GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pedobacter sp. GW460-11-11-14-LB5

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate CA265_RS19585 CA265_RS19585 pyruvate dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_479
         (423 letters)



>FitnessBrowser__Pedo557:CA265_RS19585
          Length = 562

 Score =  203 bits (516), Expect = 1e-56
 Identities = 139/434 (32%), Positives = 214/434 (49%), Gaps = 22/434 (5%)

Query: 2   GTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALG 61
           G  VI+MP + + + E  ++ WH KVGD V +D VLADV TDKA +++     G ++ +G
Sbjct: 134 GVTVIRMPLLSDTMTEGVIAEWHKKVGDKVKDDDVLADVETDKATMEVMGYATGTLLHIG 193

Query: 62  GEPGEVMAVGSELIRIEVEGAGNLKESAQQAPTPTPAAQAPKPAPVATPEPVLEKTAAPR 121
            E G    V   +  +  EG  ++         P P A++ + AP A     + +   PR
Sbjct: 194 VEKGAAAKVNGIIAIVGPEGT-DVSGILAGGSAPAPKAESAE-APKAEKSATVAEIETPR 251

Query: 122 CAPQAPVARDPDERPLASPAVRKHALDLGIQLRLVQGSGPAGRVLHEDLEAYLAQGPSVQ 181
            +       + D R  ASP  +K A D GI L  V GS   GR++ +D+E +       +
Sbjct: 252 TSSCGTTTDNGDSRVKASPLAKKIAKDKGIDLAQVAGSAEGGRIIKKDIENFKPSAAPAK 311

Query: 182 AKGGSGYAERHDEQQIPVIG---------------MRRKIAQRMQEATQRAAHFSYVEEI 226
           A+  S  A        PVI                MR+ IA+R+ E+   A HF     I
Sbjct: 312 AESASAPAAEKAAAPAPVIPQYVGEVKFTEAPVSQMRKVIAKRLAESLFTAPHFYLTISI 371

Query: 227 DITALEELRVHLNEKHGASRGKLTLLPFLVRALVVALRDFPQMNARYDDEAQVIHRSGAV 286
           D+      R  +N     +  K++    +++A+ VAL+  P +N+ +  +   I  +   
Sbjct: 372 DMDNAMAARTAIN---AVAPVKVSFNDIVIKAVAVALKKHPAVNSSWGGDK--IRFNEHT 426

Query: 287 HVGVATQSDVGLMVPVVRHAEARSLWDNAAEISRLATAARTGKASRDELSGSTITLTSLG 346
           ++GVA   + GL+VPVVR A+ +SL   +AE+      A+  K    +  GST T+++LG
Sbjct: 427 NIGVAMAVEDGLLVPVVRFADGKSLSHISAEVKDFGGKAKAKKLQPADWEGSTFTVSNLG 486

Query: 347 ALGGIVSTPVLNLPEVAIVGVNKIVERPVVIKGQIVIRKMMNLSSSFDHRVVDGMDAAQF 406
             G    T ++N P+ AI+ V  I + PVV  G +V   +M L+   DHRVVDG   AQF
Sbjct: 487 MFGIDEFTSIINSPDGAILSVGAIQQVPVVKNGAVVPGNVMKLTLGCDHRVVDGATGAQF 546

Query: 407 IQALRGLLEQPATL 420
           +Q L+GLLE+P  L
Sbjct: 547 LQTLKGLLEEPIRL 560



 Score = 57.4 bits (137), Expect = 1e-12
 Identities = 38/108 (35%), Positives = 56/108 (51%), Gaps = 4/108 (3%)

Query: 5   VIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALGGEP 64
           VIKMP + + + E  L+ WH KVGD V    VLA+V TDKA +D+ S   G ++ +G E 
Sbjct: 4   VIKMPKMSDTMTEGVLAKWHKKVGDKVKSGDVLAEVETDKATMDMESYWDGTLLYVGVEE 63

Query: 65  GEVMAVGSELIRIEVEG----AGNLKESAQQAPTPTPAAQAPKPAPVA 108
           G  + V + +  I  EG    A    E +    + +P ++    AP A
Sbjct: 64  GTAVPVDAIMAVIGKEGEDYKAALEAEQSGSQESGSPKSERKDEAPKA 111


Lambda     K      H
   0.317    0.133    0.375 

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: 562
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 423
Length of database: 562
Length adjustment: 34
Effective length of query: 389
Effective length of database: 528
Effective search space:   205392
Effective search space used:   205392
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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