GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate N515DRAFT_4327 N515DRAFT_4327 phospholipid/cholesterol/gamma-HCH transport system ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4327
          Length = 270

 Score =  108 bits (271), Expect = 1e-28
 Identities = 81/243 (33%), Positives = 120/243 (49%), Gaps = 12/243 (4%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + VRDL   FG   V + L+LD+  GE L ++G SG GKS LL  I GL   + GQ+ + 
Sbjct: 15  IQVRDLVNRFGTQAVHEHLDLDVRRGEILGVVGGSGTGKSVLLRTIVGLRRPTSGQVQVF 74

Query: 64  DRNVTWEEPKDRG-----IGMVFQSYALYPQMTVEKNLSFGL---KVAKIPPAEIEKRVK 115
            +++    P+ R       G++FQ+ AL+    V +N++  L      K P AE    VK
Sbjct: 75  GQDLLRLPPEQRSRIERRFGVLFQNGALFSSQNVVENIAMPLIEHAGLKRPEAEALGTVK 134

Query: 116 RASEILQIQPLLKRK-PSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRV 174
            A  +  + P  + K PSELSGG  +R A+ RAL  D +V   DEP + LD    +    
Sbjct: 135 LA--LAGLPPGTEHKYPSELSGGMVKRAALARALALDPEVLFLDEPTAGLDPISAAAFDQ 192

Query: 175 EIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI 234
            I  L  +L  T+  VTHD     T+ DR+AV+    +    D + +    E+ +V  + 
Sbjct: 193 LILTLRDALGLTVFLVTHDLDTLYTICDRVAVLSQKKV-LACDRLDVVAQNEDPWVQSYF 251

Query: 235 GSP 237
             P
Sbjct: 252 HGP 254


Lambda     K      H
   0.320    0.137    0.392 

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: 259
Number of extensions: 10
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: 361
Length of database: 270
Length adjustment: 27
Effective length of query: 334
Effective length of database: 243
Effective search space:    81162
Effective search space used:    81162
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 (21.8 bits)
S2: 48 (23.1 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 (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