GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Marinicella litoralis KMM 3900

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_099018480.1 CCS90_RS05525 pyruvate dehydrogenase

Query= uniprot:G1UHX5
         (328 letters)



>NCBI__GCF_002591915.1:WP_099018480.1
          Length = 701

 Score =  181 bits (460), Expect = 4e-50
 Identities = 115/325 (35%), Positives = 176/325 (54%), Gaps = 12/325 (3%)

Query: 4   ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63
           I M  A+   L   L  + + ++FGED+GA GGV  +T GL  + G+ + FDT L+E  I
Sbjct: 381 INMVTAIRKTLDYELSHNNKMLVFGEDVGAKGGVHAVTLGLQEKHGEAQVFDTSLSEEGI 440

Query: 64  LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123
           +G ++G+A+ G  PV E+QF  +A PA EQL +    +R RT      P+ +R+  GG  
Sbjct: 441 IGRSIGLALAGLLPVPEIQFRKYADPAEEQL-NETGSMRWRTNNRFAAPMVVRMA-GGYF 498

Query: 124 G-GVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY---WR 179
           G G   HS  +E+ ++   G  V  P+ A DA  LLR ++ + +P +F E +++    W 
Sbjct: 499 GCGDPWHSQCAEVKWVHAIGWQVAMPSNAEDAVGLLRYALRNNNPTIFFEHRKMLDHAWS 558

Query: 180 KEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239
           +          P G       G   T++++G  V     A E   + G   ++IDLRTL 
Sbjct: 559 RRPYPGDQYIIPFGQGNKILSGDRVTVVSWGGMVHMCQTAIE---QTGIQADLIDLRTLR 615

Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDV--P 297
           P D A V  SV++TGR ++VHE +  AG GAEIAA + +  F++L+AP+ R+   D+  P
Sbjct: 616 PWDKAMVLQSVKKTGRCLIVHEDNMSAGFGAEIAAILAKEAFFYLDAPIERLATADIGNP 675

Query: 298 YPPPLLERHYLPGVDRILDAVASLE 322
           + P L+E H LP  D I   +  L+
Sbjct: 676 HDPKLME-HALPNPDSIAQRLMELD 699


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: 544
Number of extensions: 27
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: 701
Length adjustment: 33
Effective length of query: 295
Effective length of database: 668
Effective search space:   197060
Effective search space used:   197060
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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