GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Streptacidiphilus oryzae TH49

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_051939761.1 BS73_RS09785 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_000744815.1:WP_051939761.1
          Length = 465

 Score =  135 bits (339), Expect = 4e-36
 Identities = 136/439 (30%), Positives = 193/439 (43%), Gaps = 40/439 (9%)

Query: 9   IRGTL---WEKVTPELAMKVGMA-VGTYKSGKALVGRDGRTSSVMLKNAMISGLLSTGME 64
           IRG +   W++ T EL    G A V    +G  + G D R SS  L  A   G  + G +
Sbjct: 24  IRGVVPDDWDEATAEL---FGAAFVRVTGAGAIVTGHDMRPSSPGLAAAFARGATAQGAD 80

Query: 65  VLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGL---- 120
           V +  L  T  L + +  L  AG M TASHNP   NG+K+         V Q+ GL    
Sbjct: 81  VTEIGLCSTDQLYFASGSLGLAGAMFTASHNPARYNGIKLCRAGAEP--VGQDTGLAAIR 138

Query: 121 ---EEIIFSGNFRKARWDEIKPVRNVEVIPDY---INAVLDFVGHETNLKVLYDGANGAG 174
              EE + +G   +          + E + DY   + +++D +G    LKV+ D  NG G
Sbjct: 139 ALVEEWLDAGRGPEPAAGPRGRTTSRETLADYAAHLRSLVD-LGAIRPLKVVVDAGNGMG 197

Query: 175 SLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYE-NIAYLGKLVRELGVDLAIAQDGD 233
               P +L  +   V+ +   +DG FP  +  P    NI  L   VR  G DL +A DGD
Sbjct: 198 GHTVPTVLAGLPLTVVPMYFELDGTFPHHEANPLDPANIVDLRARVRAEGADLGLAFDGD 257

Query: 234 ADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRI 293
           ADR  V DE+G  V    V AL A   + EH G  V+ ++ T   +  VV  AGG  VR 
Sbjct: 258 ADRCFVVDERGEPVSPSAVTALVAARELAEHPGAAVIHNLITSRTVPEVVREAGGIPVRT 317

Query: 294 PLGQPHDGIK----RYKAIFAAEPWKLVHPKFGPWIDP----FVTMGLLIKLIDENGPLS 345
            +G  H  IK    R  A+F  E     H  F  + +        + +L  L ++  PLS
Sbjct: 318 RVG--HSFIKAEMARAGAVFGGE--HSAHYYFRDFWNADTGMLAALHVLAALGEQPRPLS 373

Query: 346 ELVKEIPTYYLK-KANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGS 404
           EL      Y    + N    D+ +     RAA      ++ +  + LT++G         
Sbjct: 374 ELTARYERYAASGEINSTVADQAERIAAVRAAWSGRPGVTLDELDGLTVAG------RDW 427

Query: 405 WILIRPSGTEPKIRVVAEA 423
           W  +RPS TEP +R+  EA
Sbjct: 428 WFNLRPSNTEPLLRLNVEA 446


Lambda     K      H
   0.318    0.138    0.402 

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: 492
Number of extensions: 29
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: 450
Length of database: 465
Length adjustment: 33
Effective length of query: 417
Effective length of database: 432
Effective search space:   180144
Effective search space used:   180144
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: 51 (24.3 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