GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Dyella japonica UNC79MFTsu3.2

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate N515DRAFT_0361 N515DRAFT_0361 homogentisate 1,2-dioxygenase

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



>FitnessBrowser__Dyella79:N515DRAFT_0361
          Length = 430

 Score =  652 bits (1682), Expect = 0.0
 Identities = 302/425 (71%), Positives = 345/425 (81%)

Query: 20  TPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRI 79
           T GYQSGF NEFATEA+ G LP GQNSPQR  +GLYAEQ+SG+AFTAPR  NRRSW YRI
Sbjct: 3   TKGYQSGFGNEFATEAVAGVLPHGQNSPQRVAHGLYAEQLSGSAFTAPRHSNRRSWLYRI 62

Query: 80  RAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
           R AA+H PF         + FD  P +PNQ+RW P  +P  PTDFVDG++T+AGNGGP  
Sbjct: 63  RPAAVHRPFEPRAHEHFHNRFDEAPATPNQLRWDPWPLPARPTDFVDGLVTLAGNGGPAE 122

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
            +GCGIH+Y ANRSM  RFFY+ADGE+L+VPQQGRLR+ TE+G+LDV P EI VIPRGVR
Sbjct: 123 QAGCGIHIYAANRSMLGRFFYDADGELLLVPQQGRLRVCTELGVLDVAPLEIAVIPRGVR 182

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           FRVEL DGEARGY+CEN+GAL RLPDLG IG+N +A PRDFLTP AWYED EGDFEL+AK
Sbjct: 183 FRVELIDGEARGYVCENFGALLRLPDLGPIGANSMALPRDFLTPQAWYEDVEGDFELIAK 242

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
           FQG+LW AAI HSPLDVVAWHGNYAPYKYDL  +NT+GSIS DHPDPSIF VL SPSDTP
Sbjct: 243 FQGSLWTAAIDHSPLDVVAWHGNYAPYKYDLTTYNTVGSISVDHPDPSIFTVLTSPSDTP 302

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           G  ++DFVIF PRWL  ++TFRPP+FHRN+ASEFMGLI+G YDAK  GF PGGASLHNCM
Sbjct: 303 GTANVDFVIFPPRWLVAEHTFRPPYFHRNVASEFMGLIQGAYDAKEGGFVPGGASLHNCM 362

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           SGHGPDA +F KA+ AD S+P  +  TMAFMFET  VIRPT  A ++ QLQ  YY CWQG
Sbjct: 363 SGHGPDAASFEKASGADVSKPDHLTGTMAFMFETRKVIRPTRQALDAPQLQGSYYECWQG 422

Query: 440 LKKHF 444
           ++KHF
Sbjct: 423 IRKHF 427


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: 803
Number of extensions: 27
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: 449
Length of database: 430
Length adjustment: 32
Effective length of query: 417
Effective length of database: 398
Effective search space:   165966
Effective search space used:   165966
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 N515DRAFT_0361 N515DRAFT_0361 (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.23699.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23699.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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