GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate 3607838 Dshi_1246 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::WCS417:GFF4322
         (281 letters)



>lcl|FitnessBrowser__Dino:3607838 Dshi_1246
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 282

 Score =  176 bits (446), Expect = 5e-49
 Identities = 94/272 (34%), Positives = 157/272 (57%), Gaps = 6/272 (2%)

Query: 13  SRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGI---GWVKAWAT 69
           +++    ++ LA++L+L+PL+ + + S K   D ++GN   WP    G      V   + 
Sbjct: 13  AQLTYQGMIPLALILWLLPLIAVAIFSVKPAGDFAAGNYWGWPAEFAGFENYARVFTDSE 72

Query: 70  VDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPA 129
           +  Y  NS  IT+P V+ + A+  + G+ L  +RF+G+ L F + + G F+PFQ +++P 
Sbjct: 73  MPRYILNSFMITIPTVIGAVALSCMTGFALGIYRFRGNLLIFFMFIAGNFVPFQILMVPV 132

Query: 130 SFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQ 189
                 MGL +T TGLV  H+ +   F TLF RN+  ++P  LI+AAR++G   + IF  
Sbjct: 133 RDLTVDMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPYELIEAARVEGVAEWRIFWF 192

Query: 190 IILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSG-DSQPITVALNNLVNTSTGAKEYNVD 248
           ++LP+  P I    +  FT IWND+ + VV + G ++QP+T  + +  N   G   YN+ 
Sbjct: 193 VVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGPNAQPVTAGITSF-NAQFGI-AYNML 250

Query: 249 MAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVK 280
            A ++IA LP ++++ +  K+F+ GLT GAVK
Sbjct: 251 SAGSLIAALPPVMMFFLMQKHFIAGLTLGAVK 282


Lambda     K      H
   0.328    0.141    0.435 

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: 211
Number of extensions: 12
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: 281
Length of database: 282
Length adjustment: 26
Effective length of query: 255
Effective length of database: 256
Effective search space:    65280
Effective search space used:    65280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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