GapMind for catabolism of small carbon sources

 

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

Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate 3609944 Dshi_3326 TRAP dicarboxylate transporter, DctP subunit (RefSeq)

Query= uniprot:Q930R1
         (334 letters)



>FitnessBrowser__Dino:3609944
          Length = 325

 Score =  167 bits (423), Expect = 3e-46
 Identities = 96/287 (33%), Positives = 153/287 (53%), Gaps = 7/287 (2%)

Query: 46  IKAMQACLDQKSGGKLKLTAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGV 105
           + A   C + K G   ++  F    LG D +  Q L+ G Q  +   SS +  + P  G+
Sbjct: 42  VNAFAECANGKLGDAAEVQTFGASQLGNDREMLQKLKLG-QVHMSLPSSVMSSVAPEFGI 100

Query: 106 FDLPFLFANAQEAYTVLDGDFGDMMNEKLEAAGLVNLAYWENGFRNLSNSVRPVTKWEDF 165
           F++P++  + +    V   + GD   E     G   + Y ENGFR+++N+VRP+   ED 
Sbjct: 101 FEMPYIIRDREHMKRV-QAELGDTFQEAALGQGYRIIGYMENGFRHITNNVRPINTPEDL 159

Query: 166 EGMKVRVMQNNIFLDTFQNLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQ 225
            G+K+R       +  FQ  GAN TPM+F EVF+AL+TK ID QENPY  I ++KF EVQ
Sbjct: 160 AGVKLRTPNGEWRVKMFQEYGANPTPMSFSEVFTALQTKVIDGQENPYAQIASAKFQEVQ 219

Query: 226 KYVTETNHAYTPFLFLFSKPIFDSYTPEEQAALRECAVVGRDEERKVIQDLNKKSLEKIK 285
            Y++ T H YTP   L ++  + S+  + +AAL  C    +D   ++  +L  + L+ IK
Sbjct: 220 SYLSITGHVYTPAYVLVAENQWQSWPEDVRAALESCGTETQDTVYEIAANLETELLDVIK 279

Query: 286 EAGLEVNTLSAEEQARIREKSMVVYEKHKAEI--GAEVVDAILAKLE 330
            AG+EVN     ++A     S  +Y+   A++   AE+++ + +  E
Sbjct: 280 AAGVEVN---EADKAAFVAASTPIYDAFAAQVEGAAEMIETVQSLAE 323


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: 231
Number of extensions: 7
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: 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