GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Azospirillum brasilense Sp245

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AZOBR_RS04800 AZOBR_RS04800 pyruvate dehydrogenase subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>FitnessBrowser__azobra:AZOBR_RS04800
          Length = 343

 Score =  207 bits (528), Expect = 2e-58
 Identities = 132/327 (40%), Positives = 173/327 (52%), Gaps = 12/327 (3%)

Query: 3   EITMAKALNTALRDALRDDPRTILFGEDI----------GALGGVFRITDGLAAEFGDER 52
           +I+M  A+N AL   +R DP  IL GEDI           A GGV  +T GL A+ GD R
Sbjct: 4   KISMKTAINEALDLEMRRDPTVILMGEDIVGGTGAPGEDDAWGGVLGVTKGLFAKHGD-R 62

Query: 53  CFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLP 112
             DTPL+ESA +G A+G A  G RPV E+ F  F    F+Q+ +  AK R    G    P
Sbjct: 63  LLDTPLSESAYIGAAIGAATCGMRPVAELMFMDFMGVCFDQIFNQAAKFRYMFGGKAETP 122

Query: 113 LTIRIPYGGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLE 172
           + IR   G G      HS      +   PGL VV P+ A DA  LL +SI   DPV+F E
Sbjct: 123 VVIRGMVGAGFRAAAQHSQMLTPLFTHIPGLKVVCPSNAYDAKGLLIQSIRDNDPVIFCE 182

Query: 173 PKRLYWRKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEV 232
            K LY  +  +       P G A + R G H T+++YG  V  A+EAA+A A+   + EV
Sbjct: 183 HKNLYGHETEVPAESYAIPFGEANVLRDGDHVTIVSYGLTVHRAMEAADALAKDKVEAEV 242

Query: 233 IDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVT 292
           IDLRTL P+D  T+  SV RTGR VVV EAH       +I+A + +  F  L++ ++ VT
Sbjct: 243 IDLRTLSPIDWDTIIDSVERTGRLVVVDEAHPRCNLATDISAFVAQNAFGALKSGIQMVT 302

Query: 293 GFDVPYP-PPLLERHYLPGVDRILDAV 318
               P P  P LE  Y+P  + +  AV
Sbjct: 303 PPHTPVPFSPSLEDLYIPSAEAVAAAV 329


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: 326
Number of extensions: 17
Number of successful extensions: 3
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: 343
Length adjustment: 28
Effective length of query: 300
Effective length of database: 315
Effective search space:    94500
Effective search space used:    94500
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: 49 (23.5 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