRPGKAAGAGF 596

Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQ---GRISAPQVAERCVMLMLNEAVRCVDEQVIR 640
           Y Y   G+K        ++P + ++ +   G+IS   + +R + +   E VRC++E V+ 
Sbjct: 597 YEYPANGQK-------YLWPQLKSRFEKTDGQISPQDIRDRLLFIQALETVRCIEEGVLT 649

Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700
           S  D +IG++FGIGF  + GG  ++I+  G  + V   Q LA QYG RF+P   L+E  A
Sbjct: 650 STADANIGSIFGIGFAAWTGGALQFINQYGLQDFVGRAQYLAEQYGERFSPPALLLEKAA 709

Query: 701 RGESF 705
           R E F
Sbjct: 710 RHELF 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: 984
Number of extensions: 39
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