GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Caulobacter crescentus NA1000

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate CCNA_02325 CCNA_02325 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Caulo:CCNA_02325
          Length = 311

 Score =  320 bits (821), Expect = 2e-92
 Identities = 170/307 (55%), Positives = 206/307 (67%), Gaps = 9/307 (2%)

Query: 4   RHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTR-----PLEGKVLAMIFDKPSTRTRV 58
           RHF DL  +    LR +LDDA  RKA  K   + +     P + +VL+MIF K STRTR 
Sbjct: 5   RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQGKVDADAPAKDRVLSMIFQKNSTRTRF 64

Query: 59  SFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENA 118
           SFD  MRQLGG  I+ T ++MQLGR ETI DTAKVLSR VDA+MIR  SH  +    + +
Sbjct: 65  SFDAAMRQLGGSAIISTASDMQLGRGETIEDTAKVLSRMVDAVMIRANSHADVERFAQVS 124

Query: 119 TVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNL 178
           TVP+INGLTD +HPCQ+MADI+T EEHRGP+AGKTIAW GDGNNV  S + A+    F L
Sbjct: 125 TVPIINGLTDKSHPCQIMADILTIEEHRGPIAGKTIAWVGDGNNVCSSFIHAAPLLGFEL 184

Query: 179 NVAVPEGSEPAQKHIDWSKAHG--GKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGH 236
            +A P     A  H D ++A G  GK+  T  P+ AV  AD VV D WVSMG        
Sbjct: 185 KIACP-AVYHADLH-DLARAEGLQGKVSMTTDPKAAVSGADVVVADTWVSMGDTDHDERL 242

Query: 237 NVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAV 296
               PYQV+ +LM  A  + +F+HCLPAHRGEEVTD V+DGP S+V+DEAENR+HAQK+V
Sbjct: 243 AALEPYQVDDRLMDLAAGNGVFLHCLPAHRGEEVTDAVLDGPRSLVWDEAENRIHAQKSV 302

Query: 297 LAWCLGA 303
           LAWC GA
Sbjct: 303 LAWCFGA 309


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: 335
Number of extensions: 10
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: 311
Length adjustment: 27
Effective length of query: 276
Effective length of database: 284
Effective search space:    78384
Effective search space used:    78384
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 CCNA_02325 CCNA_02325 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.6775.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6775.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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