GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Burkholderia phytofirmans PsJN

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate BPHYT_RS12835 BPHYT_RS12835 dihydrolipoamide acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542
         (425 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS12835 BPHYT_RS12835
           dihydrolipoamide acetyltransferase
          Length = 550

 Score =  224 bits (571), Expect = 5e-63
 Identities = 152/444 (34%), Positives = 242/444 (54%), Gaps = 45/444 (10%)

Query: 2   GTHVIKMPDIGE--GIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIA 59
           G   +K+PDIG+   I  +E++V   KVGD V ++Q L  + +DKA +D+PS   G V  
Sbjct: 115 GLQEVKVPDIGDYKDIPVIEVAV---KVGDRVEKEQSLVTLESDKATMDVPSSAAGVVKE 171

Query: 60  LGGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAP 119
           +  + G+ ++ GSV++ +E EG      +A PAP    AP  A +  +   + P  APA 
Sbjct: 172 VKVKVGDTVSEGSVIVIVEAEGGA----AAAPAP----APKQAVEKPSDAPATPSPAPAA 223

Query: 120 KAAVCQGPMV------AREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDA 173
            +A+ Q P++      AR A     ASP+VRK A +LG+ +  V+GTGP  R+   D+ A
Sbjct: 224 PSALAQAPVIPAGEGGARHASH---ASPSVRKFARELGVDVTQVQGTGPKNRITQADVTA 280

Query: 174 YLA---QGQ----SNASAPVAAAYAQRTDEQQIPVIGMRR------KIAQRMQDATQRAA 220
           ++     GQ    + A+AP AA      +    P +   +      K   R++  +    
Sbjct: 281 FIKGVMTGQRAAPAGAAAPAAAGGGGELNLLPWPKVDFTKFGPVDPKPLSRIKKISGANL 340

Query: 221 HFSYV--------EEIDVTAVEELRAHLNEKHGATRGKLTLLPFLVRALVVALRDFPQIN 272
           H ++V        +E D+T +E LR  LN+++  +  K+T+L F+++A+V AL+ FP  N
Sbjct: 341 HRNWVMIPHVTNNDEADITELEALRVKLNKEYEKSGVKITMLAFVIKAVVSALKQFPTFN 400

Query: 273 ARYDDEAQVITRLGAVHVGIATQADIGLMVPVVRHAEARSLWDSAAEISRLATAARNGKA 332
           A  D +  V  +    H+G A     GL+VPV+R A+ + L D A E++ L+  AR+GK 
Sbjct: 401 ASLDGDNLVFKQY--FHIGFAADTPNGLVVPVIRDADKKGLIDIAKEMAELSKLARDGKL 458

Query: 333 SRDELSGSTITLTSLGALGGIVSTPVLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLS 392
             D++ G   +++SLG +GG   TP++N PEVAI+G+++   +P+    Q V R  + LS
Sbjct: 459 KPDQMQGGCFSISSLGGIGGTNFTPIINAPEVAILGLSRGAMKPVWDGKQFVPRLTLPLS 518

Query: 393 SSFDHRVVDGMDAALFIQAIRGLL 416
            S+DHRV+DG  AA F   +  LL
Sbjct: 519 LSYDHRVIDGAAAARFNAYLGALL 542



 Score = 58.2 bits (139), Expect = 6e-13
 Identities = 39/117 (33%), Positives = 63/117 (53%), Gaps = 11/117 (9%)

Query: 6   IKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIALGGQPG 65
           +K+PDIG+   ++ +    VK GD V ++Q L  + +DKA +D+PS   G V  +  + G
Sbjct: 7   VKVPDIGD-YKDIPVIEVLVKAGDTVEKEQSLVTLESDKATMDVPSSAAGVVKEVKVKVG 65

Query: 66  EVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPKAA 122
           + ++ GS+++ +  EGA     +  PAP    AP AA        + P AAP P A+
Sbjct: 66  DNVSEGSLIVVL--EGAEGGAAAPAPAPAAAPAPSAA--------AAPAAAPVPAAS 112


Lambda     K      H
   0.318    0.133    0.368 

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: 514
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 425
Length of database: 550
Length adjustment: 34
Effective length of query: 391
Effective length of database: 516
Effective search space:   201756
Effective search space used:   201756
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: 52 (24.6 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 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