GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF2174
          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.

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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