GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Desulfoscipio geothermicus DSM 3669

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_092483299.1 BM299_RS09265 TRAP transporter substrate-binding protein

Query= SwissProt::P37735
         (333 letters)



>NCBI__GCF_900115975.1:WP_092483299.1
          Length = 343

 Score =  168 bits (426), Expect = 2e-46
 Identities = 95/302 (31%), Positives = 163/302 (53%), Gaps = 10/302 (3%)

Query: 29  IVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNSQLYKDKEELEALQLGAVQ 88
           I++K  H VA   P   G  KF+++ E+ T G V +++Y N  +  +++ +E LQLG + 
Sbjct: 41  IILKAGHAVAESHPYHLGLEKFKQIVEEKTGGQVQIDIYANGTIGSERDMIEGLQLGTID 100

Query: 89  MLAPSLAKFGPL--GVQDFEVFDLPYIFKDYEALHKVTQGEAGKMLLSKLEAKGITGLAF 146
           ++   L   GP+   V +  V DLP++F   E  ++V  GE G+ LL +    GI GLAF
Sbjct: 101 LV---LTSTGPVINFVPEMGVVDLPFLFSSREHAYQVLDGEIGQDLLEQFGDIGIVGLAF 157

Query: 147 WDNGFK-IMSANTPLTMPDDFLGLKMRIQSSKVLEAEMNALGAVPQVMAFSEVYQALQTG 205
           W+NGF+ + ++  P+   +D  GLK+R   ++V +A    LGA P  MA+ EVY ALQ  
Sbjct: 158 WENGFRNLTNSERPINSVEDIQGLKIRTMENEVHQAAFKELGADPTPMAWGEVYTALQQK 217

Query: 206 VVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWDGLPADVRTGLEKAMAE 265
            +DG ENP   ++  K+ EVQK+  ++ H Y    +++ ++  D L  + +  ++KA  E
Sbjct: 218 TIDGQENPIPIIYNMKIYEVQKYLALTGHFYSPALLLIGQKSLDKLSPEQQNIIKKAAVE 277

Query: 266 STDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAAWEEVLTPVHDEMAERIGAETIA 325
           +  Y     K + ++ L  +++ G      +T  ++ A  E    V+++   R G +TI 
Sbjct: 278 AATYEREQIKVQEDEQLAKLEEKGMV----ITRPDKNALREATMAVYEKYEGRFGKDTIQ 333

Query: 326 AV 327
            +
Sbjct: 334 KI 335


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: 233
Number of extensions: 10
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: 333
Length of database: 343
Length adjustment: 28
Effective length of query: 305
Effective length of database: 315
Effective search space:    96075
Effective search space used:    96075
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 Apr 09 2024. 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