GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Cupriavidus basilensis 4G11

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate RR42_RS31275 RR42_RS31275 homogentisate 1,2-dioxygenase

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



>FitnessBrowser__Cup4G11:RR42_RS31275
          Length = 449

 Score =  943 bits (2437), Expect = 0.0
 Identities = 449/449 (100%), Positives = 449/449 (100%)

Query: 1   MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60
           MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS
Sbjct: 1   MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60

Query: 61  GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120
           GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE
Sbjct: 61  GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120

Query: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180
           PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE
Sbjct: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180

Query: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240
           MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF
Sbjct: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240

Query: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300
           LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS
Sbjct: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300

Query: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360
           FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV
Sbjct: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360

Query: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420
           YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT
Sbjct: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420

Query: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449
           PYAAESAQLQDDYYRCWQGLKKHFNPNER
Sbjct: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449


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: 973
Number of extensions: 31
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: 449
Length adjustment: 33
Effective length of query: 416
Effective length of database: 416
Effective search space:   173056
Effective search space used:   173056
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 RR42_RS31275 RR42_RS31275 (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.12485.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12485.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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