GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Novosphingobium fuchskuhlense FNE08-7

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_067911252.1 AQZ52_RS12615 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase

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



>NCBI__GCF_001519075.1:WP_067911252.1
          Length = 430

 Score =  196 bits (499), Expect = 9e-55
 Identities = 141/429 (32%), Positives = 214/429 (49%), Gaps = 19/429 (4%)

Query: 6   IKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALGGEPG 65
           IKMP +   + E  L+ W VKVGD V    ++A++ TDKA ++  +   G V+A+    G
Sbjct: 5   IKMPALSPTMEEGTLAKWLVKVGDKVSSGDIMAEIETDKATMEFEAVDEGTVVAIEVAEG 64

Query: 66  -EVMAVGSELIRIEVEGAGNLKESAQQAPTPTPAAQAPKPAPVATPEPVLEKTAAPRCAP 124
            E + VG+ +  I  E  G+   +A     P PA  AP PAPVA P       AAP  AP
Sbjct: 65  TEGVKVGTVIATIAGEDDGDAAPAAAAVSAPAPAPVAPMPAPVAAPAAA-PVAAAPAPAP 123

Query: 125 QAPVARDPDERPLASPAVRKHALDLGIQLRLVQGSGPAGRVLHEDLE--------AYLAQ 176
            APVA   D R +ASP  ++ A + GI L  V GSGP GR++  DL+        A  A 
Sbjct: 124 -APVAAAGD-RIVASPLAKRIASEKGIDLGTVTGSGPHGRIIKADLDVAAPKAAVAAPAA 181

Query: 177 GPS-----VQAKGGSGYAERHDEQQIPVIGMRRKIAQRMQEATQRAAHFSYVEEIDITAL 231
            P+     V A   + ++     + + +  MR+ IA+R+ EA     H+    +I +  L
Sbjct: 182 VPAPVAAPVAAPAAAPFSTDIPHEAVKLSSMRKTIARRLTEAKATVPHYYLTVDISLDKL 241

Query: 232 EELRVHLNEKHGASRGKLTLLPFLVRALVVALRDFPQMNARYDDEAQVIHRSGAVHVGVA 291
            +LR  LN        KL++   L++AL  AL   P  N  +  +  +  R     + VA
Sbjct: 242 LKLRAELNAALAGEGVKLSVNDLLIKALGKALMLAPDANVSFAGDNLI--RYSRADIAVA 299

Query: 292 TQSDVGLMVPVVRHAEARSLWDNAAEISRLATAARTGKASRDELSGSTITLTSLGALGGI 351
                GL+ P+V  A+ +S+     +++ LA  A+ GK +  E  G T +L++LG  G  
Sbjct: 300 VSIPGGLITPIVTGADVKSISAIQKDMADLAARAKAGKLAPHEYQGGTASLSNLGMFGIK 359

Query: 352 VSTPVLNLPEVAIVGVNKIVERPVVIKGQIVIRKMMNLSSSFDHRVVDGMDAAQFIQALR 411
               V+N P+  I+ +    +RP VI   + I  +M+ + SFDHR +DG + AQ +QA +
Sbjct: 360 QFVAVINPPQGMIMAIGAGEKRPYVIDDALGIATVMSATGSFDHRAIDGAEGAQLMQAFK 419

Query: 412 GLLEQPATL 420
            L+E P  L
Sbjct: 420 TLVEAPLAL 428


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: 439
Number of extensions: 32
Number of successful extensions: 7
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: 423
Length of database: 430
Length adjustment: 32
Effective length of query: 391
Effective length of database: 398
Effective search space:   155618
Effective search space used:   155618
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: 51 (24.3 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