GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Cupriavidus basilensis 4G11

Align propionate kinase (EC 2.7.2.15) (characterized)
to candidate RR42_RS03800 RR42_RS03800 acetate kinase

Query= BRENDA::O06961
         (402 letters)



>FitnessBrowser__Cup4G11:RR42_RS03800
          Length = 408

 Score =  262 bits (669), Expect = 2e-74
 Identities = 167/405 (41%), Positives = 243/405 (60%), Gaps = 27/405 (6%)

Query: 5   PVVLVINCGSSSIKFSVLDV-----ATCD---VLMA-------GIADGMNTENAFLSING 49
           P +LV+N GSSS+K SV  V     A  D   VL A       G++  ++   A   I  
Sbjct: 6   PTILVVNAGSSSVKVSVYAVPEAAHANADINPVLSAHGQIEGIGVSPRLSASMADGRIVA 65

Query: 50  DKPINLAH-SNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNI 108
           D+   +A  ++++ A + I   L           IGHR+ HGG  F+ +V I D++I  +
Sbjct: 66  DERFPVAQVADHDAAFRLIRLVLSIGLRDAPPVAIGHRVVHGGADFSAAVKIDDDVITKL 125

Query: 109 RRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLG 168
             + PLAPLH   NL+ I A R   PA+ QVA FDT+FH    P A L  LP+EYF   G
Sbjct: 126 EALIPLAPLHQPHNLTAIRAVRAAVPALLQVACFDTAFHAGHDPLAQLLALPYEYFER-G 184

Query: 169 VRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPL 228
           +RRYGFHG S+ Y++RR  ++   D     +IVAHLGNGAS+CA+R+G+SV+++MG+T L
Sbjct: 185 IRRYGFHGLSYEYIARRLQQIAP-DLAQGRVIVAHLGNGASLCAMRDGRSVESTMGLTAL 243

Query: 229 EGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHE 288
           +GL MGTR G +D GA+ W++++ G +  D+E ++ +ESGL G+SG+SSD+R L  +   
Sbjct: 244 DGLPMGTRCGAIDAGAILWLSQQ-GMSTKDIETMLYQESGLKGLSGVSSDMRALLAS--- 299

Query: 289 GHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLG-VLGL 347
              RARLAI  + +R A+ I   AA+L  LD ++FT GIG NS  +R+ +   L  + G+
Sbjct: 300 DAPRARLAIDFYAYRAAQEIGKLAATLGGLDALVFTAGIGANSPPVREKICARLADLFGI 359

Query: 348 TLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHL 392
           +LD   N   N + +R IS + S+V   V+PT+EE MIAL+   +
Sbjct: 360 SLDAGAN---NENRQR-ISRDNSRVPVLVLPTDEEGMIALNTARI 400


Lambda     K      H
   0.320    0.137    0.397 

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: 396
Number of extensions: 20
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: 402
Length of database: 408
Length adjustment: 31
Effective length of query: 371
Effective length of database: 377
Effective search space:   139867
Effective search space used:   139867
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 RR42_RS03800 RR42_RS03800 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.10170.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10170.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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