GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Dinoroseobacter shibae DFL-12

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate 3608617 Dshi_2010 phosphonate ABC transporter, ATPase subunit (RefSeq)

Query= CharProtDB::CH_088321
         (255 letters)



>FitnessBrowser__Dino:3608617
          Length = 265

 Score =  137 bits (345), Expect = 2e-37
 Identities = 87/245 (35%), Positives = 133/245 (54%), Gaps = 10/245 (4%)

Query: 3   LRTENLTVSYGT-DKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFL 61
           LR E LT +Y T DK L ++ L +P+G++ ALIGP+G GKST++ C +RL+ P SG V+L
Sbjct: 2   LRLEKLTKTYKTGDKALTEIDLEVPSGQVLALIGPSGAGKSTMIRCINRLVPPTSGAVWL 61

Query: 62  GDNPINMLSS---RQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLW----GRLSAE 114
            D  I  L S   R+  R + ++ Q +   E +TV E V  GR  ++  W     R    
Sbjct: 62  DDVNITALGSGGLRRARREMGMIFQEYALVERLTVMENVLSGRLGFVGFWRSFLRRYPQS 121

Query: 115 DNARVNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQ 174
           D       +++  + H+A +R  ELSGGQRQR  +   L QN  ++L+DEPT  LD    
Sbjct: 122 DVDEAFRLLDRVGLLHMADKRADELSGGQRQRVGICRALIQNPKLLLVDEPTASLDPKTS 181

Query: 175 VDLMRLMGEL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRT 233
             +MRL+ EL   +G   +  +HD+  A  +  ++V +  G ++  G P   +TP  L  
Sbjct: 182 RQIMRLITELCAERGLAAIINIHDVALAQMFVPRVVGLRFGEIVYDGGPTG-LTPDKLTE 240

Query: 234 VFSVE 238
           ++  E
Sbjct: 241 IYGEE 245


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: 166
Number of extensions: 6
Number of successful extensions: 4
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: 265
Length adjustment: 24
Effective length of query: 231
Effective length of database: 241
Effective search space:    55671
Effective search space used:    55671
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