GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Limnohabitans curvus MWH-C5

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_108402619.1 B9Z44_RS12860 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_003063475.1:WP_108402619.1
          Length = 291

 Score =  140 bits (352), Expect = 4e-38
 Identities = 89/285 (31%), Positives = 152/285 (53%), Gaps = 10/285 (3%)

Query: 2   DLSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWL 61
           D  QL F+G+A GSI AL A+G TL +      NFA G+F+ L A++      +G  L L
Sbjct: 3   DFLQLFFSGLATGSIYALAALGFTLLWQASGTINFAQGEFVMLPAFMMLGFLAAGFPLVL 62

Query: 62  SMALGCVGTIIAMFIGEWLLWKPM--RARRATATTLIIISIGLALFLRNGILLIWGGNNQ 119
           S A  CV   +++F+  WL  + +     +     +++ +IGL++ +RN +    G + +
Sbjct: 63  SFAASCV---VSVFVLGWLFKRGVVDPLFKFGMMPIVVATIGLSIAMRNAVRA--GYSAE 117

Query: 120 NYRVP-IVPAQ--DFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDL 176
            +  P + P +  +  G+      +     AIA ++V    L +T  G+AM+AVA N + 
Sbjct: 118 PHPFPNLFPDEVYNIAGVTISATDIGTFVFAIALVLVTQAFLAKTVTGRAMQAVAQNTES 177

Query: 177 AKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNP 236
           A V GINV  ++ +T+ + A+L A    +       K +MG  L    F + I+GG  N 
Sbjct: 178 ASVLGINVPRMIFYTFAINALLAAAAAILVTPTYLAKFDMGASLGNKAFFAAIIGGFNNS 237

Query: 237 YGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
            GA+ GG+I+GV + ++  +   +YK  VAL++ ++++  +PQGL
Sbjct: 238 RGALLGGVIVGVCENLAAAYISPAYKDAVALVIFMVVILFKPQGL 282


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: 176
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: 286
Length of database: 291
Length adjustment: 26
Effective length of query: 260
Effective length of database: 265
Effective search space:    68900
Effective search space used:    68900
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