GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Phaeobacter inhibens BS107

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF2286 PGA1_c23180 dihydrolipoyllysine-residue acetyltransferase-like protein

Query= reanno::Smeli:SMc03203
         (426 letters)



>FitnessBrowser__Phaeo:GFF2286
          Length = 292

 Score =  166 bits (420), Expect = 9e-46
 Identities = 104/303 (34%), Positives = 155/303 (51%), Gaps = 33/303 (10%)

Query: 140 LASPAVRLRARESGIDLRQVAG------------------TGPAGRITHEDLDLFISRGA 181
           +A P+VR  AR+ GIDL ++A                   +GPAG  ++ D+D       
Sbjct: 5   IAPPSVRALARQKGIDLEKLAKELGRTSIVREDLESGKTTSGPAGDTSYWDVD------- 57

Query: 182 EPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEVDMTALEDLRATMN 241
               +Q G V +  +     +      A  +S + + IP +T+ +  D+TA+E LR  + 
Sbjct: 58  ---HSQFGSVGEELMSRFAQVA-----AANLSAANALIPQVTHHDRADVTAIEALRKELK 109

Query: 242 RDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAVHIGIATQTPAGLT 301
            + +    KLT L F  +AL + + E P  NA+       +     VHIGIA  T  GL 
Sbjct: 110 PEAQARGVKLTALAFQAKALARALREFPRFNASLSPDGKTLTLKGYVHIGIAVDTAHGLM 169

Query: 302 VPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLGAIGGIASTPVINH 361
           VPVV   + +G+W  AAE++ LA  A+      DE+ G+++TI++LG IGGI  TP++N 
Sbjct: 170 VPVVHDVDRKGLWQIAAEISDLASRAQNRKVGPDEMGGASMTITNLGGIGGIGFTPIVNP 229

Query: 362 PEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVFVQRLKTLLETPAL 421
           PEVAI+G+ +     VWD     P  ++ L  S+DHRVI+G DAA FV     L+  P  
Sbjct: 230 PEVAILGITRTETVTVWDDDTPRPVTMVPLDLSYDHRVINGADAARFVSYFAGLIADPRR 289

Query: 422 IFV 424
           I V
Sbjct: 290 IMV 292


Lambda     K      H
   0.317    0.133    0.384 

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: 290
Number of extensions: 11
Number of successful extensions: 2
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: 426
Length of database: 292
Length adjustment: 29
Effective length of query: 397
Effective length of database: 263
Effective search space:   104411
Effective search space used:   104411
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: 49 (23.5 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