GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sinorhizobium meliloti 1021

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 SMc02227 SMc02227 fatty oxidation complex enoyl-COA hydratase/3-hydroxyacyl-COA dehydrogenase/3-hydroxybutyryl-COA epimerase

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Smeli:SMc02227
          Length = 737

 Score =  404 bits (1039), Expect = e-117
 Identities = 255/723 (35%), Positives = 381/723 (52%), Gaps = 27/723 (3%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F +    D IA++T D+P + MN    E   ++ AII Q   +  ++GVV  S K  +F 
Sbjct: 6   FKIETDADGIALVTWDMPDKSMNVFTEEVMKELDAIIDQTTADPAVKGVVITSGK-SSFS 64

Query: 67  AGADINMIGNCKTAQEAEA------LARQGQQLMAEIHALPIQV-------IAAIHGACL 113
            GAD++MI +  T Q  E        AR+   L+  +  L  ++       ++AI+G C+
Sbjct: 65  GGADLSMIKSMFTFQAEERKKDPDNAARKLFDLVGRMTGLFRKLETSGKPWVSAINGTCM 124

Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173
           GG  E++LACHGRV ++     + LPEV++G+ PG+GGTQR+PRL     AL+M+ TG  
Sbjct: 125 GGAFEMSLACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLTNTQDALQMMTTGSS 184

Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG----PLGRALLF 229
           L   +A  +GLV +VV    L+EAA  + K      +P   +   L G        A L+
Sbjct: 185 LTPARAKAMGLVHEVVDPDKLIEAAKAMIKNGLKPVQPWDEKGFKLPGGGIWTPASAQLW 244

Query: 230 KMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS-QALRSI 288
                    +T GNYP    IL+ V  GL     +    E R F E+  T ++   +RS+
Sbjct: 245 PAASGILRRETYGNYPGAIAILKCVYEGLQVPFDTALKIEQRYFTEILQTTEAFSMIRSL 304

Query: 289 FFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346
           F +  ++ K     A  P   L  VG++G G MG  IAYVTA   GIPV + D + +   
Sbjct: 305 FVSMQELGKGARRPAGVPKTELKKVGVVGAGFMGASIAYVTAA-GGIPVTLIDRDMEAAE 363

Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406
               +S   ++  + +  L   E +  L+ I+ + DY       L+IEAVFE+ ++K+ +
Sbjct: 364 KGKTHSEGLVKDAIGKGRLTKEEGEALLSRITPSADYGDLRDAGLVIEAVFEDRQVKKDV 423

Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466
           + +VE   A   IFASNTS+LPI  +A ++ RP++ IG+HFFSPVEKM L E+I    T 
Sbjct: 424 IEKVEAVIAEDAIFASNTSTLPITGLARNSKRPDRFIGIHFFSPVEKMMLTEVILGKETG 483

Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526
            + +A  +       KTPIVV D  GFYVNR +  YI+EA  ML +G     I+ A    
Sbjct: 484 DRALAAALDYVAAIRKTPIVVNDTRGFYVNRCVFRYIHEAYDMLIEGVPPAMIENAAKMA 543

Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGER---FSAPANVVSSILNDDRKGRKNGRGF 583
           G PVGP+ L DEV ID   KI+    A  G++       A +   +   DR+GRKNG+GF
Sbjct: 544 GMPVGPLSLNDEVAIDLSQKILKAAVADLGDKAVDLRHMALIDKMVDELDRRGRKNGKGF 603

Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVR 643
           Y Y  K   ++K + P +  L   +  G I    + +R ++ +  EA R ++E ++   R
Sbjct: 604 YEYPAK--PARKYLWPGLKELYPQKDAGEIEVGVLKQRLLVTIALEAARTIEEGIVTDPR 661

Query: 644 DGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGE 703
           + D+G++ G GF P+ GG   YID +GA   V + ++LA  +G  F P   L EM  +GE
Sbjct: 662 EADVGSILGFGFAPYTGGTLSYIDGMGAKAFVELCEKLAADHGDHFRPTPLLKEMAEKGE 721

Query: 704 SFW 706
           +F+
Sbjct: 722 TFY 724


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: 1024
Number of extensions: 40
Number of successful extensions: 6
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: 737
Length adjustment: 40
Effective length of query: 674
Effective length of database: 697
Effective search space:   469778
Effective search space used:   469778
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