GapMind for catabolism of small carbon sources

 

Aligments for a candidate for msdB2 in Dinoroseobacter shibae DFL-12

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 3607127 Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= uniprot:A3DE71
         (289 letters)



>lcl|FitnessBrowser__Dino:3607127 Dshi_0549
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 272

 Score =  140 bits (352), Expect = 4e-38
 Identities = 82/267 (30%), Positives = 140/267 (52%), Gaps = 9/267 (3%)

Query: 24  ILAILVVLTLGPIVFMVLTSLMDHNAIARGK--WIAPTRFSNYVEVFQKLPFGIYFRNSL 81
           +L +++ + + P  +MV TSL            WI     SNY E   +        NSL
Sbjct: 13  LLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSL 72

Query: 82  IVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKIKQ 141
           I+      +ALV+   A ++LA+++F G        +  +++  ++  LP +L       
Sbjct: 73  IIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLI------ 126

Query: 142 ATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRVML 201
           A  + L++    L+++Y  F +P  IWI+   F  IP +L+EAAR++G ++FT   ++ L
Sbjct: 127 ARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICL 186

Query: 202 PLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARYDLLMAAGT 261
           PLA+PG+  +AI+ F+ +W+EL+F  +L + ++  T PA    F+      Y  +MA  T
Sbjct: 187 PLAMPGVAVSAIFSFIFSWNELMFGLILTR-SEAKTAPAMAVSFMEGYNLPYGKIMATST 245

Query: 262 IVTIPVLIMFFTMQKKFISGMTAGAVK 288
           ++ IPVLI      K+ + G+T GAVK
Sbjct: 246 LIVIPVLIFALIASKQLVRGLTMGAVK 272


Lambda     K      H
   0.332    0.145    0.434 

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: 221
Number of extensions: 8
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: 289
Length of database: 272
Length adjustment: 26
Effective length of query: 263
Effective length of database: 246
Effective search space:    64698
Effective search space used:    64698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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