GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylB in Sinorhizobium meliloti 1021

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate SMc02341 SMc02341 sugar kinase

Query= reanno::Dino:3608604
         (480 letters)



>lcl|FitnessBrowser__Smeli:SMc02341 SMc02341 sugar kinase
          Length = 477

 Score =  252 bits (644), Expect = 2e-71
 Identities = 173/484 (35%), Positives = 238/484 (49%), Gaps = 17/484 (3%)

Query: 1   MYLGLDLGTSGLKAVLIDENQALVAEATAPLEVARPHPGWSEQMPCDWLAATEAAMAAL- 59
           MYLG+DLGT  +KA+LID +   VAEA     V+ P PG++E  P DW A T AA+ A  
Sbjct: 1   MYLGIDLGTGSVKALLIDGDGKAVAEAARAYPVSSPMPGYAETSPADWWAQTVAAVRACC 60

Query: 60  -GARADLSGVRAIGLSGQMHGATLLDASHEVLRPCILWNDTRAAAEAAALDADP-AFRSV 117
            G   D   VR IGLSGQ HG   + A  + LRP ILW D RA AE  A+ A P A R  
Sbjct: 61  DGHGGD---VRGIGLSGQAHGLVAVGADAKPLRPAILWADQRATAEMEAVLALPEAVRRP 117

Query: 118 TGNIVFPGFTAPKLAWVRAHEPDVFDRTALVLLPKDYLRLWLTGEAVAEMSDAAGTSWLD 177
             N V  G     L W+R +EP  +     +L PKD+LRL +TGEA  E SDA+ T   D
Sbjct: 118 LANPVVSGMAGLSLLWLRRNEPATYAAIRRILAPKDWLRLVMTGEAATEPSDASMTLLYD 177

Query: 178 TGARDWSAPLLAATGLSRDHMPRLVEGSEVSGTLRDSLADAWGLPRGVPVAGGGGDNAAS 237
            GA  W+  +L++  +    +  +VE   ++G L  + A   GL  G PVA G  D A+ 
Sbjct: 178 VGAGRWATDVLSSLSIDPAILAPIVESHSIAGRLSAAAAAELGLAAGTPVAAGLSDTASC 237

Query: 238 GIGMGVVRAGDGFVSLGTSGVLFAACDAYAPDPATAVHTFCHALPETWHQMGVILAATDA 297
             GMG  + G   + +G+   + +  ++  P      +++   +    + M  +      
Sbjct: 238 LFGMGQTKPGSTILQVGSGIQIMSVVESIEPRVQPFYNSY-RGIGGNLYSMAALQNGGTV 296

Query: 298 LNWFARTCGTDAATL-TGGLGPLQAPGRPVFLPYLGGERTPHNDAAIRGAFARIDHAADR 356
             W     G   A +   G    +  G  +FLPY+ GER P  D     A+A +     R
Sbjct: 297 FEWARTVLGASWAEMYRSGFEENEGNGGVIFLPYVTGERAPLLDPNASAAWANMRLGCTR 356

Query: 357 DALARAVLEGVAFAFRDSFDALAATGTRLERLVAVGGGAKSDTWVRMIATLIGLPIDLPQ 416
             L R+V EGVA A RDS+DAL   G   +R++  GGG+    W +M+A ++ +P  L  
Sbjct: 357 GQLIRSVFEGVALAVRDSWDALRGVGVSADRILLTGGGSTDPRWQQMLADILEVP--LVP 414

Query: 417 AGDYGGA-FGAARLGMMAATGQGAALATRP---PIARSLDPVPALADAFGEAHATYRATY 472
           A D G A  GAA LG MAA G    +   P    + R ++P P            +RATY
Sbjct: 415 AHDLGNATIGAAYLGGMAA-GHWRCIEAIPFPDDLGRPIEPRP--FQGLDALLPRFRATY 471

Query: 473 TALK 476
             LK
Sbjct: 472 RGLK 475


Lambda     K      H
   0.320    0.135    0.418 

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: 642
Number of extensions: 39
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: 480
Length of database: 477
Length adjustment: 34
Effective length of query: 446
Effective length of database: 443
Effective search space:   197578
Effective search space used:   197578
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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