GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Pseudomonas fluorescens FW300-N2E2

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate Pf6N2E2_165 Ribokinase (EC 2.7.1.15)

Query= reanno::pseudo5_N2C3_1:AO356_00950
         (304 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165
          Length = 304

 Score =  554 bits (1427), Expect = e-162
 Identities = 287/304 (94%), Positives = 294/304 (96%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60
           MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESF+TIPGGKGANQAVAAARLGA+VSMVG
Sbjct: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFSTIPGGKGANQAVAAARLGAEVSMVG 60

Query: 61  CVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAE 120
           CVG+DAYGEQLRG LLAEGIDCQAV V +G+SGVALIVVDDNSQNAIVIVAGANGALTAE
Sbjct: 61  CVGNDAYGEQLRGGLLAEGIDCQAVSVVEGASGVALIVVDDNSQNAIVIVAGANGALTAE 120

Query: 121 VLDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACID 180
           VLD VD+VLQSADVIICQLEVPDATVGHALKR R LGKIVILNPAPASH LPADWYACID
Sbjct: 121 VLDSVDEVLQSADVIICQLEVPDATVGHALKRARELGKIVILNPAPASHTLPADWYACID 180

Query: 181 YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA 240
           YL+PNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANG SFEHFPA
Sbjct: 181 YLVPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGVSFEHFPA 240

Query: 241 PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 300
           PRVKAVDTTAAGDTFVGGFAAALA GKSEVDAIRFGQ AAALSVTRAGAQPSIPTLLEVQ
Sbjct: 241 PRVKAVDTTAAGDTFVGGFAAALASGKSEVDAIRFGQAAAALSVTRAGAQPSIPTLLEVQ 300

Query: 301 AFKS 304
           AFKS
Sbjct: 301 AFKS 304


Lambda     K      H
   0.318    0.133    0.377 

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: 484
Number of extensions: 12
Number of successful extensions: 2
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: 304
Length of database: 304
Length adjustment: 27
Effective length of query: 277
Effective length of database: 277
Effective search space:    76729
Effective search space used:    76729
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: 48 (23.1 bits)

Align candidate Pf6N2E2_165 (Ribokinase (EC 2.7.1.15))
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

Software error:

../bin/blast/fastacmd -i /tmp/list.13271.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13271.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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