GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Sphingomonas koreensis DSMZ 15582

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate Ga0059261_1694 Ga0059261_1694 homogentisate 1,2-dioxygenase (EC 1.13.11.5)

Query= SwissProt::Q9X4F5
         (453 letters)



>FitnessBrowser__Korea:Ga0059261_1694
          Length = 441

 Score =  644 bits (1660), Expect = 0.0
 Identities = 296/437 (67%), Positives = 349/437 (79%), Gaps = 2/437 (0%)

Query: 13  SGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERS 72
           S   +A GYMPGFGNDFETE+LPGALPQGQNSPQKC YGLYAEQLSG+ FTAPRG NERS
Sbjct: 3   SHNMQAVGYMPGFGNDFETEALPGALPQGQNSPQKCPYGLYAEQLSGTAFTAPRGQNERS 62

Query: 73  WLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTM 132
           W YRIRPSVRH GRF  ++ PHWK+AP++     +LGQ RW+P+P  +  L +L G+RT+
Sbjct: 63  WCYRIRPSVRHVGRFAAIELPHWKSAPNIVPGVASLGQYRWNPVPHGAGELTWLTGMRTV 122

Query: 133 TTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEI 192
           TTAGD  TQ GMA+H Y   A MVD YF++ADGELL+VP+ G ++  TELG +++ P EI
Sbjct: 123 TTAGDVNTQTGMASHVYLVTASMVDSYFYSADGELLVVPQEGRLRFCTELGVIEIAPGEI 182

Query: 193 CLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYED 252
            ++PRG++++V  +  +   RG++CENYG  F LPDRGPIGANC+ANPRDFKTPVAA+ED
Sbjct: 183 AVLPRGLVYRVEVI--DGPCRGFVCENYGQPFALPDRGPIGANCMANPRDFKTPVAAFED 240

Query: 253 KETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIF 312
           +ETP  + +KWCG FH   I HSPLDVVAWHGNYAPYKYDL T+SPVGAILFDHPDPSIF
Sbjct: 241 RETPSTLTIKWCGQFHQSAIPHSPLDVVAWHGNYAPYKYDLSTYSPVGAILFDHPDPSIF 300

Query: 313 TVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFV 372
           TVLTA S   GTAN+DFV+F  RWLVAEH+FRPPWYH+N+MSE MG IYG YDAK +GF 
Sbjct: 301 TVLTARSEIPGTANIDFVLFRERWLVAEHSFRPPWYHKNVMSELMGNIYGEYDAKPDGFA 360

Query: 373 PGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQ 432
           PGGMSLHN ML HGPD + FEKASN  LKP KLD TM+FMFETRFPQ LT +AA    LQ
Sbjct: 361 PGGMSLHNCMLPHGPDRNAFEKASNAALKPEKLDKTMSFMFETRFPQHLTDWAAREAPLQ 420

Query: 433 DDYMDCWSGLERKFDGT 449
            DY DCW GL++KFDG+
Sbjct: 421 SDYADCWDGLDKKFDGS 437


Lambda     K      H
   0.320    0.138    0.442 

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: 829
Number of extensions: 37
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: 453
Length of database: 441
Length adjustment: 33
Effective length of query: 420
Effective length of database: 408
Effective search space:   171360
Effective search space used:   171360
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 Ga0059261_1694 Ga0059261_1694 (homogentisate 1,2-dioxygenase (EC 1.13.11.5))
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.19203.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19203.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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