GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N2E3

Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate AO353_04155 AO353_04155 ornithine carbamoyltransferase

Query= SwissProt::Q02047
         (306 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04155
          Length = 306

 Score =  538 bits (1386), Expect = e-158
 Identities = 268/306 (87%), Positives = 284/306 (92%)

Query: 1   MNARHFLSMMDYTPDELLGLIRRGVELKDLRIRGELFEPLKNRVLGMIFEKSSTRTRLSF 60
           M+ARHFLS+MD TP+EL+ +IRRG+ELKDLR RG LFEPLKNRVLGMIFEKSSTRTRLSF
Sbjct: 1   MSARHFLSLMDCTPEELVSVIRRGIELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRLSF 60

Query: 61  EAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSRV 120
           EAGMIQLGGQAIFLS RDTQLGRGEPI D A VMSRMLDAVMIRT+AHS LTEFAANSRV
Sbjct: 61  EAGMIQLGGQAIFLSPRDTQLGRGEPIGDCAIVMSRMLDAVMIRTFAHSTLTEFAANSRV 120

Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180
           PVINGLSDDLHPCQLLADMQTFLEHRGSI+GKTVAWIGDGNNMCNSYIEAAIQFDFQLR+
Sbjct: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAIQFDFQLRI 180

Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240
           ACP GYEPNPEF+A AG+RVTIVRDP+ AV GAHLVSTDVWTSMGQEEETA+R+ LFAPF
Sbjct: 181 ACPEGYEPNPEFVAKAGDRVTIVRDPREAVRGAHLVSTDVWTSMGQEEETAKRLKLFAPF 240

Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300
           QV RA LDLA  DVLFMHCLPAHRGEEIS+DLLDD RSVAWDQAENRLHAQKALLEFLV 
Sbjct: 241 QVNRALLDLAAADVLFMHCLPAHRGEEISLDLLDDPRSVAWDQAENRLHAQKALLEFLVP 300

Query: 301 PSHQRA 306
           PS+  A
Sbjct: 301 PSYHHA 306


Lambda     K      H
   0.322    0.135    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: 370
Number of extensions: 4
Number of successful extensions: 1
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate AO353_04155 AO353_04155 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.30723.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30723.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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