GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Dechlorosoma suillum PS

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate Dsui_2532 Dsui_2532 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= SwissProt::P37735
         (333 letters)



>FitnessBrowser__PS:Dsui_2532
          Length = 341

 Score =  145 bits (367), Expect = 1e-39
 Identities = 104/337 (30%), Positives = 178/337 (52%), Gaps = 16/337 (4%)

Query: 10  LVGATALSLAL-----SVPALAE-PIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVD 63
           LV A +L+LAL     SV   A+     + S V+ P  P GK   ++ EL ++ T G ++
Sbjct: 4   LVAAASLALALLPLGHSVAHAADYKSEYRLSTVLGPAFPWGKAGERWAELVKQKTEGRIN 63

Query: 64  VEVYPNSQLYKDKE--ELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALH 121
           +++YP + L    +  E  A++ G + +   S   + P  V+   +F LP++  D ++L 
Sbjct: 64  IKLYPGTSLVGGDQTREFSAIRQGVIDLAIGSSINWSPQ-VKQLNLFSLPFLTPDEKSLD 122

Query: 122 KVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMS-ANTPLTMPDDFLGLKMRIQSSKVLE 180
            + +G  GK L + LE +G+  LA+ +NGF+ +S +  P+  P D  G+K+R+  S +  
Sbjct: 123 ALIKGPVGKDLFAVLEKQGVVPLAYGENGFRELSNSRHPIRTPADLKGMKIRVVGSPIFI 182

Query: 181 AEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEV-QKHATVSNHGYLGY 239
              +ALGA P  M++++   AL T  VDG ENP S     K++ + Q+H T+  +     
Sbjct: 183 DAFSALGANPTQMSWADAQPALATKAVDGQENPLSVFNAAKLHTLGQQHLTLWGYMTDPL 242

Query: 240 AVIVNKQFWDG-LPAD---VRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHE 295
             +VN+  W+    AD   VR   E+A AE+   A       ++  L+ ++  G T    
Sbjct: 243 IFVVNRNVWNNWSEADRKAVREAAEQAAAENLVAARKGVSPGDDALLKDIEKNGVT-ITR 301

Query: 296 LTAEERAAWEEVLTPVHDEMAERIGAETIAAVKAATA 332
           LTAE+R A++++  PV+D+ AE +G + +   +AA A
Sbjct: 302 LTAEQRKAFKDLTRPVYDKWAETVGKDLVKKAEAAIA 338


Lambda     K      H
   0.314    0.130    0.364 

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: 8
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: 333
Length of database: 341
Length adjustment: 28
Effective length of query: 305
Effective length of database: 313
Effective search space:    95465
Effective search space used:    95465
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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