GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Erythrobacter marinus HWDM-33

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_047093915.1 AAV99_RS08480 alpha-ketoacid dehydrogenase subunit beta

Query= uniprot:G1UHX5
         (328 letters)



>NCBI__GCF_001013305.1:WP_047093915.1
          Length = 355

 Score =  261 bits (668), Expect = 1e-74
 Identities = 154/332 (46%), Positives = 193/332 (58%), Gaps = 21/332 (6%)

Query: 4   ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63
           + M +A+N+AL   L  D    L GEDIG  GGVFR T GL  + G  R FDTP++E  I
Sbjct: 22  MNMIEAINSALDVMLTRDSDVTLLGEDIGYFGGVFRCTAGLQEKHGKTRVFDTPISECGI 81

Query: 64  LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123
           +G AVGM  YG RPV E+QF  + YP  +QL+S  A+LR R+      P+T+R P+GGGI
Sbjct: 82  IGVAVGMGAYGLRPVPEIQFADYIYPGLDQLISEAARLRYRSAAEFIAPMTVRSPFGGGI 141

Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY------ 177
            G + HS S E  +    GL  V PAT  DA  LL   I   DPV+F EPKR+Y      
Sbjct: 142 FGGQTHSQSPESIFTHVCGLKTVIPATPYDAKGLLISCIEDNDPVIFFEPKRIYNGPFDG 201

Query: 178 --------WR-KEALGLP--VDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEH 226
                   W+ +E   +P      PLG A     G   T++AYG  V     A     E 
Sbjct: 202 YYDRPAKNWKGREDAQVPDGYYKIPLGKARTVTEGDAMTILAYGTMVHV---AESVCREK 258

Query: 227 GWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEA 286
           G   E++DLRTL+PLD   + ASV+RTGR ++VHEA   +G GAE++A +TERCFYHLEA
Sbjct: 259 GVAAEILDLRTLVPLDIEAIEASVKRTGRCLIVHEATRTSGFGAELSALVTERCFYHLEA 318

Query: 287 PVRRVTGFDVPYPPPLLERHYLPGVDRILDAV 318
           PV RVTGFD PYP   LE  Y PG  RI +A+
Sbjct: 319 PVERVTGFDTPYPHS-LEWAYFPGPVRIGEAI 349


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: 377
Number of extensions: 19
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: 355
Length adjustment: 29
Effective length of query: 299
Effective length of database: 326
Effective search space:    97474
Effective search space used:    97474
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 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