GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfovibrio vulgaris Miyazaki F

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__Miya:8501893
          Length = 302

 Score =  131 bits (329), Expect = 2e-35
 Identities = 88/293 (30%), Positives = 159/293 (54%), Gaps = 23/293 (7%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWW-ANTSGINLWLSM 63
           +L F G+  GSI AL A+G T+ YGI+ L NFAHG+   + A+     A   GI  + ++
Sbjct: 8   ELFFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGALGIYGFPAL 67

Query: 64  ALGCVGTIIAMFIG-------EWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGG 116
           A+  +  ++A+          E + +KP+R   A   + +I +IG+++FL+N ++L    
Sbjct: 68  AILIIAAVVAVIYCAAYGLTLEKIAYKPLRD--APRLSPLISAIGMSIFLQNYVILAQTS 125

Query: 117 NNQNYRVPIVPAQDF-------MGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRA 169
           +   +   +VP  DF       MG       +L+I  +  +M  L L ++ T++GKAMRA
Sbjct: 126 DFMPFP-NLVPQPDFLEPIAHIMGAS----EVLIIVTSAISMAALTLFIKYTRMGKAMRA 180

Query: 170 VADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASV 228
            A N  +A + GI+ + V+  T+V+ + L A+GG +    +  +   +G+   +  F + 
Sbjct: 181 TAQNRKMAMLLGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAFTAA 240

Query: 229 ILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
           +LGGIG+  GA+ GG+++G  +  +  +  + Y+  +A  L+++IL  RP G+
Sbjct: 241 VLGGIGSIPGAMLGGLVLGWCESFATGYISSDYEDALAFALLVLILIFRPSGI 293


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: 212
Number of extensions: 14
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: 302
Length adjustment: 26
Effective length of query: 260
Effective length of database: 276
Effective search space:    71760
Effective search space used:    71760
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 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