GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Klebsiella michiganensis M5al

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate BWI76_RS20235 BWI76_RS20235 acetate kinase

Query= BRENDA::P63411
         (400 letters)



>FitnessBrowser__Koxy:BWI76_RS20235
          Length = 400

 Score =  773 bits (1997), Expect = 0.0
 Identities = 388/400 (97%), Positives = 393/400 (98%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60
           MSSKLVLVLNCGSSSLKFAI+DAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEA LGAG
Sbjct: 1   MSSKLVLVLNCGSSSLKFAILDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAELGAG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120
           AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVID+SVIQGIKDSASFA
Sbjct: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDDSVIQGIKDSASFA 120

Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180
           PLHNPAHLIGIAEALKSFP LKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG
Sbjct: 121 PLHNPAHLIGIAEALKSFPNLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
           AHGTSHFYVTQEAAK+LNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM
Sbjct: 181 AHGTSHFYVTQEAAKVLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTRSGDIDPAIIFHLHD LGMSVD INKMLTKESGLLGLTEVTSDCRYVEDNY  K DAK
Sbjct: 241 GTRSGDIDPAIIFHLHDALGMSVDAINKMLTKESGLLGLTEVTSDCRYVEDNYQEKADAK 300

Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER
Sbjct: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360

Query: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLAARFGKSGFINKEGTRPA+VIPTNEELVIAQDA+RLTA
Sbjct: 361 NLAARFGKSGFINKEGTRPAIVIPTNEELVIAQDANRLTA 400


Lambda     K      H
   0.318    0.134    0.384 

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: 628
Number of extensions: 9
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 BWI76_RS20235 BWI76_RS20235 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.20970.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20970.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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