GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Magnetospirillum magneticum AMB-1

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011383016.1 AMB_RS02965 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_000009985.1:WP_011383016.1
          Length = 460

 Score =  124 bits (311), Expect = 6e-33
 Identities = 119/441 (26%), Positives = 190/441 (43%), Gaps = 41/441 (9%)

Query: 9   IRGTLWEKVTPELAMKVGMAVGTY--KSGKALV--GRDGRTSSVMLKNAMISGLLSTGME 64
           IRG + E +    A  +G A GT   ++G  +V  G DGR SS  +  A+  GL++ G  
Sbjct: 15  IRGIIGETLFAADAEAIGRAFGTRVRRNGGHVVCLGWDGRLSSPEMAEALTKGLMAAGCT 74

Query: 65  VLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEI 123
           V      PTP L +  + + AD G+M+T SHNPP  NG K+    G  F+    + L  I
Sbjct: 75  VRRVGRGPTPMLYFAAKVRDADGGIMVTGSHNPPNHNGFKMVLA-GRPFFGPDIQSLGTI 133

Query: 124 IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLR 183
             +G+F       ++      V  +Y++ +        +L+V++D  NGA   V   L++
Sbjct: 134 AAAGDFASGEGKAVED----SVFEEYVSRLAQDYDGLRDLRVVWDCGNGATGEVLHALVK 189

Query: 184 EMGAKVLSVNAHVDGHFPGRKPEPRY-ENIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242
            +      +   +DGHFP   P+P    N+  L   V      L IA DGD DRI V D 
Sbjct: 190 RLPGTHTVLFGEIDGHFPNHHPDPTEPHNLVALQDKVLTESAHLGIAFDGDGDRIGVVDA 249

Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302
           +G  +  D ++ + A+  ++   G T++  +         V R GG  V    G  H  I
Sbjct: 250 EGRILYGDQILVILAEDLLKSLPGATIIADVKASKVFFDEVRRMGGNAVMGRTG--HSLI 307

Query: 303 KRYKA-------------IFAAEPWKLVHPKFGPWIDPFVTMGLLIKLID--ENGPLSEL 347
           K   A             IF A+       ++  + D       L+ ++   ++  + + 
Sbjct: 308 KTQMAETGAPLAGEMSGHIFFAD-------RYYGFDDALYAAIRLLGIVARWDHTTIGQR 360

Query: 348 VKEIP-TYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWI 406
              +P      +    CP+E K  VV     EV+ +L +E      I G R+   DG W 
Sbjct: 361 RDRLPHMVNTPELRFDCPEERKFAVV----AEVKARLEAEGASFSAIDGVRVDTPDG-WW 415

Query: 407 LIRPSGTEPKIRVVAEAPTEK 427
           L+R S T+  +    EA + +
Sbjct: 416 LLRASNTQAVLVARCEAASSE 436


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: 497
Number of extensions: 31
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: 460
Length adjustment: 33
Effective length of query: 417
Effective length of database: 427
Effective search space:   178059
Effective search space used:   178059
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 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