GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntK in Caldicellulosiruptor hydrothermalis 108

Align Gluconokinase; EC 2.7.1.12; Gluconate kinase (uncharacterized)
to candidate WP_013403936.1 CALHY_RS10535 xylulokinase

Query= curated2:P46834
         (513 letters)



>NCBI__GCF_000166355.1:WP_013403936.1
          Length = 502

 Score =  270 bits (690), Expect = 9e-77
 Identities = 157/490 (32%), Positives = 250/490 (51%), Gaps = 7/490 (1%)

Query: 4   YMLGIDIGTTSTKAVLFSEKGDVIQKESIGYALYTPDISTAEQNPDEIFQAVIQSTAKIM 63
           Y +GID+GT+ TK +L   KG+++   +  Y LY P I  AEQNP++ + A ++    ++
Sbjct: 2   YFIGIDVGTSGTKTILTDSKGNILATATFEYPLYQPQIGWAEQNPEDWWDASVKGIKAVL 61

Query: 64  QQHP--DKQPSFISFSSAMHSVIAMDENDKPLTSCITWADNRSEGWAHKIKEEMNGHNVY 121
           ++     K+   +  +  MH ++ +D+N   +   I W D R+     +I E++    + 
Sbjct: 62  EKSKVDPKEVKAVGLTGQMHGLVMLDKNYNVIRPSIIWCDQRTAKECDEITEKIGKERLI 121

Query: 122 KRTGTPIHPMAPLSKITWIVNEHPEIAVKAKKYIGIKEYIFKKLFDQYVVDYSLASAMGM 181
           + T  P       SKI W+ N  P+   K  K +  K+YI  KL  ++  D S AS M +
Sbjct: 122 EITANPALTGFTASKILWVRNNEPQNYEKVYKILLPKDYIRFKLTGEFATDVSDASGMQL 181

Query: 182 MNLKTLAWDEEALAIAGITPDHLSKLVPTTAIFHHCNPELAAMMGIDPQTPFVIGASDGV 241
           +++K   W +E L    I  D L K+  +  +    + + + + G+   T  V G  D  
Sbjct: 182 LDIKNRCWSDEVLEKLEIDKDLLGKVYESPEVTGKVSRQASEITGLWEGTLVVAGGGDQA 241

Query: 242 LSNLGVNAIKKGEIAVTIGTSGAIRPIIDKPQTDEKGRI--FCYALTENHWVIGGPVNNG 299
              +G   +K G I+ TIG+SG +   +D+ + D +GR+  FC+A+    W + G     
Sbjct: 242 AGAVGNGIVKTGVISSTIGSSGVVFAHLDEFKIDPQGRVHTFCHAV-PGKWHVMGVTQGA 300

Query: 300 GIVLRWIRDEFASSEIETAKRLGIDPYDVLTKIAERVRPGADGLLFHPYLAGERAPLWNP 359
           G+ L+W RD FA  E    + +  DPY ++ + AE   PG+DGL+F PYL GER P+ +P
Sbjct: 301 GLSLKWFRDNFAHIEKAAFEFIDKDPYILMDQEAELANPGSDGLVFLPYLMGERTPILDP 360

Query: 360 DVPGSFFGLTMSHKKEHMIRAALEGVIYNLYTVFLALTECMDGPVARIQATGGFARSDVW 419
              G FFG+T  H +   IRA +EGV+++L      L E M   V  ++ +GG A+S +W
Sbjct: 361 YAKGIFFGITAKHTRREFIRAVMEGVVFSLKNCLDILHE-MGIEVKEVRVSGGGAKSKLW 419

Query: 420 RQMMADIFESEVVVPESYESSCLGACILGLYATGKIDSFDVVSD-MIGSTHRHAPKEESA 478
           RQM ADIFE +V    S E    GA IL     G  +  +   D MI      +P ++  
Sbjct: 420 RQMQADIFEMDVWTLNSKEGPAFGAAILATVGAGVYNKVEEACDTMIQKVESCSPNKDLF 479

Query: 479 KEYRKLMPLF 488
           + YRK   L+
Sbjct: 480 EVYRKTYKLY 489


Lambda     K      H
   0.318    0.134    0.401 

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: 552
Number of extensions: 33
Number of successful extensions: 4
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: 513
Length of database: 502
Length adjustment: 34
Effective length of query: 479
Effective length of database: 468
Effective search space:   224172
Effective search space used:   224172
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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