GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaB in Bacteroides thetaiotaomicron VPI-5482

Align Rhamnulokinase (EC 2.7.1.5) (characterized)
to candidate 353289 BT3763 rhamnulose kinase/L-fuculose kinase (NCBI ptt file)

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



>FitnessBrowser__Btheta:353289
          Length = 485

 Score =  365 bits (937), Expect = e-105
 Identities = 210/464 (45%), Positives = 275/464 (59%), Gaps = 9/464 (1%)

Query: 8   AVDLGASSGRVMLASYQPGQQTLALREIHRFTNSLQKVDGFDCWDLDSLEGEIRRGLEKV 67
           AVDLGA+SGR +L S+  G   L L EI+RF N L +V G   WD+ +L   I  GL+ V
Sbjct: 7   AVDLGATSGRTILGSFIEGG--LNLEEINRFPNHLIEVGGHFYWDIYALYRHIIDGLKLV 64

Query: 68  CEQGILIDSIGIDTWGVDYVLLDKRGQRVGLPVSYRDSRTQGLMRHAEAQLGRAEIYRRS 127
             +G  I SIGIDTWGVD+VLL K G  +  P +YRD  T G      +++ R+E+Y ++
Sbjct: 65  AHRGESIASIGIDTWGVDFVLLGKDGNLLRQPYAYRDPHTVGAPEAFFSRISRSEVYGKT 124

Query: 128 GIQFLPFNTLYQLRALVEQQPELVSQAAHALLIPDYFSFRLTGNMNWEYTNATTTQLVNI 187
           GIQ + FN+L+QL  L       +  A   L +PD  S+ LTG M  EYT A+T QLVN 
Sbjct: 125 GIQVMNFNSLFQLDTLRRNHDSALEAADKVLFMPDALSYMLTGKMVTEYTIASTAQLVNA 184

Query: 188 NSDSWDEDLLNWSGAPREWFGTPTHPGNVIG------HWICPQGNHIPVVAVASHDTASA 241
           ++   + +LL   G   E FG    PG  IG        I   G  IPV+AVA HDT SA
Sbjct: 185 HTQRLEPELLKAVGLQEENFGRFVFPGEKIGTLTEEVQKITGLGA-IPVIAVAGHDTGSA 243

Query: 242 VIASPLASKNAAYLSSGTWSLMGFESKIPCTSDAALRANITNEGGAEGRYRVLKNIMGLW 301
           V A P   +N AYLSSGTWSLMG E+  P  +      N TNEGG EG  R+LKNI G+W
Sbjct: 244 VAAVPALDRNFAYLSSGTWSLMGVETDAPVITAETEALNFTNEGGVEGTIRLLKNICGMW 303

Query: 302 LLQRVLREQNVSDLPALIARTAALPACRFVIDCNDDRFINPDDMSAEIQAACRESGQPVP 361
           LL+R       +  P LI    +    R +I+ +DD F NP DM   I+  CR +GQPVP
Sbjct: 304 LLERCRLNWGDTSYPELITEADSCEPFRSLINPDDDCFANPADMEQAIREYCRTTGQPVP 363

Query: 362 DTDAELARCIFDSLALLYTRVLNELAALRGQPFSQLHIVGGGCQNELLNQLCADACGITV 421
           +   ++ RCIF+SLAL Y +VL  L AL  +P   LH++GGG +N+LLNQ  A+A GI V
Sbjct: 364 EQRGQIVRCIFESLALRYRQVLENLRALSPRPIETLHVIGGGSRNDLLNQFTANAIGIPV 423

Query: 422 VAGPVEASTLGNIGIQLMTLDELNNVDEFRQVVRQNYALTTFTP 465
           VAGP EA+ +GN+ IQ MT+ E  +V   RQ++ ++  L T+ P
Sbjct: 424 VAGPSEATAIGNVMIQAMTVGEATDVAGMRQLISRSIPLKTYHP 467


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: 596
Number of extensions: 22
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: 488
Length of database: 485
Length adjustment: 34
Effective length of query: 454
Effective length of database: 451
Effective search space:   204754
Effective search space used:   204754
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)

Align candidate 353289 BT3763 (rhamnulose kinase/L-fuculose kinase (NCBI ptt file))
to HMM TIGR02627 (rhaB: rhamnulokinase (EC 2.7.1.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.9345.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9345.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.