GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02227 SMc02227 fatty oxidation complex
           enoyl-COA hydratase/3-hydroxyacyl-COA
           dehydrogenase/3-hydroxybutyryl-COA epimerase
          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 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