GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Rhizobium freirei PRF 81

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_004110897.1 RHSP_RS06555 ROK family transcriptional regulator

Query= BRENDA::Q5RLG0
         (302 letters)



>NCBI__GCF_000359745.1:WP_004110897.1
          Length = 408

 Score =  109 bits (272), Expect = 1e-28
 Identities = 93/306 (30%), Positives = 140/306 (45%), Gaps = 30/306 (9%)

Query: 4   VGLDLGGTKIAAGVFDG------KRLLSKVVVPTPKEGGERVAEALAEAAERAEREAGVR 57
           +GL+LG  + AAGV          R+   V  P P E     A  + +  E    +   R
Sbjct: 86  IGLELGRQR-AAGVLTDLSGTVCARIDRHVDRPGPTEAMPVFAAIVRDLQEAFSFD---R 141

Query: 58  GEAIGLGTPGPLDFRRG-VIRFAP-NIPGVQDFPIRRILEEATGRPVFLENDANAAALAE 115
              +G+G   P  +  G V   +P N+PG Q+FP+ R LE   G PV +ENDA A A+ E
Sbjct: 142 DRLLGVGIALPGRYADGGVTSLSPLNLPGWQNFPVARELERLIGLPVLVENDATAGAIGE 201

Query: 116 HHLGAAQGEESSLYLTVS--TGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGPACGCGL 173
              G A+G  S +YL ++   GIG G+ L G + +G R   GE+GH+ + P G  C CG 
Sbjct: 202 RLYGVARGLGSFVYLFLAGDGGIGAGMFLDGHLYKGSRANAGEIGHIIVEPHGRLCTCGK 261

Query: 174 EGCLEALAAGRALERDATYAFQC-------PVDTRELFRLFQAGDPKAERLVLQAARYVG 226
            GCL+   +        + A++C        +D  +L  +  A     +  + QA + + 
Sbjct: 262 RGCLDRYVS-------PSVAYECLGIEDAQELDPDDLDAMIAANSRGLQTWLEQAVQPLR 314

Query: 227 IGLASLVKAFDPGVVVLGGGVALNAPEGYWEAL--LEAYRRYLQGWEAPPLRRARLGAEA 284
             +  L  AFDP  +VLGG    +   G  E +  L      ++  + P L     G + 
Sbjct: 315 QTIDFLELAFDPQTIVLGGSAPPSLMTGLAERVEPLHIPVNPMEERKIPRLMVGATGKDT 374

Query: 285 GLLGAA 290
            +LGAA
Sbjct: 375 AILGAA 380


Lambda     K      H
   0.319    0.141    0.416 

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: 192
Number of extensions: 12
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: 302
Length of database: 408
Length adjustment: 29
Effective length of query: 273
Effective length of database: 379
Effective search space:   103467
Effective search space used:   103467
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 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