GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Burkholderia phytofirmans PsJN

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate BPHYT_RS26200 BPHYT_RS26200 acetate kinase

Query= SwissProt::P74879
         (404 letters)



>FitnessBrowser__BFirm:BPHYT_RS26200
          Length = 386

 Score =  243 bits (621), Expect = 5e-69
 Identities = 157/398 (39%), Positives = 206/398 (51%), Gaps = 28/398 (7%)

Query: 5   IMAINAGSSSLKFQLLEMPQGD--MLCQGLIERIGMADAQVTIKTHSQKW--QETVPVAD 60
           I+ +N+GSSSLKF L      D  +L +G  E IG  D  + IK    +   Q+   +  
Sbjct: 12  ILVLNSGSSSLKFGLFRRAGNDESLLLEGSAEGIGRDDGSLRIKAPDGRVLVQQERVLES 71

Query: 61  HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAELAP 120
             DA+  L + L              VGHRV HGG   +    +T +   Q+      AP
Sbjct: 72  QIDALQKLAQVLKEQHHARPA----AVGHRVVHGGPRLRTHQRITADVRRQLHEAVHFAP 127

Query: 121 LHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGFHG 180
           LH P     I    ++  DAP  A FDTAFH TL   A    LP   YAE G+ RYGFHG
Sbjct: 128 LHIPPALALIDEAEKIFDDAPHFACFDTAFHATLPLRAAHLALP-RRYAEAGVMRYGFHG 186

Query: 181 TSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMGTR 240
            S++     L  +LG  L A R +  HLGNGSS+CA+++GRS++TSMG TP  GV MGTR
Sbjct: 187 LSYES----LVTRLGADLPA-RAVFAHLGNGSSVCALRDGRSIDTSMGLTPTGGVPMGTR 241

Query: 241 SGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAKLA 300
           SGD+DP +L ++ + E      L  LLN +SGL G +   SD + +E+ A  G+  A LA
Sbjct: 242 SGDLDPGVLLYLMRVEKLDAGALETLLNRQSGLAGYADGESDMQALEKRAAAGDTNASLA 301

Query: 301 LTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKNQR 360
           L  FA  +R TIG Y   +GG+D LVFTGGIGE+S   R  VC  L F+GL   +     
Sbjct: 302 LDAFATAVRKTIGGYAALLGGIDLLVFTGGIGEHSQEIRKRVCDGLAFMGLTQSDPAG-- 359

Query: 361 NATFIQTENALVKVAVINTNEELMIAQDVMRIALPATE 398
                       KV  I+T EE  IA+    +   AT+
Sbjct: 360 ------------KVRAIHTEEEKQIARHCRTLLQQATQ 385


Lambda     K      H
   0.319    0.135    0.392 

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: 371
Number of extensions: 14
Number of successful extensions: 4
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: 386
Length adjustment: 31
Effective length of query: 373
Effective length of database: 355
Effective search space:   132415
Effective search space used:   132415
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: 50 (23.9 bits)

Align candidate BPHYT_RS26200 BPHYT_RS26200 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.26655.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26655.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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