GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Paraburkholderia bryophila 376MFSha3.1

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate H281DRAFT_04741 H281DRAFT_04741 homogentisate 1,2-dioxygenase

Query= reanno::Cup4G11:RR42_RS31275
         (449 letters)



>FitnessBrowser__Burk376:H281DRAFT_04741
          Length = 448

 Score =  723 bits (1865), Expect = 0.0
 Identities = 339/430 (78%), Positives = 377/430 (87%), Gaps = 1/430 (0%)

Query: 21  PGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIR 80
           PGYQSGF NEFATEALPGALP G+NSPQRA YGLYAEQ+SGTAFTAPR HNRR+W YRIR
Sbjct: 19  PGYQSGFGNEFATEALPGALPEGRNSPQRAAYGLYAEQLSGTAFTAPRGHNRRTWLYRIR 78

Query: 81  AAAMHEPFTRVEQSRIVSHFDAVPPSP-NQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
            AA+H+PFT +   R+V++F  VPP+P NQ+RW    MP EPTDFVDG +TMAGNG  ++
Sbjct: 79  PAAVHKPFTPLPSERLVANFAEVPPTPPNQLRWDALPMPGEPTDFVDGWVTMAGNGAADS 138

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
           MSGC IHLY ANRSMTDRFFY+ADGE+LIVPQ+GRL +ATE+G L+V P EI VIPRGVR
Sbjct: 139 MSGCAIHLYAANRSMTDRFFYSADGELLIVPQEGRLDIATELGRLEVRPFEIAVIPRGVR 198

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           F V LPDG ARGYICEN+GAL RLPDLG IGSNGLANPRDFLTPHA YEDREGDFELVAK
Sbjct: 199 FAVSLPDGTARGYICENFGALLRLPDLGPIGSNGLANPRDFLTPHAAYEDREGDFELVAK 258

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
             GNLWRA IGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQS SDTP
Sbjct: 259 MNGNLWRADIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSQSDTP 318

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           GVDS+DFVIF PRWLA ++TFRPPWFHRN+ASEFMGL+ GVYDAKA+GF PGGASLHNCM
Sbjct: 319 GVDSLDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGVYDAKAEGFVPGGASLHNCM 378

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           SGHGPDA+TF KA+ +DTS+P ++GDTMAFMFET  +I+PT +A E+AQLQ  YY CWQG
Sbjct: 379 SGHGPDADTFEKASHSDTSKPVKVGDTMAFMFETRTLIKPTRFALETAQLQAHYYECWQG 438

Query: 440 LKKHFNPNER 449
           LKKHFNP +R
Sbjct: 439 LKKHFNPEQR 448


Lambda     K      H
   0.320    0.138    0.439 

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: 852
Number of extensions: 33
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: 449
Length of database: 448
Length adjustment: 33
Effective length of query: 416
Effective length of database: 415
Effective search space:   172640
Effective search space used:   172640
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_04741 H281DRAFT_04741 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.32662.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32662.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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