GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Halococcus hamelinensis 100A6

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase

Query= SwissProt::P50845
         (324 letters)



>NCBI__GCF_000336675.1:WP_049904537.1
          Length = 318

 Score =  244 bits (623), Expect = 2e-69
 Identities = 136/319 (42%), Positives = 180/319 (56%), Gaps = 1/319 (0%)

Query: 1   MKLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGND 60
           M    VT GE+M + Y +  G +     F K LAGAE+NVA GLARLG  +GW SK+G D
Sbjct: 1   MSSRVVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTD 60

Query: 61  QLGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEGDPQVTYYRKNSAASTLTTAE 120
             G ++   ++ EGVD + V    DE PTG++ K + + G+P V YYR  SAAS ++  +
Sbjct: 61  PHGEYLEFFVRGEGVDTTTV-EFTDEAPTGIMFKERREFGEPAVHYYRHGSAASLMSPDD 119

Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180
            P DY   A +LH+TGI PALS   +D T         AG T+SFDPNVR  LW     M
Sbjct: 120 LPVDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERM 179

Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240
             T+ DL  L+D   PGI EG  L G   PE IA   L  GA    +KLG  GA    G+
Sbjct: 180 RETMLDLVSLSDIVLPGIEEGAALFGTDDPEAIAAACLDHGAGTAVVKLGAAGAVVADGS 239

Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300
           +   + G  V+RVVD VGAGDGFA G ++  ++G    +A +  NA+GA      GD +G
Sbjct: 240 TTERVSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTEG 299

Query: 301 LPTREKLASFLSAQRTVHQ 319
           LPTR++L  F+  +  V +
Sbjct: 300 LPTRKELDVFVGERDAVRR 318


Lambda     K      H
   0.317    0.135    0.399 

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: 294
Number of extensions: 16
Number of successful extensions: 2
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: 324
Length of database: 318
Length adjustment: 28
Effective length of query: 296
Effective length of database: 290
Effective search space:    85840
Effective search space used:    85840
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: 48 (23.1 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