GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Dechlorosoma suillum PS

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo5_N2C3_1:AO356_00470
         (220 letters)



>FitnessBrowser__PS:Dsui_0636
          Length = 245

 Score =  106 bits (265), Expect = 3e-28
 Identities = 68/215 (31%), Positives = 107/215 (49%), Gaps = 12/215 (5%)

Query: 18  LWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLAC 77
           L+ G   +V  SL A V+  ++G + G++ T    W+      YV+  R  P+ V + + 
Sbjct: 25  LFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPNRWLSGFAAVYVECFRNVPLLVQLFSW 84

Query: 78  FY-----MAPALGWQ-------IGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEAS 125
           ++     + PALG         +  F A +L L LF  + VAE VR  +++LPRGQ  A 
Sbjct: 85  YFVLPELLPPALGNAYKQSDPLLQQFLAAMLCLGLFTAARVAEQVRAGIESLPRGQRNAG 144

Query: 126 QAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIART 185
            A+G T  Q   +VLLP A R I+P   +    I K S + + IG+ EL    QQ++  T
Sbjct: 145 LAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATTIGLIELSRQAQQLVDYT 204

Query: 186 FMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP 220
               E ++    L+  IN  +  L R +E++V +P
Sbjct: 205 AQPYEAFIAVTLLYVCINVTVMFLMRRLEEKVRVP 239


Lambda     K      H
   0.330    0.142    0.443 

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: 149
Number of extensions: 4
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: 220
Length of database: 245
Length adjustment: 23
Effective length of query: 197
Effective length of database: 222
Effective search space:    43734
Effective search space used:    43734
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: 46 (22.3 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