GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Rhodanobacter denitrificans 2APBS1

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  139 bits (351), Expect = 7e-38
 Identities = 86/231 (37%), Positives = 128/231 (55%), Gaps = 7/231 (3%)

Query: 36  EKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKI 95
           ++ G    ++  SLA   G    ++G SGSGKST++RLL  L  P  G V +DG  + + 
Sbjct: 19  KRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRS 78

Query: 96  SDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKA--LDALRQVG 153
               LR    +++  V Q   L PH+T L N A      G   +  R++A  L AL  + 
Sbjct: 79  DVLPLR----RRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLP 134

Query: 154 LENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAK 213
                  YP ELSGG RQRV L RAL  +PD LL+DE   ALDP++R E+QDEL ++  +
Sbjct: 135 T-GVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQ 193

Query: 214 HQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
             +T++ ++HDL EA    +R+ +++ G V+Q GT  ++   PA+ +V  F
Sbjct: 194 LGKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRF 244


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: 227
Number of extensions: 13
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: 400
Length of database: 255
Length adjustment: 27
Effective length of query: 373
Effective length of database: 228
Effective search space:    85044
Effective search space used:    85044
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 (21.8 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