GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Phaeobacter inhibens BS107

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate GFF3085 PGA1_c31360 putative hydroxypyruvate reductase

Query= BRENDA::O58231
         (440 letters)



>FitnessBrowser__Phaeo:GFF3085
          Length = 424

 Score =  229 bits (583), Expect = 2e-64
 Identities = 153/437 (35%), Positives = 236/437 (54%), Gaps = 20/437 (4%)

Query: 5   DIREIGLRLVGEAIKAADPYRAVLNAVKVSDDKIIVQGKEFEIKGKVYVIALGKAACEMA 64
           D+R I  R    A+  A+P  A+  +++     +   G      G++ ++ALGKAA  M 
Sbjct: 3   DLRSIARRFFAAAVARANPATALAESLRQHPPTLPQPG------GRLILVALGKAAIPMI 56

Query: 65  RAIEDILDVED-GVAVTKYGYGKELKRIKVIEAGHPIPDEKSILGAKEALSILNRAREND 123
           R    +L   D  +AVT      +L  ++V+   HP+P   S+       S L+     D
Sbjct: 57  RQAMAMLPPPDRAIAVTNPENVADLSDVEVLAGNHPVPHHMSLAAGDALRSALSNLNAKD 116

Query: 124 IVFILISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKGGKLAK 183
            V  LISGGGSAL   P  G++L D    TDLLL  G  I ++N +R+ +S++KGG L +
Sbjct: 117 RVIALISGGGSALAVAPAGGLTLADKTAVTDLLLGGGVDITQMNLIRQQLSELKGGGLLR 176

Query: 184 MIKGTGIV-LIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESVRLHIE 242
             +   +   I+SDV+GD+L AIASGPTV    +   A+  L  +++WE +P +V+ H+ 
Sbjct: 177 AAQPAQVFSYILSDVIGDDLRAIASGPTVAPLGSRAMARDCLLSHNLWEGLPHAVQTHLT 236

Query: 243 RGLRGEVEETLKEDLPNVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLEGEAKDAGL 302
                + +      + + H  LI SN  S  A+  +A R G+ A+I++  L G+ + A  
Sbjct: 237 TPEEPQ-QSPANSSVTSAH--LIGSNRHSLGAVRDQATRDGWSAHIVSDALIGDVEVAAT 293

Query: 303 FIGSIVQEIAERGRPFEPPVVLVFGGETTVTIEGKGGKGGPNQEIALSAT---RKISDLE 359
            I +  +E  E GR    P  L+FGGETTV + G  G+GG NQE+AL      R+     
Sbjct: 294 EILAATKE-QETGR----PTALIFGGETTVQLTG-SGRGGRNQELALHIARLGRRALKER 347

Query: 360 ALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKKVGGLLFTG 419
              ++  TDG DGPTDAAGG+VD  T++++ + G + + +L+ ++S  ALK  G LL TG
Sbjct: 348 WTFLSAGTDGRDGPTDAAGGVVDSGTWQRIGDNGGNPDALLRNNDSNAALKLAGDLLITG 407

Query: 420 PTGTNVNSIVIAIVTSK 436
            TGTNV  + I +++ +
Sbjct: 408 GTGTNVADVQIMLLSPR 424


Lambda     K      H
   0.315    0.137    0.376 

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: 427
Number of extensions: 17
Number of successful extensions: 6
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: 440
Length of database: 424
Length adjustment: 32
Effective length of query: 408
Effective length of database: 392
Effective search space:   159936
Effective search space used:   159936
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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