GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Dinoroseobacter shibae DFL-12

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 3608244 Dshi_1648 ABC transporter related (RefSeq)

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__Dino:3608244
          Length = 373

 Score =  154 bits (389), Expect = 2e-42
 Identities = 94/240 (39%), Positives = 139/240 (57%), Gaps = 11/240 (4%)

Query: 2   IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61
           ++L  V K YG   VL NINL +++GE +V +GPSG GKST +R + GLE+++ G + ++
Sbjct: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63

Query: 62  NLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKE---AEETAFK 118
             V+   N +   ++  AMVFQ + LYPHMTV +N++ A +K+ KKS+ E   A E A +
Sbjct: 64  GTVV---NDVPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAAE 119

Query: 119 YLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPE-TIQEVLDV 177
            L++   LD+    P  LSGGQ+QRVAI RS+       LFDEP S LD    +   L++
Sbjct: 120 KLQLGQYLDR---LPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEI 176

Query: 178 MKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLG 237
            +       +TMV VTH+   A  +A RI+ +  G I +   P E +  P+ E    F+G
Sbjct: 177 AQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIG 236


Lambda     K      H
   0.317    0.133    0.372 

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: 184
Number of extensions: 9
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: 242
Length of database: 373
Length adjustment: 27
Effective length of query: 215
Effective length of database: 346
Effective search space:    74390
Effective search space used:    74390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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