GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS12835
          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:

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