GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfovibrio vulgaris Hildenborough

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= TCDB::P74318
         (286 letters)



>MicrobesOnline__882:209487
          Length = 302

 Score =  129 bits (323), Expect = 1e-34
 Identities = 86/288 (29%), Positives = 158/288 (54%), Gaps = 13/288 (4%)

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

Query: 64  ALGCVGTIIAM-------FIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGG 116
            +  +  I+A+       F  E + +KP+R   A   + +I +IG+++FL+N ++L    
Sbjct: 68  GILIIAAIVAVIYCAAYGFTLEKVAYKPLRD--APRLSPLISAIGMSIFLQNYVILAQTS 125

Query: 117 NNQNYR--VPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNV 174
           +   +   VP +   + +        +L+I  +   MV L L ++ T++GKAMRA A N 
Sbjct: 126 DFVPFPRLVPDLAILEPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMRATAQNR 185

Query: 175 DLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGI 233
            +A + GI+ + V+  T+++ + L A+GG +    +  +   +G+   +  F + +LGGI
Sbjct: 186 KMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTAAVLGGI 245

Query: 234 GNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
           G+  GA+AGG+++G+ +  +  +  + Y+  +A  L+++IL  RP G+
Sbjct: 246 GSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGI 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: 204
Number of extensions: 14
Number of successful extensions: 4
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