GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Rhodococcus qingshengii djl-6-2

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 WP_050655910.1 C1M55_RS30490 2-oxo acid dehydrogenase subunit E2

Query= SwissProt::O06159
         (393 letters)



>NCBI__GCF_002893965.1:WP_050655910.1
          Length = 407

 Score =  273 bits (697), Expect = 8e-78
 Identities = 168/398 (42%), Positives = 225/398 (56%), Gaps = 24/398 (6%)

Query: 10  FPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGGAEG 69
           F +PDLGEGL E  +  W V VGD V I+Q +  VETAKA V++P P+AG ++EL G +G
Sbjct: 6   FMLPDLGEGLAEADIAEWHVKVGDVVTIDQIVVEVETAKAAVDVPIPFAGTVIELHGKDG 65

Query: 70  DVLKVGAELVRIDTGPT--AVAQPNGE--------GAVPTLVGYGADTAIETSRRTSRP- 118
           D LKVG  L+ +  G +  AV   N E        G+   L+GYG        RR + P 
Sbjct: 66  DTLKVGTPLITVSGGESVDAVVSANHERYREEERAGSGNVLIGYGTSEDAPLRRRRAAPS 125

Query: 119 --LAAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAARGGVG-----AGPDVRPVH 171
             + +P+VRKLA + ++DL  +  GSGAGGVITRADV A +  G       A     P+ 
Sbjct: 126 VRVISPIVRKLASDNSIDLTTIS-GSGAGGVITRADVEAGSNTGTELETSHAADQRIPIK 184

Query: 172 GVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPE---ITPFALTLRLLVI 228
           G+   +A+K++ S +EIP A   V+V   ELL  R     + P+   I+  AL  RL + 
Sbjct: 185 GLRKVVADKLSTSRREIPDATTWVDVDATELLAARAEINKSLPDSDKISLMALLARLTIA 244

Query: 229 ALKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVA 288
           AL     LNS+ VD+  G  V  H   HLG  A T +GL+VPV+ +A   +T ELA  + 
Sbjct: 245 ALAQYPELNSS-VDTARGEIVR-HARTHLGIAAQTPKGLMVPVIRNADALSTVELAQALR 302

Query: 289 ELITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGG 348
                AR+G L PA L G TFT++N+G  GVD   P+INHPEAAILG+G I  +P VV G
Sbjct: 303 VTTDLARDGKLEPARLTGGTFTLNNYGVFGVDGSTPIINHPEAAILGIGRIIDKPWVVNG 362

Query: 349 EVVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESP 386
           E+  R    ++  FDHRV DG +   F+    D IE+P
Sbjct: 363 ELTVRKVTQISLSFDHRVCDGGEAGGFLRLFGDYIENP 400


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: 419
Number of extensions: 20
Number of successful extensions: 5
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: 407
Length adjustment: 31
Effective length of query: 362
Effective length of database: 376
Effective search space:   136112
Effective search space used:   136112
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 24 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:

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