GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3796 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__pseudo1_N1B4:Pf1N1B4_3796
          Length = 714

 Score =  377 bits (969), Expect = e-109
 Identities = 270/733 (36%), Positives = 374/733 (51%), Gaps = 49/733 (6%)

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

Query: 62  PDNFIAGADINMIGNCKTAQ-EAEA-----LARQGQQLMAEIHALPIQVIAAIHGACLGG 115
              F AG D+N +   K  + EA+A     L  +GQ    E    P  V+AAI+GA LGG
Sbjct: 61  K-TFFAGGDLNEL--IKVGKPEAKAFYDMVLILKGQLRTLETLGKP--VVAAINGAALGG 115

Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175
           G E+ LACH RV  DDP  +LGLPEV LGLLPG GG  R+ R++G+  AL  +L GK++R
Sbjct: 116 GWEICLACHHRVVLDDPSVLLGLPEVTLGLLPGGGGVVRMVRMLGIEKALPYLLEGKKIR 175

Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERP--SSRPLPVRERILAG---PLGR----- 225
            +QAL+  L+D+      L     EL  K R      P+ V+   + G   P G      
Sbjct: 176 PQQALQARLIDE------LAADRDELMAKARAWIVDHPVAVQRWDVKGYQIPGGTPSDPK 229

Query: 226 -ALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284
            A +  +       KTQG  PA E+IL     G      + +  E R F EL     S+ 
Sbjct: 230 LAPMLAITPSILRSKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVSKN 289

Query: 285 LRSIFFASTDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDIN 341
           L   F+   +     GS      P     VG+LG G+MG GIA+V+A  AGI V +KDIN
Sbjct: 290 LIGTFWFQLNEINAGGSRPQGIAPYVTKKVGVLGAGMMGAGIAFVSAL-AGIDVVLKDIN 348

Query: 342 PQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLE 401
                    +S   L+ KV R  L   +R++ LA I  T +    A  DL+IEAVFE+ E
Sbjct: 349 LAAAEKGKAHSAALLDKKVARGQLTREQREEILARIHATENDADLAGCDLVIEAVFEDRE 408

Query: 402 LKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIP 461
           LK ++ +  +       + ASNTS+LPI  +A       + IGLHFFSPVEKMPLVEII 
Sbjct: 409 LKTKVSSAAQAVVGPDAVIASNTSTLPISGLAIAVPDQTKFIGLHFFSPVEKMPLVEIIK 468

Query: 462 HAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDA 521
              TS +T+A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+ 
Sbjct: 469 GVHTSDETLARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIET 528

Query: 522 ALVKFGFPVGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPANVVSSILNDD--RK 575
              K G PVGP+ + DEV +   + I       L A        PA  V  +L  +  R 
Sbjct: 529 EARKAGMPVGPLAISDEVSLSLMSHIREQTAKDLRAEGKTLIEHPAFAVIDLLLKEYKRP 588

Query: 576 GRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVR 632
           G+  G GFY Y   G+K        ++P + +   +  G+IS   + +R + +   E VR
Sbjct: 589 GKAAGGGFYDYPATGQKH-------LWPELKSRFEKADGQISPQDIRDRLLFVQAIETVR 641

Query: 633 CVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPC 692
           C++E V+ S  D ++G++FGIGF  + GG  ++I+  G  + VA  Q LA QYG RFTP 
Sbjct: 642 CMEEGVLTSTADANVGSIFGIGFAAWTGGALQFINQYGVKDFVARAQYLAEQYGERFTPP 701

Query: 693 ERLVEMGARGESF 705
             L+E  A+   F
Sbjct: 702 ALLLEKAAKNALF 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: 1011
Number of extensions: 42
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