GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Echinicola vietnamensis KMM 6221, DSM 17526

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate Echvi_1518 Echvi_1518 chorismate synthase

Query= BRENDA::B5AAU3
         (442 letters)



>FitnessBrowser__Cola:Echvi_1518
          Length = 360

 Score =  420 bits (1080), Expect = e-122
 Identities = 211/352 (59%), Positives = 263/352 (74%), Gaps = 5/352 (1%)

Query: 55  GNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKET 114
           GN FG  F+++T+GESHG G+G +I GCP  +P+ E  ++ +L RR+PGQS+ITT RKE 
Sbjct: 2   GNSFGKVFKISTFGESHGKGLGVIIDGCPAGLPIDEAFIRQELQRRKPGQSKITTQRKEE 61

Query: 115 DTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQG 174
           D C+ILSG +EG +TGTPI + + NTDQ+  DY+ +A  YRPSHAD TY  K+GVR  +G
Sbjct: 62  DECQILSGVFEGKSTGTPIAIVIMNTDQKSKDYSHIADKYRPSHADYTYQEKFGVRDYRG 121

Query: 175 GGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIES 234
           GGRSSARET  RVAAGAVAK  LK   GVEI A+VS+   + L +    Y+ L   +IE 
Sbjct: 122 GGRSSARETAARVAAGAVAKLFLK-HIGVEINAYVSQAGHIKLDK---PYQELDFAEIEK 177

Query: 235 NICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAML 294
           NI RCPDPE AQ MID ID++R N +++GGVV+C+A+NVP GLG PVFD+L A L K+ML
Sbjct: 178 NIVRCPDPEVAQDMIDYIDEIRKNRDTVGGVVSCVAKNVPVGLGEPVFDRLHADLGKSML 237

Query: 295 SLPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKV 354
           S+ A KGFE GSGF G  + GSEHND FYMD G  VRT+TN SGG+QGGISNGE IYF+V
Sbjct: 238 SINAVKGFEYGSGFEGVTMLGSEHNDAFYMD-GDTVRTKTNHSGGIQGGISNGEDIYFRV 296

Query: 355 AFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMD 406
           AFKP ATI K Q++V +  + + +  +GRHDPCVVPRAVP+VE MAALVL D
Sbjct: 297 AFKPVATIMKDQDSVNQAGDQVTVSGKGRHDPCVVPRAVPIVEAMAALVLAD 348


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: 457
Number of extensions: 18
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: 360
Length adjustment: 31
Effective length of query: 411
Effective length of database: 329
Effective search space:   135219
Effective search space used:   135219
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 Echvi_1518 Echvi_1518 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.4812.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4812.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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