GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCbeta in Dyella japonica UNC79MFTsu3.2

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate N515DRAFT_0481 N515DRAFT_0481 2-oxoisovalerate dehydrogenase E1 component

Query= uniprot:G1UHX5
         (328 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0481 N515DRAFT_0481
           2-oxoisovalerate dehydrogenase E1 component
          Length = 755

 Score =  135 bits (339), Expect = 4e-36
 Identities = 110/333 (33%), Positives = 153/333 (45%), Gaps = 25/333 (7%)

Query: 6   MAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAILG 65
           +A  +  AL + +   P ++LFGED+   GGV+ +T GL   F   R F+T L E+ ILG
Sbjct: 422 LAIQIGQALHEVMAKYPESLLFGEDVALKGGVYTVTKGLFKTFKGNRVFNTLLDETVILG 481

Query: 66  TAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIP---YGGG 122
            A G A  G  P+ E+Q+ A+ + A +Q+      L+  +      PL +R+    Y  G
Sbjct: 482 LAQGYANMGMLPMPEIQYLAYFHNACDQIRGEACSLQFFSNDQYRNPLVMRVAALGYQKG 541

Query: 123 IGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLR--RSIASPDPVV--FLEPKRLYW 178
            GG   H+D+S       PGL V  P+   DA ++LR   ++A  D  V  FLEP  LY 
Sbjct: 542 FGG-HFHNDNSIAALRDIPGLVVGCPSRGDDAAAMLRTLMALAKVDGRVCAFLEPIALYM 600

Query: 179 RKE-----------ALGLPVDTGPLGSA-VIRRHGTHATLIAYGPAVTTALEAA-EAAAE 225
            K+           A   P +  PLG   V  +      +  +G  V  AL AA E   +
Sbjct: 601 TKDLYEAGDGQWQFAYPAPGEALPLGEGRVYEQDADDLVVFTFGNGVPMALRAAREIEKK 660

Query: 226 HGWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITE-RCFYHL 284
           HGW   V+DLR L PL+D  +    R   R +V+ E    AG G  I   I E  C    
Sbjct: 661 HGWRTRVVDLRWLAPLNDKFIAGQARNARRILVLDEGRRSAGVGEGIITAIVEGGCG--- 717

Query: 285 EAPVRRVTGFDVPYPPPLLERHYLPGVDRILDA 317
             P++RV G D   P        LPG   I+ A
Sbjct: 718 ATPLQRVVGADTYTPLAGAALLVLPGEAEIVAA 750


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: 594
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: 755
Length adjustment: 34
Effective length of query: 294
Effective length of database: 721
Effective search space:   211974
Effective search space used:   211974
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: 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 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