GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntC in Sinorhizobium meliloti 1021

Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate SM_b21353 SM_b21353 periplasmic C4-dicarboxylate transport protein

Query= uniprot:Q930R1
         (334 letters)



>FitnessBrowser__Smeli:SM_b21353
          Length = 325

 Score =  175 bits (443), Expect = 2e-48
 Identities = 102/302 (33%), Positives = 165/302 (54%), Gaps = 10/302 (3%)

Query: 30  IRVSNGINEDHPVGNGIKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAV 89
           +R S+   + +P   G+K     + +++ G+  +  +    LG +    + +RSGV E  
Sbjct: 28  LRSSDTHPDGYPTVEGVKYFGELVKERTAGRYSVEVYHSAQLGEEKDTIEQVRSGVIELN 87

Query: 90  VTSSSPLVGIIPALGVFDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGF 149
             S +P  G +    V  LP+LF + +  + V+DG  GD + +  E AG+V LA+++ G 
Sbjct: 88  RVSMAPFNGTVKESIVPALPYLFRSEEHMHKVMDGAIGDQIKKAFEGAGVVVLAFYDAGA 147

Query: 150 RNLSNSVRPVTKWEDFEGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQ 209
           R+  N  +P+   ED +G+K RV+Q++IF+D    LGANATPM +GEV+S +ET  ID  
Sbjct: 148 RSFYNKQKPINTVEDMKGLKFRVIQSDIFVDMVAALGANATPMPYGEVYSGIETGVIDGA 207

Query: 210 ENPYVTIDTSKFFEVQKYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEE 269
           EN + + DT+K FEV K  +   H   P +F+ +K  FD  TPE+Q   ++ A     ++
Sbjct: 208 ENNFPSYDTAKHFEVAKNYSLDEHTILPEVFVMNKAAFDKLTPEDQEIFKQAAKDSVAKQ 267

Query: 270 RKVIQDLNKKSLEKIKEAGLEVNTLSAEEQARIREKSMVVYEKHKAEIGAEVVDAILAKL 329
           R++     K+S  K++ AG ++ T   E+Q  I +    VYEKH       V D +L K+
Sbjct: 268 RELWAAKVKESRAKVEAAGAKITT--PEKQGFI-DAMKPVYEKH-------VTDEVLKKM 317

Query: 330 EE 331
            E
Sbjct: 318 VE 319


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: 244
Number of extensions: 9
Number of successful extensions: 1
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: 325
Length adjustment: 28
Effective length of query: 306
Effective length of database: 297
Effective search space:    90882
Effective search space used:    90882
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 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