GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Burkholderia phytofirmans PsJN

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate BPHYT_RS20695 BPHYT_RS20695 ribokinase

Query= reanno::pseudo1_N1B4:Pf1N1B4_6031
         (305 letters)



>FitnessBrowser__BFirm:BPHYT_RS20695
          Length = 310

 Score =  315 bits (808), Expect = 7e-91
 Identities = 167/300 (55%), Positives = 213/300 (71%), Gaps = 2/300 (0%)

Query: 4   KVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVGCVG 63
           +V+V+GS+N DLV RAP LPR GET+ G  F+ V+GGKG NQAVAAAR+GAQV+MVGCVG
Sbjct: 9   RVLVVGSINTDLVARAPHLPRPGETIGGHEFSQVAGGKGGNQAVAAARIGAQVAMVGCVG 68

Query: 64  NDAYGEALRGALLAEQIDCQAVSTVEDS-SGVALIVVDDNSQNAIVIVAGANGALTPEVI 122
            DA G      L AE IDC  +       +GVA++ V D+ QN IV+VAG+NG LTPE +
Sbjct: 69  KDANGAQRVKDLEAEGIDCSGIEVHPGQPTGVAMVTVSDDGQNTIVVVAGSNGELTPESV 128

Query: 123 DRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAIDYL 182
            R +A ++A DV++CQLE P  +V   L   R LGK  +LNPAPA+ PLP +W   +DYL
Sbjct: 129 ARHEAAIKACDVVVCQLETPWDSVHATLALARRLGKITVLNPAPATGPLPAEWLPLVDYL 188

Query: 183 IPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGS-LFADGQRFEHFPAA 241
           +PNE EA++L+GLPV+S S A  AAT L   GA  VI+TLG+QG+ L  +G    HFPA 
Sbjct: 189 VPNEVEAAILAGLPVESQSGARRAATELQQGGARNVIVTLGAQGAYLLVEGGEGMHFPAP 248

Query: 242 KVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQA 301
           +V+AVDTTAAGDTF+G FAA LA+ +    AI   Q AA++SVTRAGAQPSIPT ++V +
Sbjct: 249 QVQAVDTTAAGDTFIGVFAAQLASRQPLESAISLAQRAASISVTRAGAQPSIPTRAEVDS 308


Lambda     K      H
   0.316    0.132    0.369 

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: 306
Number of extensions: 10
Number of successful extensions: 3
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: 305
Length of database: 310
Length adjustment: 27
Effective length of query: 278
Effective length of database: 283
Effective search space:    78674
Effective search space used:    78674
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: 48 (23.1 bits)

Align candidate BPHYT_RS20695 BPHYT_RS20695 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

Software error:

../bin/blast/fastacmd -i /tmp/list.30278.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30278.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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