GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Dechlorosoma suillum PS

Align Malate synthase (EC 2.3.3.9) (characterized)
to candidate Dsui_0019 Dsui_0019 malate synthase A

Query= reanno::BFirm:BPHYT_RS12305
         (536 letters)



>FitnessBrowser__PS:Dsui_0019
          Length = 532

 Score =  766 bits (1979), Expect = 0.0
 Identities = 374/529 (70%), Positives = 438/529 (82%), Gaps = 5/529 (0%)

Query: 10  SLQLPQGMEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGER 69
           SL LP GM+ITA I+P Y++IL+ EALE VA LHR FE RRQ+LL+AR ER  R+DAGE 
Sbjct: 2   SLNLPAGMQITAPIQPQYESILTLEALEFVAKLHRAFEGRRQELLKARVERQARIDAGEM 61

Query: 70  PDFLAETKSVRDGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNA 129
           PDFL ETK +R+GDW +APLP  L+ RR EITGPVE KMIINA NSGADSYMTDFEDSN+
Sbjct: 62  PDFLPETKHIREGDWKVAPLPAALERRRTEITGPVEAKMIINAFNSGADSYMTDFEDSNS 121

Query: 130 PSWDNQITGHINLKDAVRRTISLEQN-GKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKR 188
           P+WDNQI G +NL  A+RR +S +   GK Y LND++ATL +RPRGWHLDEKHV VDG+R
Sbjct: 122 PNWDNQIQGQVNLYQAIRRQLSFKNEAGKEYKLNDQIATLQIRPRGWHLDEKHVTVDGQR 181

Query: 189 VSGGIFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTI 248
           V+GGIFDFAL   HNAKE +ARG+GP++YLPKMESHLEARLWNDIFV AQ+ +G+P+GTI
Sbjct: 182 VAGGIFDFALVFFHNAKEQIARGAGPFYYLPKMESHLEARLWNDIFVMAQDHIGLPQGTI 241

Query: 249 RATVLIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITM 308
           +ATVL+ETI+A FEM+EILYELR HS+GLNAGRWDYIFS IKKFK ++DFCLA R  ITM
Sbjct: 242 KATVLVETILATFEMEEILYELRNHSAGLNAGRWDYIFSCIKKFKKNKDFCLAQRGVITM 301

Query: 309 TSPFMRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYD 368
             PFMR+YAL L++ CH+R APA+GGMSALIPIKNDP AN+KA++G+R DKARDA DG+D
Sbjct: 302 EVPFMRSYALALVQACHKRGAPAMGGMSALIPIKNDPVANEKALAGIRHDKARDAKDGFD 361

Query: 369 GGWVAHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNI 428
           GGWVAHPGLV IA EEFVKVLGDKPNQ  KQ +       D  +F+PE PITE GLRNNI
Sbjct: 362 GGWVAHPGLVSIAHEEFVKVLGDKPNQWEKQVEGSF-GPKDWLNFQPEQPITEAGLRNNI 420

Query: 429 NVGIHYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVRE 488
           NVGIHYLG+WLAGNGCVPIHNLMEDAATAEISRSQVWQW+ SPKG L+DGRKVT E+VR 
Sbjct: 421 NVGIHYLGSWLAGNGCVPIHNLMEDAATAEISRSQVWQWVVSPKGILDDGRKVTVEMVRP 480

Query: 489 LSAQELEKVKQAV---GGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYE 534
           + A+EL KVK  V   G DT  Y++AA IF++MS +  + +FLTLPLYE
Sbjct: 481 MIAEELAKVKATVAAQGEDTATYDQAAVIFDKMSLTPDYPEFLTLPLYE 529


Lambda     K      H
   0.318    0.134    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: 808
Number of extensions: 17
Number of successful extensions: 5
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: 536
Length of database: 532
Length adjustment: 35
Effective length of query: 501
Effective length of database: 497
Effective search space:   248997
Effective search space used:   248997
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: 52 (24.6 bits)

Align candidate Dsui_0019 Dsui_0019 (malate synthase A)
to HMM TIGR01344 (aceB: malate synthase A (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.22373.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22373.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.