GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxC in Cupriavidus basilensis 4G11

Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate RR42_RS35130 RR42_RS35130 benzoyl-CoA-dihydrodiol lyase

Query= SwissProt::Q84HH6
         (555 letters)



>FitnessBrowser__Cup4G11:RR42_RS35130
          Length = 552

 Score =  749 bits (1933), Expect = 0.0
 Identities = 371/550 (67%), Positives = 439/550 (79%), Gaps = 5/550 (0%)

Query: 10  AELVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDAL 69
           A  V+Y+T+PS+Y+H  L  DG IATL ++IDE+ G+RPGYKLKLNSYDLGVDIEL+DA+
Sbjct: 4   APRVEYQTDPSQYKHLKLTFDGPIATLAVDIDENAGLRPGYKLKLNSYDLGVDIELNDAV 63

Query: 70  QRVRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQY 129
            R+RFEHPEVRTVVVTSGK K+FCSGANI+MLG+S+H+WKVNFCKFTNETRNG+EDSS++
Sbjct: 64  NRIRFEHPEVRTVVVTSGKDKVFCSGANIFMLGVSSHSWKVNFCKFTNETRNGLEDSSKH 123

Query: 130 SGLKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDK 189
           SGLKFLAA NG  AGGGYELALACDEI+LVDDR+S+VSLPEVPLLGVLPGTGGLTRVTDK
Sbjct: 124 SGLKFLAAVNGACAGGGYELALACDEIILVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDK 183

Query: 190 RRVRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAK 249
           R VR D ADIFCT +EGVRGQRAKDWRLVDD+ K   FA+ +Q RA+ALA  SDRPA A 
Sbjct: 184 RHVRHDLADIFCTTTEGVRGQRAKDWRLVDDIAKPAVFAQKVQERAQALAALSDRPANAS 243

Query: 250 GVKLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPL 309
           GV LT L RT++     Y +V   ID  GR  T TV+ P+A    + A I   G  W+PL
Sbjct: 244 GVALTPLARTLETDALRYTYVTVEIDRVGRKATFTVKGPSATQPTSVAAIAEAGAAWYPL 303

Query: 310 QMARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRT 369
           Q+AREL+DAIL++RTN LD+G W ++TEGDA  VL +DAT+ AN+D+W VRETIG+LRRT
Sbjct: 304 QLARELEDAILSMRTNELDIGTWLIKTEGDAANVLAMDATLLANQDHWLVRETIGLLRRT 363

Query: 370 LARIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML----DAAEAKNVVGLSAMNFGT 425
            +R+DVSSRSL+ALIEPGSCFAGT LE+ALA DRSY L    D A A  +  ++  NFG 
Sbjct: 364 FSRLDVSSRSLFALIEPGSCFAGTFLELALACDRSYHLALPDDEARAPRIT-VAETNFGL 422

Query: 426 FPMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAI 485
           +PMV G SR+  RFY E+  + AV+AK G  L    A  +GLVTA PDD+DW +EVRIA+
Sbjct: 423 YPMVTGQSRLGRRFYDEQPALDAVRAKAGQPLDADAAFAVGLVTANPDDIDWTDEVRIAL 482

Query: 486 EERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSG 545
           EERAA+SPDALTG+EANLRF   E M TRIFGRL+AWQNWIF RPNAVGE GALK++G G
Sbjct: 483 EERAAMSPDALTGMEANLRFNGQENMFTRIFGRLTAWQNWIFQRPNAVGEKGALKVYGKG 542

Query: 546 KKAQFDWNRV 555
            KA FDWNRV
Sbjct: 543 DKAAFDWNRV 552


Lambda     K      H
   0.318    0.134    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: 830
Number of extensions: 28
Number of successful extensions: 2
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: 555
Length of database: 552
Length adjustment: 36
Effective length of query: 519
Effective length of database: 516
Effective search space:   267804
Effective search space used:   267804
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate RR42_RS35130 RR42_RS35130 (benzoyl-CoA-dihydrodiol lyase)
to HMM TIGR03222 (boxC: benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))

Software error:

../bin/blast/fastacmd -i /tmp/list.3982.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3982.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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