GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pobA in Sphingomonas koreensis DSMZ 15582

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Ga0059261_0531 Ga0059261_0531 4-hydroxybenzoate 3-monooxygenase

Query= reanno::Cup4G11:RR42_RS21940
         (389 letters)



>FitnessBrowser__Korea:Ga0059261_0531
          Length = 389

 Score =  459 bits (1181), Expect = e-134
 Identities = 226/387 (58%), Positives = 281/387 (72%)

Query: 1   MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60
           MRTQVAI+GAGP+GLLLG LL +AG+D VIVE++S  Y+LGRIRAG+LE+VT D + R G
Sbjct: 1   MRTQVAIVGAGPSGLLLGHLLLQAGVDCVIVERQSASYVLGRIRAGVLETVTTDLMTRLG 60

Query: 61  VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI 120
           +  R+  +GL+  G  L+      RID  AL GR V VYGQTE+TRDLM A +      +
Sbjct: 61  IDARMNAEGLIEQGFNLATSDRVIRIDIAALTGRHVMVYGQTELTRDLMDAARDRGLEIV 120

Query: 121 YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY 180
           Y+A+DV++HD ++  P V Y K G+   + C FIAGCDGFHG +RR++P  + R +ER Y
Sbjct: 121 YEAKDVALHDVESGAPYVTYAKDGKAQRIDCAFIAGCDGFHGPSRRAIPASAAREYEREY 180

Query: 181 PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD 240
           PFGWLG+LAD PP   ELIYA+ ++GFAL SMRS TRSRYY+QV   +RVEDWS++R WD
Sbjct: 181 PFGWLGILADVPPCHPELIYANTDQGFALASMRSATRSRYYIQVPLTDRVEDWSEERLWD 240

Query: 241 ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL 300
           EL +R D  ++  +  G ++E SIAPLRS+V E MR G LFLAGD+AHIVPPTGAKGLNL
Sbjct: 241 ELAARFDPLSSAGVTRGPALEMSIAPLRSYVFETMRHGRLFLAGDSAHIVPPTGAKGLNL 300

Query: 301 AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL 360
           AASDV YL+  LIA + R D   L  Y  K L R+WKAERFSW++T L+HRFPD   F  
Sbjct: 301 AASDVAYLSTALIAFFARGDEEGLAGYQAKALARIWKAERFSWYLTKLMHRFPDDGSFEH 360

Query: 361 RIQQAELDYLAGSRAAQMSLAENYVGL 387
           R+Q AELDYLA S A Q  +AENYVGL
Sbjct: 361 RMQAAELDYLAHSEAMQRVIAENYVGL 387


Lambda     K      H
   0.323    0.137    0.414 

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: 422
Number of extensions: 16
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: 389
Length of database: 389
Length adjustment: 30
Effective length of query: 359
Effective length of database: 359
Effective search space:   128881
Effective search space used:   128881
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: 50 (23.9 bits)

Align candidate Ga0059261_0531 Ga0059261_0531 (4-hydroxybenzoate 3-monooxygenase)
to HMM TIGR02360 (pobA: 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.29073.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29073.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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