GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pantoea rwandensis LMG 26275

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_084934374.1 HA51_RS09990 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_002095475.1:WP_084934374.1
          Length = 363

 Score =  280 bits (715), Expect = 6e-80
 Identities = 151/300 (50%), Positives = 200/300 (66%), Gaps = 11/300 (3%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84
           +L I  GEF+V VGPSGCGKST LRM+AGLE ++DG + I   D+TH    +R IAMVFQ
Sbjct: 23  DLTINSGEFVVFVGPSGCGKSTLLRMIAGLEEISDGKLLIEGADMTHQPATERGIAMVFQ 82

Query: 85  NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144
           +YALYP+MTV  N+ + L++  KS+ EI + +++ AA L LTE L+R P+ALSGGQRQRV
Sbjct: 83  SYALYPNMTVRGNLAYPLEVMKKSKAEIEQAINQTAARLHLTELLDRLPRALSGGQRQRV 142

Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204
           A+GRAI+R+P++FL DEPLSNLDA+LR+Q R +IA L   LG T +YVTHDQ EA+T+ D
Sbjct: 143 AIGRAIIRHPRIFLFDEPLSNLDAELRLQMRIEIARLHSSLGNTMIYVTHDQLEAMTLAD 202

Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARIKLSP 264
           RI VL+ G ++QVGAP  LY  P N+FVAGFIGSP MN      +    T G  ++++  
Sbjct: 203 RIVVLRQGKIEQVGAPMTLYHDPDNLFVAGFIGSPKMNF--LPAEVAAVTPGAVQLRVPA 260

Query: 265 ETLAAMTPEDNG------RITIGFRPEALEIIPEGESTD-LSIPIKLDFVEELGSDSFLY 317
             +  +    N       ++T+G RPE    IP     + LS    L F E LG  ++LY
Sbjct: 261 LGIHNLKMNINAACREGQKVTLGVRPE--HFIPASSDAEALSFSADLSFSEMLGHTNYLY 318


Lambda     K      H
   0.316    0.135    0.380 

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: 349
Number of extensions: 15
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: 376
Length of database: 363
Length adjustment: 30
Effective length of query: 346
Effective length of database: 333
Effective search space:   115218
Effective search space used:   115218
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: 49 (23.5 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