GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaB in Kocuria turfanensis HO-9042

Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate WP_062735671.1 AYX06_RS10180 rhamnulokinase

Query= reanno::Koxy:BWI76_RS00680
         (488 letters)



>NCBI__GCF_001580365.1:WP_062735671.1
          Length = 487

 Score =  319 bits (818), Expect = 1e-91
 Identities = 196/491 (39%), Positives = 266/491 (54%), Gaps = 27/491 (5%)

Query: 4   RHCVAVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVD-----GFDCWDLDSLEG 58
           R   AVDLGA+SGRV+L   + G+  L LR + RF N   ++      G   W++  L  
Sbjct: 3   RTVAAVDLGATSGRVILGGIEDGR--LRLRHLARFPNQPVRLHEGGRTGLH-WNITELHR 59

Query: 59  EIRRGLEKVCEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQL 118
            +  GL +   QG L+ SIGID+W VDY LL + G+ +G P SYRD RT   +     ++
Sbjct: 60  SLTAGLAQALRQGELVVSIGIDSWAVDYALL-RDGRMLGAPYSYRDERTAVGVEAVHGRV 118

Query: 119 GRAEIYRRSGIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTN 178
              E++ R+G+Q LPFNT+YQL   V++    +  A   LL+PD   + LTG    E TN
Sbjct: 119 SPEELHARTGLQHLPFNTVYQLA--VDRVRGDLDLADRMLLVPDLIGYWLTGRQVAEATN 176

Query: 179 ATTTQLVNINSDSWDEDLLNWSGAPREWFGTPTHPGNVIGHWICPQGNHI------PVVA 232
           A+TT L++  +  WD  L++  G PRE F     PG  IG  +      +       V A
Sbjct: 177 ASTTGLLDARTRQWDTGLMDRLGYPRELFAPVVTPGTRIGELLPDVAAELGAAPGLAVTA 236

Query: 233 VASHDTASAVIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYR 292
           V SHDTASAV+A P     AA++SSGTWSL+G E   P  +  +  AN TNEGG +GR R
Sbjct: 237 VGSHDTASAVVAVPTTDDAAAFISSGTWSLVGIELDAPVLTPESRAANFTNEGGLDGRVR 296

Query: 293 VLKNIMGLWLLQRVLRE---------QNVSDLPALIARTAALPACRFVIDCNDDRFINPD 343
            LKN+ GLWLL   +R          Q  SDL AL+A  AA+     V+D  D+RF  P 
Sbjct: 297 FLKNVSGLWLLSESIRTWDGPGASDAQRSSDLAALLAEAAAVTRPVSVVDATDERFTAPG 356

Query: 344 DMSAEIQAACRESGQPVPDTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGG 403
           DM A + A C E G   P T AE+ RCI +SLA  Y   + +   L G+    +H+VGGG
Sbjct: 357 DMPARVVAWCEERGLEPPRTRAEVVRCILESLAAAYATTIEQAEHLSGKRIRTIHVVGGG 416

Query: 404 CQNELLNQLCADACGITVVAGPVEASTLGNIGIQLMTLDEL-NNVDEFRQVVRQNYALTT 462
            QN LL QL AD  G TV AGPVEA+ +GN+ +Q      +  +++  R +V   +    
Sbjct: 417 SQNALLCQLTADRTGRTVAAGPVEATAVGNVLVQARAAGLVTGDLEALRGIVATTFEPVR 476

Query: 463 FTPNPENEIAR 473
           + P    + AR
Sbjct: 477 YQPRTVTDTAR 487


Lambda     K      H
   0.320    0.135    0.413 

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: 615
Number of extensions: 33
Number of successful extensions: 6
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: 488
Length of database: 487
Length adjustment: 34
Effective length of query: 454
Effective length of database: 453
Effective search space:   205662
Effective search space used:   205662
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: 52 (24.6 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