GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein

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



>NCBI__GCF_000009985.1:WP_011384263.1
          Length = 273

 Score =  151 bits (382), Expect = 2e-41
 Identities = 86/214 (40%), Positives = 129/214 (60%), Gaps = 3/214 (1%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + ++ LS++FGA   ++  +L+I+ GEF+ LLG SGCGKST LN +AG L  + G++ + 
Sbjct: 17  IGIQRLSVSFGAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVD 76

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
              VT   P+    GMVFQ ++L+P  TV +N++FG ++     AE     +   +++ +
Sbjct: 77  GVEVTGPGPER---GMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGL 133

Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183
               +R P+ LSGG  QRV I RALV    V L DEP   LDA+ RS ++  + RL   +
Sbjct: 134 GGSAQRYPAALSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQI 193

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLAD 217
            NT+++VTHD  EAL LADR+ VM +   + L D
Sbjct: 194 GNTVLFVTHDIDEALFLADRVVVMSAAPGRVLLD 227


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: 246
Number of extensions: 13
Number of successful extensions: 2
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: 273
Length adjustment: 27
Effective length of query: 334
Effective length of database: 246
Effective search space:    82164
Effective search space used:    82164
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