GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Sinorhizobium meliloti 1021

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate SMc00670 SMc00670 histidine transport ATP-binding ABC transporter protein

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__Smeli:SMc00670
          Length = 275

 Score =  302 bits (774), Expect = 7e-87
 Identities = 149/260 (57%), Positives = 198/260 (76%)

Query: 5   LEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64
           +EI+N+YKIFG   ++A   +E GL K  IL ++G ++G+ D SL I  G+IFVIMGLSG
Sbjct: 4   IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63

Query: 65  SGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVL 124
           SGKST+VR +NRLIEPT G+VL DG +I  +    LR  R ++++MVFQSFALMPH TVL
Sbjct: 64  SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123

Query: 125 DNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPD 184
            N  +G  + G++ ++ RE  +  +  VGL  Y   +P +LSGGM+QRVGLARALA + D
Sbjct: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183

Query: 185 ILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVV 244
           ++LMDEAFSALDPLIR +MQD+L++LQ    +TIVFI+HDLDEA+RIG  IAI+++G+VV
Sbjct: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243

Query: 245 QVGTPDEILNNPANDYVRTF 264
           QVGTP++IL+NPANDYV  F
Sbjct: 244 QVGTPNDILDNPANDYVARF 263


Lambda     K      H
   0.319    0.137    0.378 

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: 347
Number of extensions: 13
Number of successful extensions: 1
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: 400
Length of database: 275
Length adjustment: 28
Effective length of query: 372
Effective length of database: 247
Effective search space:    91884
Effective search space used:    91884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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