GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Dechlorosoma suillum PS

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate Dsui_3057 Dsui_3057 phosphoglucosamine mutase

Query= metacyc::MONOMER-13382
         (455 letters)



>FitnessBrowser__PS:Dsui_3057
          Length = 451

 Score =  177 bits (450), Expect = 5e-49
 Identities = 146/446 (32%), Positives = 207/446 (46%), Gaps = 28/446 (6%)

Query: 3   KLFGTFGVRGIANEK-ITPEFAMKIGMAFGTLLKRE----GRKKPLVVVGRDTRVSGEML 57
           K FGT GVRG   E  ITP+FAM++G + G +L  +      ++P V++G+DTR+SG ML
Sbjct: 4   KYFGTDGVRGRVGEAPITPDFAMRLGYSAGQVLVAQDGLPAGERPAVLIGKDTRISGYML 63

Query: 58  KEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNG 117
           + AL +G  + G DV  VG  PTPAV + T+      G VI+ASHNP   NGIK     G
Sbjct: 64  EAALEAGFSAAGVDVCLVGPMPTPAVAYLTRALRLQAGIVISASHNPFYDNGIKFFSAQG 123

Query: 118 MGLKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS----KVDVEAIKK 172
             L    E  + E   +          +G+ RR +D    YIE  KS     +D+  +K 
Sbjct: 124 TKLPDAVEHAI-EAGVEAPMGCVPSDRLGKARRIDDARGRYIEFCKSTFPNDLDLRGLK- 181

Query: 173 RKPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVK 232
               +VVD ++GA     P +  ELG  V+ +  +PDG     N        K   E V 
Sbjct: 182 ----IVVDCAHGAAYHIAPDVFHELGADVVAIGNRPDGL--NINAAVGATAPKALKEAVL 235

Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNLL 291
              AD G+A DGD DR V +D  G    GD+  +A+V          G +  T+ T+  L
Sbjct: 236 GQRADLGIALDGDGDRLVMVDGEGNVYDGDQLLYAIVRGRQALGPVAG-VAGTLMTNLAL 294

Query: 292 DDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVE 351
           +D  K       R  VGD  V   L +N    GGE +G ++  +     DG +   +V+ 
Sbjct: 295 EDALKALDIPFARAAVGDRYVLEKLVQNGWLYGGENSGHILCLDRHTTGDGIIAALQVLA 354

Query: 352 IFAKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIF 411
              + G     L+ +L  Y Q K             +  A  A +R    +  DG     
Sbjct: 355 ALRQQGGSLKALLGDLVLYPQ-KLINVPMPKGFPWQDSPAIAAAQRAVEAE-LDGR---- 408

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKE 437
             G VL+RASGTEP++R+  E +  E
Sbjct: 409 --GRVLLRASGTEPLLRVMVEGRDGE 432


Lambda     K      H
   0.317    0.138    0.391 

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: 501
Number of extensions: 36
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: 455
Length of database: 451
Length adjustment: 33
Effective length of query: 422
Effective length of database: 418
Effective search space:   176396
Effective search space used:   176396
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