GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCbeta in Magnetospirillum magneticum AMB-1

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_011384714.1 AMB_RS11710 pyruvate dehydrogenase complex E1 component subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384714.1 AMB_RS11710 pyruvate
           dehydrogenase complex E1 component subunit beta
          Length = 452

 Score =  207 bits (527), Expect = 4e-58
 Identities = 125/325 (38%), Positives = 177/325 (54%), Gaps = 6/325 (1%)

Query: 5   TMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAIL 64
           T+ +AL  A+ + +R DP   L GE++    G ++++ GL  EFG ER  DTP+ E    
Sbjct: 130 TVREALRDAMAEEMRADPNVFLMGEEVAQYQGAYKVSQGLLDEFGAERVIDTPITEMGFA 189

Query: 65  GTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGIG 124
           G A G    G +P+VE     F+  A + +++  AK    + G     +  R P G    
Sbjct: 190 GLACGAGYAGLKPIVEFMTMNFSMQAIDHVINSAAKTLYMSGGQQPCSIVFRGPNGAASR 249

Query: 125 GVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKEALG 184
               HS     +Y   PGL V+ P +AADA  LL+ +I  P+PVVFLE + LY   ++  
Sbjct: 250 VGAQHSQDYASWYAHCPGLKVLAPWSAADAKGLLKAAIRDPNPVVFLENELLY--GQSFD 307

Query: 185 LPVDTG---PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPL 241
           +P D     P+G A I R G H T+ AY   V  AL+AAE     G + EVI+LR++ PL
Sbjct: 308 VPDDPDFVLPIGKAKIERAGAHVTITAYSRMVQVALDAAEILKAEGIEAEVINLRSIRPL 367

Query: 242 DDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP-P 300
           D AT+ ASV++T R V V E    AG G+EIAA + E+ F  L+APV RV G DVP P  
Sbjct: 368 DVATIVASVQKTNRIVSVEEGWPVAGIGSEIAALMMEQAFDWLDAPVVRVAGADVPMPYA 427

Query: 301 PLLERHYLPGVDRILDAVASLEWEA 325
             LE+  LP ++ ++ A  S+ + A
Sbjct: 428 ANLEKLALPQIEHVVAAARSVCYRA 452


Lambda     K      H
   0.322    0.138    0.418 

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: 2
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: 328
Length of database: 452
Length adjustment: 30
Effective length of query: 298
Effective length of database: 422
Effective search space:   125756
Effective search space used:   125756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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