GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Marivita geojedonensis DPG-138

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 WP_085636206.1 MGEO_RS08035 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_002115805.1:WP_085636206.1
          Length = 728

 Score =  400 bits (1029), Expect = e-116
 Identities = 265/724 (36%), Positives = 372/724 (51%), Gaps = 33/724 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FT+    D IA IT DVP + MN L  E    +  ++     ++ ++G++  S K D F 
Sbjct: 4   FTMTKDADGIATITWDVPEKSMNVLSFEGLQTLNDLVDDALADEAVKGIIITSGKAD-FA 62

Query: 67  AGADINMIGNCKTAQEAEA--------------LARQGQQLMAEIHALPIQVIAAIHGAC 112
           AG D+N++   K A  AEA              + R G          P  V A + G  
Sbjct: 63  AGMDLNVLATLKEAG-AEAVFDGIMKMHGVLRKIERAGMDAKTNKGGKP--VAAVLPGTA 119

Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172
           LG GLE+ LACH     D+PK  +GLPE+ +G+ PG+GGT R+ R +G   A   +L GK
Sbjct: 120 LGIGLEIPLACHRVFAADNPKAKIGLPEILVGIFPGAGGTTRVARKMGAMAASPFLLEGK 179

Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG--PLGRALLFK 230
                +A   GL+D+V    +    A  L+  +    +P   +   + G  P   A    
Sbjct: 180 LSDPAKAKAAGLIDEVSADPMADARAWVLSAGDADILKPWDAKGYKMPGGAPYHPAGFMT 239

Query: 231 MVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RS 287
            VG       KT+G YPA + +L  V  G      +    EAR F  + M P S A+ RS
Sbjct: 240 FVGASAMVNGKTKGVYPAAKALLSAVYEGALVPFDTALKIEARWFTSVIMNPSSSAMIRS 299

Query: 288 IFFASTDVKKDP--GSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGI 345
           +F     ++K     +D     +  VG+LG G+MG GIA V+A +AGI V + D +    
Sbjct: 300 LFINKQALEKGAVRPADVDDQRVKKVGVLGAGMMGAGIALVSA-QAGIDVVLLDRDQAAA 358

Query: 346 NHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQ 405
           +    YS D     V RR +   + D  LA I+ TTDY   A  DLI+EAVFE+ ++K  
Sbjct: 359 DKGKAYSADYAAKGVSRRKITQDKADAMLARITATTDYNDLAGCDLIVEAVFEDPKIKAD 418

Query: 406 MVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGT 465
           + A+VE       IFA+NTS+LPI D+A  + RPEQ IG+HFFSPVEKM LVEII    T
Sbjct: 419 VTAQVEAVIGEDCIFATNTSTLPISDLAKASKRPEQFIGIHFFSPVEKMMLVEIIKGKET 478

Query: 466 SAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVK 525
             + +A  +   ++  KTPIVV D   FY NR + PYINE IRM+ +G     I+ A   
Sbjct: 479 GDRAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVKEGVAPALIENAAKM 538

Query: 526 FGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGRKNGRGF 583
            G P+GP+QL+DE  ID G KI    +AA G+ +   A   V+  +  + R GRK   GF
Sbjct: 539 VGMPLGPLQLVDETSIDLGAKIARATKAAMGDAYPDGAVDEVIFWMEGEGRLGRKAKAGF 598

Query: 584 YLYGQKG-RKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642
           Y Y  KG R+    V  A YP    Q + +     V  R + +   EAVR +++ V+  +
Sbjct: 599 YDYDDKGKRQGLSSVVAAQYP----QAEDQPDLIDVQHRLLFVQSLEAVRALEDGVLMDI 654

Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702
           R+GD+GA+ G GF P+ GGP  ++D LG+        +L   YG RF   + L EM A+G
Sbjct: 655 REGDVGAILGWGFAPWSGGPLSWLDMLGSEYAAERCDQLVETYGDRFACPDLLREMAAKG 714

Query: 703 ESFW 706
           +SF+
Sbjct: 715 QSFY 718


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: 1048
Number of extensions: 50
Number of successful extensions: 8
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: 728
Length adjustment: 40
Effective length of query: 674
Effective length of database: 688
Effective search space:   463712
Effective search space used:   463712
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 24 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