GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Erythrobacter gangjinensis K7-2

Align Glucose kinase (characterized, see rationale)
to candidate WP_047007751.1 AAW01_RS12295 glucokinase

Query= uniprot:Q8P6M4
         (344 letters)



>NCBI__GCF_001010925.1:WP_047007751.1
          Length = 324

 Score =  168 bits (425), Expect = 2e-46
 Identities = 112/320 (35%), Positives = 164/320 (51%), Gaps = 8/320 (2%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRAVDA---VV 79
           +  D+GGTH R    +H  D  I + +  T    DHAS      D+ R  +  D    V 
Sbjct: 4   VTVDIGGTHARFAIATHADDGSITMDEPVTLHTDDHASFQTAWEDY-RAQKGGDIPSRVA 62

Query: 80  IASAGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQL 139
           +A AG    +    +NN PW I P  +++ LGV +  +VNDFEAVA+A  +  +   + L
Sbjct: 63  MAIAGPVGGEVIRFTNN-PWIIRPALVKEKLGVDSFKIVNDFEAVAHAVARAGEDEYLHL 121

Query: 140 SGPTPRHAQPGGPILVVGPGTGLGAA-VWINGPRQPTVLATEAGQVALASNDPDTAQVLR 198
           +GP      P G + V+GPGTGLG A ++        V ATE G +  A  D     +L 
Sbjct: 122 TGPEGP-LPPTGRLTVMGPGTGLGVAHLYREADGTYRVSATEGGHIDFAPLDSIEDAILA 180

Query: 199 ILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQ 258
            L +  + + +E V++GP + ++Y  L  L   +       +I    ++ +D+LA   + 
Sbjct: 181 RLRKRHTRVSVERVVAGPAISDIYHTLASLERKSVPELDDVEIWTRGMNGEDSLAAAAVD 240

Query: 259 LFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIP 318
            FC  LGS  GDMALA+GA   V +AGG+   +   L  S F ERF AKGR   ++  +P
Sbjct: 241 RFCLSLGSVAGDMALAHGAK-AVVIAGGLGYRLRDHLPKSGFAERFRAKGRFAGLMAGLP 299

Query: 319 VKLVEHGQLGVLGAASWYLQ 338
           VKL+ H Q G+ GAA+ Y Q
Sbjct: 300 VKLITHPQPGLFGAAAAYCQ 319


Lambda     K      H
   0.321    0.136    0.410 

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: 405
Number of extensions: 24
Number of successful extensions: 5
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: 344
Length of database: 324
Length adjustment: 28
Effective length of query: 316
Effective length of database: 296
Effective search space:    93536
Effective search space used:    93536
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 (21.9 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