GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Rhodobacter viridis JA737

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_110804047.1 C8J30_RS02045 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_003217355.1:WP_110804047.1
          Length = 335

 Score =  164 bits (415), Expect = 2e-45
 Identities = 114/324 (35%), Positives = 173/324 (53%), Gaps = 44/324 (13%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMT----LAAYLTWWANTSGIN 58
           L+ +I    A G+ +ALGA+G+TL YGILR SNFAHGD M     L   +TW   ++G++
Sbjct: 11  LNYIIVPATAYGAQLALGALGVTLIYGILRFSNFAHGDTMAFGTGLTILVTWAMQSAGLS 70

Query: 59  LW------LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILL 112
                   L++ +G   T   +   + +++   R  RA    + ++S+G+ +F+ NG+  
Sbjct: 71  FGPLPTALLALPIGIALTAALVLATDKVVYSYYRKVRAAPIYITMVSVGV-MFVMNGLTR 129

Query: 113 IWGGNNQNYRVP----IVPAQDFMGIKFEYYRLLV-----IAMAIAAMVV--LHLILQRT 161
           +  G ++         ++ A DF  +      L +     I +  AA+VV  L   L RT
Sbjct: 130 VLIGVDEIKFADGARFLISAPDFKAMTGLTEPLAIRATTAITVITAALVVWALFWFLART 189

Query: 162 KVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLI 221
           + GK+MRA ADN DLA +SGI+   VV  TWV+ A L  + G++YGL  + K    + L+
Sbjct: 190 RTGKSMRAYADNEDLALLSGIDPNRVVAVTWVIAAALATIAGTLYGLDKSFKAFNYFQLL 249

Query: 222 LPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW---------------------FGTS 260
           LP+FA+ I+GG+GNP GAIAGG +I  + EVSV +                       T 
Sbjct: 250 LPIFAAAIVGGLGNPLGAIAGGFVIAFS-EVSVTYAWKKVAMYLIPGYEPEGLLQLLSTE 308

Query: 261 YKMGVALLLMIIILFIRPQGLFKG 284
           YK  V+  ++II+L  +P GLFKG
Sbjct: 309 YKFAVSFAILIIVLLFKPTGLFKG 332


Lambda     K      H
   0.329    0.143    0.450 

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: 258
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: 286
Length of database: 335
Length adjustment: 27
Effective length of query: 259
Effective length of database: 308
Effective search space:    79772
Effective search space used:    79772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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