GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21220 in Rhodobacter viridis JA737

Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_110804310.1 C8J30_RS03235 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21220
         (293 letters)



>NCBI__GCF_003217355.1:WP_110804310.1
          Length = 290

 Score =  126 bits (317), Expect = 5e-34
 Identities = 93/286 (32%), Positives = 148/286 (51%), Gaps = 12/286 (4%)

Query: 8   TRAWLLMLPLLVVMTAVIGW---PLVDTVRLSFTDAKLVGTE-GGFVGTANYIKMLGGSN 63
           T A L++ P ++++   +GW   PL  T+  S     L+    GGF G  NY   L    
Sbjct: 8   TAARLMISPAVILL---LGWMIVPLAMTLWFSMQRYNLLMPGMGGFTGFDNYSYFLTDPA 64

Query: 64  FQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWR 123
           F  A+  T    +  +A   V G+L ALLL+Q F G+  +R L+I P+ +   V+A +W+
Sbjct: 65  FFDAIKNTLVLVLGVLAITTVGGLLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWK 124

Query: 124 LIY-NPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQA 182
            ++ NP  G        +GL      +L +   A   LIVA  W+  P   LI L ALQ+
Sbjct: 125 NMFMNPVNGVFAHLAKSIGLQPY--DFLAQSPLASIVLIVA--WQWLPFATLILLTALQS 180

Query: 183 VPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPAN 242
           +  +   A+ +DGAGP +RF +V++P+LA  + V ++++TI     F  I V T GGP  
Sbjct: 181 LDSEQLEAAEMDGAGPISRFFYVMLPHLARAITVVILIQTIFLLSTFAEILVTTNGGPGT 240

Query: 243 STRTLSILVYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288
           ++ TL+ LVY ++      GSGA+  ++  +L  I+A     ++ K
Sbjct: 241 ASTTLTYLVYVQSLLQFDVGSGAAGGIVAVVLANIVAIFLMRMIGK 286


Lambda     K      H
   0.326    0.138    0.417 

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: 218
Number of extensions: 16
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: 293
Length of database: 290
Length adjustment: 26
Effective length of query: 267
Effective length of database: 264
Effective search space:    70488
Effective search space used:    70488
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 (21.7 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