GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dyella japonica UNC79MFTsu3.2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate N515DRAFT_2456 N515DRAFT_2456 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2456
          Length = 401

 Score =  258 bits (658), Expect = 3e-73
 Identities = 162/398 (40%), Positives = 223/398 (56%), Gaps = 15/398 (3%)

Query: 5   NGNILVINSGSSSIKYRLIA--LPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQS 62
           NG IL +N+GSSSIK+ L    L  ++++  G +E IG  E R      D   ++    +
Sbjct: 2   NGIILALNAGSSSIKFALHEHRLAAQRLILRGAIEGIGA-EPRFTAWQPDGAIIDREAWA 60

Query: 63  VIAADHHQAFKAVFEILGEN---CSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRI 119
             AA H Q  + +   +        +  +GHRVVHGG  F  P  +D   +  +  L  +
Sbjct: 61  DAAAPHEQLLQPLLAWITARLGAAELAVVGHRVVHGGPSFGQPVRIDTPVMQELERLVSL 120

Query: 120 APLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGF 179
           APLH P  L    +     PG+ QVA FDTAFH+ MP  A    +P   Y+D G+RR+GF
Sbjct: 121 APLHQPHPLAAARAIARLRPGLMQVACFDTAFHRGMPAVAASLGLPRA-YADDGMRRYGF 179

Query: 180 HGTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMG 239
           HG S+ Y+A R  EF  +  D   +I  HLGNGAS  A+ +GRS+DT+MGF+ L+GLVMG
Sbjct: 180 HGLSYEYLAGRLREFAPELAD-GRVIMAHLGNGASLCAMRHGRSIDTTMGFSALDGLVMG 238

Query: 240 TRSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTN-DLRTVLEQTNAGDERAR 298
           +R G LDP   L + Q       AI+  L +ESGL G+ G + D+R +L   +     AR
Sbjct: 239 SRCGSLDPGAVLHLLQARGLSVAAIEHLLYQESGLLGVSGISADMRALLASDSG---HAR 295

Query: 299 LALDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAAN 358
            A++L+ YRI K IGA  +V G +DALVF+ G+GE+AA +R   C  L+ LG+  DE+AN
Sbjct: 296 EAIELFVYRIVKEIGALTSVAGGLDALVFSAGIGEHAASIRSAVCRALAWLGVECDESAN 355

Query: 359 SDVTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVL 396
                 I+    A S  R+ VI+TDEE  IA  A  VL
Sbjct: 356 GLHKMLIS---TAHSAVRVFVIRTDEEAVIAAHAAGVL 390


Lambda     K      H
   0.320    0.137    0.400 

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: 417
Number of extensions: 18
Number of successful extensions: 6
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 N515DRAFT_2456 N515DRAFT_2456 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.22759.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22759.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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