GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Pedobacter sp. GW460-11-11-14-LB5

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate CA265_RS11645 CA265_RS11645 chorismate synthase

Query= BRENDA::B5AAU3
         (442 letters)



>FitnessBrowser__Pedo557:CA265_RS11645
          Length = 365

 Score =  370 bits (950), Expect = e-107
 Identities = 192/362 (53%), Positives = 245/362 (67%), Gaps = 3/362 (0%)

Query: 54  AGNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKE 113
           AGN FG  F++ T+GESHG  +G +I GCP ++ +  + +Q +LD+R+PGQS+ITT RKE
Sbjct: 2   AGNSFGQLFRITTFGESHGVAIGVIIDGCPAQLDIDMDFIQSELDKRKPGQSKITTQRKE 61

Query: 114 TDTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQ 173
           +DT +ILSG +EG +TGTPI + +PN DQR  DY      YRPSHAD  YD KYG+R  +
Sbjct: 62  SDTVQILSGVFEGKSTGTPIALLIPNEDQRSKDYGHNVDVYRPSHADYVYDAKYGIRDHR 121

Query: 174 GGGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIE 233
           GGGRSSARET  RVAAGA+AK  LK + G+EI A V+ V  +  P    +  +  L   E
Sbjct: 122 GGGRSSARETAARVAAGAIAKLFLKQQ-GIEIFAHVTSVGTIEAPNLESNDLSALLQIRE 180

Query: 234 SNICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAM 293
            NI RC DP  A +MI+ ID VR +G+++GG + C+ +  P GLG PVFDKL A L KAM
Sbjct: 181 ENIVRCADPATAHEMIEFIDSVRKDGDTVGGKIGCVVKGCPAGLGEPVFDKLHADLGKAM 240

Query: 294 LSLPASKGFEIGSGFAGTDLTGSEHND--EFYMDEGGNVRTRTNRSGGVQGGISNGETIY 351
           LS+ A  GFE GSGFAG++L GS+HND  +    +    +T TN +GG+ GGISNG  I 
Sbjct: 241 LSINAVHGFEYGSGFAGSELRGSQHNDIPQPKAADSKVFKTTTNYAGGILGGISNGMDIT 300

Query: 352 FKVAFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAH 411
           FKVAFKP ATI   Q T+    E  E+  +GRHDPCVVPRAV +VE MAALVL DQ + +
Sbjct: 301 FKVAFKPVATIMHNQQTINAAGEASEIKGKGRHDPCVVPRAVVIVEAMAALVLADQFLRN 360

Query: 412 VA 413
            A
Sbjct: 361 KA 362


Lambda     K      H
   0.317    0.135    0.396 

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: 436
Number of extensions: 23
Number of successful extensions: 4
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: 442
Length of database: 365
Length adjustment: 31
Effective length of query: 411
Effective length of database: 334
Effective search space:   137274
Effective search space used:   137274
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: 50 (23.9 bits)

Align candidate CA265_RS11645 CA265_RS11645 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.28559.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28559.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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