GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Shewanella halifaxensis HAW-EB4

Align Glycerate 3-kinase; D-Glycerate-3-kinase; Glycerate kinase 2; GK2; EC 2.7.1.31 (characterized)
to candidate WP_012277881.1 SHAL_RS14520 glycerate kinase

Query= SwissProt::P77364
         (381 letters)



>NCBI__GCF_000019185.1:WP_012277881.1
          Length = 384

 Score =  411 bits (1057), Expect = e-119
 Identities = 212/375 (56%), Positives = 273/375 (72%), Gaps = 5/375 (1%)

Query: 1   MKIVIAPDSFKESLSAEKCCQAIKAGFSTLFPDANYICLPIADGGEGTVDAMVAATGGNI 60
           MKIVIAPDSFKESL+A +    I+ GF T+ P+A YI +P+ADGGEGTV +MV AT G I
Sbjct: 1   MKIVIAPDSFKESLTAMEVANEIERGFRTVLPNAEYIKIPVADGGEGTVQSMVDATDGTI 60

Query: 61  VTLEVCGPMGEKVNAFYGLTG-----DGKTAVIEMAAASGLMLVAPEKRNPLLASSFGTG 115
           + L V GP+G KV AFYG+ G     D KTAVIEMAAASGL LVA +KRNPL+ +S+GTG
Sbjct: 61  IKLNVTGPLGHKVQAFYGILGVGYQGDKKTAVIEMAAASGLHLVAEDKRNPLMTTSYGTG 120

Query: 116 ELIRHALDNDIRHIILGIGGSATVDGGMGMAQALGVRFLDADGQALAANGGNLARVASIE 175
           ELI  AL+  I HII+G+GGSAT DGG GMAQA+G   L++ G+A++  G  L  + SI+
Sbjct: 121 ELIVDALNRGIEHIIIGLGGSATNDGGAGMAQAIGAHLLNSAGKAISPGGAALTELVSID 180

Query: 176 MDECDPRLANCHIEVACDVDNPLVGARGAAAVFGPQKGATPEMVEELEQGLQNYARVLQQ 235
           + +  P +  C  EVACDV+NPL G +GA+A+FGPQKGATPEMVE+L+  L++YA ++  
Sbjct: 181 LTDLHPLIKACSFEVACDVNNPLCGNKGASAIFGPQKGATPEMVEQLDNALKHYADIIAC 240

Query: 236 QTEINVCQMAGGGAAGGMGIAAAVFLNADIKPGIEIVLNAVNLAQAVQGAALVITGEGRI 295
               +    AG GAAGGMG+    FL A++KPGI+IV+  VNLA   +GA LVITGEGR+
Sbjct: 241 CAIQDNRDYAGAGAAGGMGLGVMAFLGAELKPGIDIVMETVNLAGLAKGADLVITGEGRL 300

Query: 296 DSQTAGGKAPLGVASVAKQFNVPVIGIAGVLGDGVEVVHQYGIDAVFSILPRLAPLAEVL 355
           DSQT  GK P+GVA VAK   + VI IAG + D   V+ ++GIDA+FSI PR  PLAEVL
Sbjct: 301 DSQTLHGKTPMGVAGVAKAQGISVIAIAGCVSDDANVLLEHGIDALFSITPRALPLAEVL 360

Query: 356 ASGETNLFNSARNIA 370
           ++ + NL+++A+NIA
Sbjct: 361 SNAKHNLYSTAKNIA 375


Lambda     K      H
   0.318    0.136    0.391 

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: 485
Number of extensions: 21
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: 381
Length of database: 384
Length adjustment: 30
Effective length of query: 351
Effective length of database: 354
Effective search space:   124254
Effective search space used:   124254
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 (21.7 bits)
S2: 50 (23.9 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