GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc02341
          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:

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