GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Pseudomonas stutzeri RCH2

Align Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex; Branched-chain alpha-ketoacid dehydrogenase complex component E2; BCKADH E2; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 (characterized)
to candidate GFF2174 Psest_2217 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes

Query= SwissProt::O06159
         (393 letters)



>lcl|FitnessBrowser__psRCH2:GFF2174 Psest_2217
           Pyruvate/2-oxoglutarate dehydrogenase complex,
           dihydrolipoamide acyltransferase (E2) component, and
           related enzymes
          Length = 382

 Score =  164 bits (415), Expect = 4e-45
 Identities = 121/386 (31%), Positives = 183/386 (47%), Gaps = 17/386 (4%)

Query: 10  FPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGAEG 69
           F +P LG  + E T+  W V  G+ +E  + +  V+TAKA V++   ++G ++EL    G
Sbjct: 4   FKLPSLGADMDEGTLLQWKVKPGERIERGEVIAVVDTAKAAVDVECWHSGEVLELLVEPG 63

Query: 70  DVLKVGAELVRIDTGPTAVAQPNGEGAVPTLVGYGAD----TAIETSRRTSRPLAAPVVR 125
             + VG  L R+     A      +   P  V   A+    TA+     TSR   +PV R
Sbjct: 64  SKIPVGTPLARLLEPGEAREAALAQSPAPVPVAVAAEQPPVTAVAPPADTSRARISPVAR 123

Query: 126 KLAKELAVDLAALQRGSGAGGVITRADVLAAARGGVGAGPDVRPVHGVHARMAEKMTLSH 185
           + A EL +D A L  GSG  G +T  DV AAA     A  +      +   +A  M+ S 
Sbjct: 124 RRAAELGIDPATLS-GSGPHGSVTLQDVEAAAAKAAPADRNA----AMRQAIAAAMSRSK 178

Query: 186 KEIPTAKASVEVICAELLRLRDRF-VSAAPE--ITPFALTLRLLVIALKHNVILNSTWVD 242
           +EIP    S  V      R    +     PE  +    L L+ + +AL+    LN  W D
Sbjct: 179 REIPHYYLSETVAFGAAARWLQAYNAERIPEERLLVSVLLLKAVALALRDYPQLNGYWRD 238

Query: 243 SGEGPQVHVHRGVHLGFGAATERG-LLVPVVTDAQDKNTRELASRVAELITGAREGTLTP 301
               P      G+HLG   +  +G L+ P + D   +   +L   + +L+  AR G+L  
Sbjct: 239 GAFQPG----EGIHLGTAISLRQGGLIAPALHDVAGQPLPQLMQALGDLVQRARAGSLRS 294

Query: 302 AELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVARPTMTLTCV 361
           +EL  +T TV+  G  GVD    VI  P+ A++G+G I  RP V  G +   P++ L+  
Sbjct: 295 SELSDATLTVTQLGEQGVDSVFGVIYPPQVALVGVGRIVERPWVEAGALCVMPSVVLSLA 354

Query: 362 FDHRVVDGAQVAQFMCELRDLIESPE 387
            DHR  DG   A+F+ E+R L+++PE
Sbjct: 355 ADHRASDGHYGARFLAEVRRLLQNPE 380


Lambda     K      H
   0.317    0.135    0.388 

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: 369
Number of extensions: 23
Number of successful extensions: 4
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 preprint 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