GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Shewanella loihica PV-4

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 5210370 Shew_2813 phosphopentomutase (RefSeq)

Query= reanno::MR1:200397
         (404 letters)



>FitnessBrowser__PV4:5210370
          Length = 405

 Score =  714 bits (1844), Expect = 0.0
 Identities = 348/404 (86%), Positives = 373/404 (92%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKADTGRKGPLALPNLARLG 60
           MKRTVIMMLDSFGVGAA DA  FGD GS+TFGHIAKACAEGKA+ GR+GPL LPNLA+LG
Sbjct: 1   MKRTVIMMLDSFGVGAAKDAEAFGDTGSNTFGHIAKACAEGKANDGREGPLKLPNLAKLG 60

Query: 61  LAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSEH 120
           LA AA ESTG+FA GF D+V++IGAYGHA ELSSGKDTPSGHWEMAGVPVL+EWGYFS+ 
Sbjct: 61  LALAAKESTGSFAEGFGDDVEVIGAYGHADELSSGKDTPSGHWEMAGVPVLYEWGYFSDL 120

Query: 121 QNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIAC 180
           ++SFPKELTDKIL RAGL GFLGNCHASGT ILEELGEEHM SG PIFYTSADSVFQIAC
Sbjct: 121 KDSFPKELTDKILERAGLSGFLGNCHASGTAILEELGEEHMTSGLPIFYTSADSVFQIAC 180

Query: 181 HEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKTV 240
           HE TFGLENLY LC+IAREELEPYNIGRVIARPF GTGPSDFARTGNRKDY++EPP+KTV
Sbjct: 181 HEETFGLENLYTLCQIAREELEPYNIGRVIARPFVGTGPSDFARTGNRKDYAVEPPSKTV 240

Query: 241 LDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNFV 300
           LDKLK AGGEVVSVGKIADIYA+CGITKKVKA GLEALFDATL +VK AG+ TIVFTNFV
Sbjct: 241 LDKLKEAGGEVVSVGKIADIYAHCGITKKVKATGLEALFDATLEQVKQAGDRTIVFTNFV 300

Query: 301 DFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTREY 360
           DFDSHYGHRRD+AGYA+ LEYFD+RLPEMLALL E+DLL+LTADHGCDPTWQGTDHTRE 
Sbjct: 301 DFDSHYGHRRDIAGYARALEYFDSRLPEMLALLGEEDLLLLTADHGCDPTWQGTDHTRER 360

Query: 361 VPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
           VPVLAYGAGL  GSLGRRNSFADIGQSIASYF LEPMEYGESF+
Sbjct: 361 VPVLAYGAGLAPGSLGRRNSFADIGQSIASYFGLEPMEYGESFV 404


Lambda     K      H
   0.318    0.137    0.412 

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: 734
Number of extensions: 15
Number of successful extensions: 1
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: 404
Length of database: 405
Length adjustment: 31
Effective length of query: 373
Effective length of database: 374
Effective search space:   139502
Effective search space used:   139502
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 5210370 Shew_2813 (phosphopentomutase (RefSeq))
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.29343.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29343.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.