GapMind for catabolism of small carbon sources

 

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

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate N515DRAFT_2514 N515DRAFT_2514 iron complex transport system ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2514
          Length = 273

 Score =  134 bits (336), Expect = 3e-36
 Identities = 88/241 (36%), Positives = 128/241 (53%), Gaps = 8/241 (3%)

Query: 3   LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62
           L   ++ + YG  +VL  V+L    G++ ALIGPNG GKS+LL   +  L P  GT  L 
Sbjct: 18  LEARDVHLHYGERRVLQAVNLRAQPGRVLALIGPNGAGKSSLLGVLAGALQPSVGTATLD 77

Query: 63  DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122
              +    + +LARR ++L Q      G   +E+   GR+P  +   R  + D   V  A
Sbjct: 78  GVALERWPATELARRRAMLSQRVQLGFGFRAEEVAMLGRSPHGATSSR--SADGRIVEEA 135

Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQ-----NTP-VVLLDEPTTYLDINHQVD 176
           +       L  R   ELSGG++QR  LA VLAQ     + P  +LLDEP   LDI HQ +
Sbjct: 136 LKAAGAWSLFGRNYLELSGGEQQRVQLARVLAQIWDCRDAPGWLLLDEPEAGLDIAHQHE 195

Query: 177 LMRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFS 236
           L+    +L  QG  V+AVLHDLN A+RY D + ++A G ++  G  E+V+   +L  ++ 
Sbjct: 196 LLAQARQLAGQGFGVIAVLHDLNLAARYADDVALLAQGRLVRHGGREQVLDAPMLSKIYG 255

Query: 237 V 237
           +
Sbjct: 256 L 256


Lambda     K      H
   0.320    0.134    0.393 

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: 165
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: 255
Length of database: 273
Length adjustment: 25
Effective length of query: 230
Effective length of database: 248
Effective search space:    57040
Effective search space used:    57040
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: 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 (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