GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Pseudomonas fluorescens FW300-N1B4

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate Pf1N1B4_6031 Ribokinase (EC 2.7.1.15)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031
          Length = 305

 Score =  583 bits (1503), Expect = e-171
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60
           MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG
Sbjct: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60

Query: 61  CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120
           CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE
Sbjct: 61  CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120

Query: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180
           VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID
Sbjct: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180

Query: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240
           YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA
Sbjct: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240

Query: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300
           AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ
Sbjct: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300

Query: 301 AFKAP 305
           AFKAP
Sbjct: 301 AFKAP 305


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: 445
Number of extensions: 7
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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 Pf1N1B4_6031 (Ribokinase (EC 2.7.1.15))
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

Software error:

../bin/blast/fastacmd -i /tmp/list.11373.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11373.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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