GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Rhizobium freirei PRF 81

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_037155072.1 RHSP_RS28510 sugar ABC transporter substrate-binding protein

Query= TCDB::P0AEE5
         (332 letters)



>NCBI__GCF_000359745.1:WP_037155072.1
          Length = 309

 Score =  159 bits (401), Expect = 1e-43
 Identities = 122/339 (35%), Positives = 177/339 (52%), Gaps = 42/339 (12%)

Query: 4   KVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMND 63
           K   L + MA +L   AAHA    IGV++  +DDNF++V+R  ++  AK    V L + D
Sbjct: 2   KKFILGSAMA-LLLSTAAHAQT--IGVSMALFDDNFLTVLRNGMQDYAKGMSGVTLQVED 58

Query: 64  SQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALD 123
           +QND +KQ  QI   +A  V A+ +N VD  A   + + A    +P+V+ N+EP+   +D
Sbjct: 59  AQNDVAKQQSQIQNFIASKVDAIIVNPVDTDATAAISKLAADAKIPLVYVNREPAN--VD 116

Query: 124 SY-DKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEART 182
           S  DK  +V ++ +ESG ++   + +             G+ + V++ GE  +  A  RT
Sbjct: 117 SLPDKQAFVASNEQESGTLETKEVCRILG----------GKGKAVVMMGELSNQAARMRT 166

Query: 183 TYVIKELND-------KGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANND 235
               K+++D       KGIK  Q Q  TA W   Q  D M  WLS  +  + + VI+NND
Sbjct: 167 ----KDVHDVLATDGCKGIKIVQEQ--TANWQRTQGADLMTNWLS--SGLEFDAVISNND 218

Query: 236 AMAMGAVEALKAHNK--SSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAK 293
            MA+GA++ALKA  K    I V GVDA  +ALA +++G L  TV  DA  Q K   D A 
Sbjct: 219 EMAIGAIQALKAAGKPMDKIVVAGVDATQDALAAMQAGDLKVTVFQDAAGQGKGAVDAAL 278

Query: 294 NLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFSKK 332
            LA G         KID KV  +P+  V   N+ +F KK
Sbjct: 279 KLAKGD--------KIDKKVY-IPFQLVTPTNVKDFVKK 308


Lambda     K      H
   0.313    0.129    0.363 

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: 238
Number of extensions: 13
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: 332
Length of database: 309
Length adjustment: 28
Effective length of query: 304
Effective length of database: 281
Effective search space:    85424
Effective search space used:    85424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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