GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Moritella dasanensis ArB 0140

Align Glucose kinase (characterized, see rationale)
to candidate WP_017222136.1 A923_RS0113155 glucokinase

Query= uniprot:Q8P6M4
         (344 letters)



>NCBI__GCF_000276805.1:WP_017222136.1
          Length = 319

 Score =  182 bits (461), Expect = 1e-50
 Identities = 103/322 (31%), Positives = 163/322 (50%), Gaps = 6/322 (1%)

Query: 23  LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRDSRAVDAVVIAS 82
           + ADVGGT++R+        A   LS+ + + CA+  +L+A LA +          +   
Sbjct: 4   VVADVGGTNIRLAVCDLETGA---LSELKEFACAEFVTLEAALAQYFAALSGEITHLCVG 60

Query: 83  AGVALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVVQLSGP 142
               +++   +  NL W  + + L+D L + ++H++ND+ A++ A P +     +Q+   
Sbjct: 61  IACPVENDHVVMTNLNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAG 120

Query: 143 TPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASNDPDTAQVLRILAR 202
                Q  G   V GPGTGLG +  +    +   L  E G V+   N P+ A +L +L  
Sbjct: 121 ---ECQTDGVTAVFGPGTGLGVSHIVKAAGKWISLDGEGGHVSFTPNTPEQADILCLLQT 177

Query: 203 DASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRCLQLFCA 262
              ++  E +LSG GL NLY  LC L         P D+T AAL     +AR+ L +FC 
Sbjct: 178 QFGHVSAERILSGQGLVNLYKCLCTLSEQEAKFDQPKDVTKAALDGSCDIARKSLAVFCQ 237

Query: 263 LLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLERIPVKLV 322
           ++G   G++AL    +GG+Y+AGGI+P    F  AS+FR  F  KGR +  L  IP  L+
Sbjct: 238 VMGGFAGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFKDYLTAIPTFLI 297

Query: 323 EHGQLGVLGAASWYLQHHTEVS 344
            H   G+LGA+ +  Q  T ++
Sbjct: 298 THDNPGLLGASVYLRQELTSIN 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: 299
Number of extensions: 12
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: 344
Length of database: 319
Length adjustment: 28
Effective length of query: 316
Effective length of database: 291
Effective search space:    91956
Effective search space used:    91956
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