GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Sphingomonas koreensis DSMZ 15582

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Ga0059261_3206 Ga0059261_3206 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Korea:Ga0059261_3206
          Length = 307

 Score =  308 bits (789), Expect = 1e-88
 Identities = 162/308 (52%), Positives = 203/308 (65%), Gaps = 10/308 (3%)

Query: 1   MSVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGE------RTRPLEGKVLAMIFDKPST 54
           M+ R+F  LS      +  ML DA+ RK R +AG+         PL G+ LAM+F+K ST
Sbjct: 1   MTYRNFLSLSDAGADGIAAMLADAIDRK-RARAGQPKGAVDADAPLAGRTLAMVFEKNST 59

Query: 55  RTRVSFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLEL 114
           RTRVSF++ +RQLGG  ++L     QLGR ET+ADTA+VLS Y DAIM+RT  H +LLE+
Sbjct: 60  RTRVSFEMAIRQLGGSAVVLDAATSQLGRGETVADTARVLSGYCDAIMVRTDDHAKLLEM 119

Query: 115 TENATVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARF 174
            + ATVPVINGLTDD+HPCQ+MAD+ T  E    + G  +AW GDGNNVL S++EA+   
Sbjct: 120 AQYATVPVINGLTDDSHPCQIMADLQTILESGKALPGLKVAWLGDGNNVLASIVEAAGLM 179

Query: 175 RFNLNVAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRAR 234
            F++  A P+     ++ +   K   G+      P EAV  AD VVTD W+SMGQ H   
Sbjct: 180 HFDVVAACPQSFALPEEAMALGK---GRARTVNDPVEAVAGADVVVTDTWISMGQAHADV 236

Query: 235 GHNVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQK 294
                +PYQV   LMA A PDA F+HCLPAHRGEEVTD VIDGP S+++ EAENRLHAQK
Sbjct: 237 KLAALAPYQVTEALMAQASPDAKFLHCLPAHRGEEVTDAVIDGPQSLIWPEAENRLHAQK 296

Query: 295 AVLAWCLG 302
           AVL WC G
Sbjct: 297 AVLRWCFG 304


Lambda     K      H
   0.320    0.133    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: 321
Number of extensions: 14
Number of successful extensions: 3
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: 303
Length of database: 307
Length adjustment: 27
Effective length of query: 276
Effective length of database: 280
Effective search space:    77280
Effective search space used:    77280
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: 48 (23.1 bits)

Align candidate Ga0059261_3206 Ga0059261_3206 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.11805.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11805.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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