GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Desulfovibrio vulgaris Miyazaki F

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate 8502088 DvMF_2801 Hydroxypyruvate reductase (RefSeq)

Query= BRENDA::O58231
         (440 letters)



>FitnessBrowser__Miya:8502088
          Length = 452

 Score =  298 bits (762), Expect = 3e-85
 Identities = 184/442 (41%), Positives = 260/442 (58%), Gaps = 19/442 (4%)

Query: 13  LVGEAIKAADPYRAVLNAVKVSDDKIIVQGKEFEIKG--KVYVIALGKAACEMARAIEDI 70
           ++  A+ A  P RAV   V+ + + + + G+++++    +VYV+  GK A  MA A+EDI
Sbjct: 12  ILSRALDAVAPDRAVHRHVRRNGNILHIAGRDYDLSAHERVYVVGAGKGAAPMAAALEDI 71

Query: 71  LD--VEDGVAVTKYGYGKELKRIKVIEAGHPIPDEKSILGAKEALSILNRARENDIVFIL 128
           L   V DGV V KYG+   LKRI + EA HP+PD      A E L ++  A   D+V   
Sbjct: 72  LGDRVHDGVVVVKYGHTAPLKRIALREAAHPVPDAAGERAANEILDLVRTAGPRDLVLCA 131

Query: 129 ISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKGGKLAKMIKGT 188
           ++GG SAL    + GI+L+D++  T LLL+ GA IHEIN +RKH+S   GG LA+     
Sbjct: 132 LTGGASALTPALQPGITLDDMRAATTLLLECGATIHEINALRKHLSAFGGGNLARAAAPA 191

Query: 189 GIV-LIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESVRLHIERGLRG 247
            +V LIISDVVGD+L+ IASGPT  D +T+ D K I   + I  ++PE V   +  GLRG
Sbjct: 192 RVVSLIISDVVGDDLDVIASGPTSPDVSTYADCKSIAYRFGILHRLPEPVVERLTAGLRG 251

Query: 248 EVEETLKEDLP---NVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLEGEAKDAGLFI 304
              ET K   P    V N ++ASN ++ EA A  A   G++  I+T T+ GEA+   +  
Sbjct: 252 MAAETPKPGDPVFGAVQNCIVASNRLALEAAAEAAAAHGYRPRILTDTMTGEAR---VRA 308

Query: 305 GSIVQEIAE--RGRPF-EPPVVLVFGGETTVTIEGKGGKGGPNQEIALSATRKISDL--- 358
             +V+E A    G P  E P  L+ GGETTVTI G GG GG NQE+AL+A  ++ +L   
Sbjct: 309 RELVEEAASAAEGLPHPEGPFCLLAGGETTVTITG-GGLGGRNQEMALAAAIRMDELADC 367

Query: 359 -EALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKKVGGLLF 417
               ++   TDGTDGPTDAAGG   G+T    R+ G+D    L ++++Y  L + G LL 
Sbjct: 368 QHIAMLCAGTDGTDGPTDAAGGYASGSTLCVARQCGVDAHGHLADNDAYHFLDRTGHLLR 427

Query: 418 TGPTGTNVNSIVIAIVTSKRGR 439
           TGPT TNV  + + +V + +G+
Sbjct: 428 TGPTLTNVMDLAVLLVDAPKGK 449


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: 449
Number of extensions: 22
Number of successful extensions: 7
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: 452
Length adjustment: 32
Effective length of query: 408
Effective length of database: 420
Effective search space:   171360
Effective search space used:   171360
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