GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Salinicoccus carnicancri Crm

Align xylulokinase (EC 2.7.1.17) (characterized)
to candidate WP_026090363.1 C792_RS0112905 gluconokinase

Query= BRENDA::Q9WXX1
         (492 letters)



>NCBI__GCF_000330705.1:WP_026090363.1
          Length = 501

 Score =  231 bits (589), Expect = 4e-65
 Identities = 137/447 (30%), Positives = 229/447 (51%), Gaps = 16/447 (3%)

Query: 5   VGLDVGTTGVKGILVNEKGEILATANERLTMFTPQPAWAEQDPLSWWEAVKKILKNLSER 64
           +GLD+GTT VK +L +  G  +        + TP    AEQDP    E   + L+ L  R
Sbjct: 2   IGLDIGTTAVKAVLFDMDGTFIDKETGDYPLHTPDAKTAEQDPEEILERTLQALRLLISR 61

Query: 65  SKEMGGKIRAISTSGQMHSLVAIDDNGKVLRNAILWCDQRTYKECEEATQILGGEENVLK 124
           +   G  I  IS S  MHS++ +D  G+ L   I W D R  +  +   +  G E  +  
Sbjct: 62  NG-CGDSIEFISFSSAMHSMILLDRKGERLTECITWADSRAAEYADRLNEADGLE--IYH 118

Query: 125 LVGNPILPGFTLPKILWIRKHEPEIYGKISKIMLPKDFINYMLTGEVKTEHSDASGTVMY 184
             G PI P   L K+   +  EPE+Y +I +IM  K+++   ++GE   + S AS   + 
Sbjct: 119 RTGTPIHPMNPLVKLFHFKNEEPELYAQIGRIMGIKEYVFAEISGEYAVDRSIASSMGLM 178

Query: 185 SVSKMEWNKDVLKELNIPESVLPEIIPSNGVVGNVKPEVASDLGLSEDTLVIGGGADNAC 244
           ++   EW+ ++L  L +    LPE++ +  +  ++  + A D+G+S+DT ++ G +D   
Sbjct: 179 NLEASEWDTELLSMLELSADQLPELVDTTEIF-SMDEDAAGDIGISQDTKLVIGASDGVL 237

Query: 245 AALGIAVVEPGDVMVSLGTSGTVLAPTKGNQPDPKGRVHFFAHTVPETRYHMGVMLSATY 304
           A LG+  +  GDV +++GTSG +       + D K R  F  H  P      G + +   
Sbjct: 238 ANLGVNAIHEGDVAITVGTSGAIRTVIDRPRTDVKMRT-FCYHLTPGAFVIGGPVNNGGV 296

Query: 305 SLEWFKEKFLSED-----------YETINEEVDKIPAGSNGIIFLPYLNGERTPHRDPFA 353
            L W +++   ++           YE + E  + +PAGS+G+IF PYL GER P  D  A
Sbjct: 297 ILRWIRDELCQQEISEADTCSRDPYEIMTEAAESVPAGSDGLIFHPYLAGERAPLWDAKA 356

Query: 354 RGVFFGISSYNTKWDMVRAIFEGVAFGIKDSFDILRELKVVLNSVRITGGGSKSRVWNKM 413
            G F+G++  + +  M+RA  EGV + +   F  LRE  + + S++ +GG ++S +W ++
Sbjct: 357 VGSFYGLTISHERKHMIRAAMEGVVYNLYSVFLALREQMMEVRSIKASGGFARSALWKQL 416

Query: 414 LADMTGLRIQKPAVDEGASYGAAILAV 440
           +AD+ G  +  P   E +++GA IL +
Sbjct: 417 MADVFGEALHVPESYESSAFGACILGL 443


Lambda     K      H
   0.316    0.135    0.397 

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: 566
Number of extensions: 18
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: 492
Length of database: 501
Length adjustment: 34
Effective length of query: 458
Effective length of database: 467
Effective search space:   213886
Effective search space used:   213886
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: 52 (24.6 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