GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntC in Desulfoscipio geothermicus DSM 3669

Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate WP_092483299.1 BM299_RS09265 TRAP transporter substrate-binding protein

Query= uniprot:Q930R1
         (334 letters)



>NCBI__GCF_900115975.1:WP_092483299.1
          Length = 343

 Score =  236 bits (602), Expect = 6e-67
 Identities = 111/297 (37%), Positives = 184/297 (61%), Gaps = 3/297 (1%)

Query: 30  IRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAV 89
           ++  + + E HP   G++  +  +++K+GG++++  +  G +G +    + L+ G  + V
Sbjct: 43  LKAGHAVAESHPYHLGLEKFKQIVEEKTGGQVQIDIYANGTIGSERDMIEGLQLGTIDLV 102

Query: 90  VTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGF 149
           +TS+ P++  +P +GV DLPFLF++ + AY VLDG+ G  + E+    G+V LA+WENGF
Sbjct: 103 LTSTGPVINFVPEMGVVDLPFLFSSREHAYQVLDGEIGQDLLEQFGDIGIVGLAFWENGF 162

Query: 150 RNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQ 209
           RNL+NS RP+   ED +G+K+R M+N +    F+ LGA+ TPMA+GEV++AL+ K ID Q
Sbjct: 163 RNLTNSERPINSVEDIQGLKIRTMENEVHQAAFKELGADPTPMAWGEVYTALQQKTIDGQ 222

Query: 210 ENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEE 269
           ENP   I   K +EVQKY+  T H Y+P L L  +   D  +PE+Q  +++ AV     E
Sbjct: 223 ENPIPIIYNMKIYEVQKYLALTGHFYSPALLLIGQKSLDKLSPEQQNIIKKAAVEAATYE 282

Query: 270 RKVIQDLNKKSLEKIKEAGLEVNTLSAEEQARIREKSMVVYEKHKAEIGAEVVDAIL 326
           R+ I+    + L K++E G+    ++  ++  +RE +M VYEK++   G + +  IL
Sbjct: 283 REQIKVQEDEQLAKLEEKGM---VITRPDKNALREATMAVYEKYEGRFGKDTIQKIL 336


Lambda     K      H
   0.317    0.133    0.374 

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: 297
Number of extensions: 12
Number of successful extensions: 2
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: 334
Length of database: 343
Length adjustment: 28
Effective length of query: 306
Effective length of database: 315
Effective search space:    96390
Effective search space used:    96390
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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