GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1A in Mesorhizobium ciceri WSM1271

Align major cell-binding factor (characterized)
to candidate YP_004143089.1 Mesci_3923 family 3 extracellular solute-binding protein

Query= CharProtDB::CH_021449
         (259 letters)



>NCBI__GCF_000185905.1:YP_004143089.1
          Length = 261

 Score = 75.9 bits (185), Expect = 8e-19
 Identities = 63/206 (30%), Positives = 92/206 (44%), Gaps = 23/206 (11%)

Query: 8   LKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVD 67
           L++A+ A  A +    A A E  L          +G +   P +  L  A G++ GF++D
Sbjct: 5   LRIALAASAALLTLGVAQAQEKTLR---------IGTEGAYPPFNNLT-ADGQLVGFDID 54

Query: 68  VAKLLAKSILGDDKKIKLVAVNAKTRG--PLLDNGSVDAVIATFTITPERKRIYNFSEPY 125
           +AK L      D+ K+K   V     G  P L  G  DA++A+ +ITPERK   +FS  Y
Sbjct: 55  IAKALC-----DEMKVKCTFVAQDWDGIIPALQAGKFDAIVASMSITPERKEKVDFSNKY 109

Query: 126 YQDAIGLLVLKEKKYKSLA--DMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYP 183
           Y     + V K+   K +   D+ G  IGVA   T        A K   D     +P  P
Sbjct: 110 YNTPSAIAVPKDSTLKGVTKEDLAGKTIGVATTTTH----FNYASKTYTDSTVKGYPSSP 165

Query: 184 SIKAALDAKRVDAFSVDKSILLGYVD 209
             +A L   R+DA   D  +L  ++D
Sbjct: 166 EEQADLANGRLDAIEDDIVVLQQFLD 191


Lambda     K      H
   0.316    0.135    0.372 

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: 154
Number of extensions: 11
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: 259
Length of database: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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