GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Collimonas arenae Ter10

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_061533630.1 CAter10_RS12285 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_001584165.1:WP_061533630.1
          Length = 296

 Score =  131 bits (330), Expect = 2e-35
 Identities = 88/290 (30%), Positives = 155/290 (53%), Gaps = 9/290 (3%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAY--LTWWANTSG---I 57
           L QL+F+GIA+G I A+ A G  LT+      NF  G+ + L A   L+   N  G   +
Sbjct: 4   LLQLVFSGIALGMIYAVIAFGYQLTFATSGTLNFGQGEALMLGALVGLSLVGNIHGGPYL 63

Query: 58  NLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGN 117
           N WL + +  V   +   + EW+  +P   +  +    I+ +I LA+  +N    IWG +
Sbjct: 64  NYWLMIPVVIVFGALQGVVVEWIGVRPA-LKIKSEFGWIMSTIALAIIFKNVAENIWGKD 122

Query: 118 NQNYRVPI--VPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVD 175
           +  +  P+   P Q  +G   +  +++V+  A+A M+ + +  +++  GKA+ A +++ D
Sbjct: 123 DLTFPTPLSATPFQ-VLGANVQPMQVVVVLGALAMMLAVEIFNRKSIYGKAVVATSNDRD 181

Query: 176 LAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGN 235
            A + GIN   V+ +++ +++   A  G +   +T     MG  L L  FA  I+GG+ +
Sbjct: 182 AAGLMGINTSMVITFSYALSSATAAFAGVLVAPLTLTGATMGTALGLKAFAVAIIGGLTS 241

Query: 236 PYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLFKGT 285
             GAI GG+I+G+A+ ++  +  T YK    LLL++++L I+P GLF  T
Sbjct: 242 GMGAIVGGLILGIAETLTGFYISTGYKEVPGLLLLLLVLAIKPAGLFGKT 291


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: 203
Number of extensions: 9
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: 296
Length adjustment: 26
Effective length of query: 260
Effective length of database: 270
Effective search space:    70200
Effective search space used:    70200
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