GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_4132 Ga0059261_4132 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= SwissProt::Q8ZPV0
         (492 letters)



>FitnessBrowser__Korea:Ga0059261_4132
          Length = 471

 Score =  472 bits (1214), Expect = e-137
 Identities = 247/457 (54%), Positives = 314/457 (68%), Gaps = 6/457 (1%)

Query: 20  TNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQAIVEKFAALLEAHKAEL 79
           TNP + E LW+G  A+A   A A + AR AFP WA Q   AR AI+ ++AA+L   K  L
Sbjct: 8   TNPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDAL 67

Query: 80  TEVIARETGKPRWEAATEVTAMINKIAISIKAYHARTGAQKSELVDGAATLRHRPHGVLA 139
            E IARETGKP WE ATEV +MI K+AISI+A  AR G ++S +  G A L HRPHGV+A
Sbjct: 68  AEAIARETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMA 127

Query: 140 VFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVIKLWERAGLPAGVLNLVQG 199
           V GPYNFPGHLPNGHIVPALLAGNTL+FKPSE TP  G+ +++    AG+P  V  L+QG
Sbjct: 128 VLGPYNFPGHLPNGHIVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQG 187

Query: 200 GRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKILALEMGGNNPLIIEDAANID 259
           GRETG AL S  D+DGLLFTGSA  G    R  + +P  ILALE+GGNNPL+  D    +
Sbjct: 188 GRETGAALVS-QDIDGLLFTGSAGAGMHFRRSFAERPAVILALELGGNNPLVAWD-GEPE 245

Query: 260 AAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVDVAGRLQPGRWDDDPQPFIG 319
           A   + + S FIT GQRC+CARRL+V +GA GDA +  +  ++ RL+ GRWD+ P+PF+G
Sbjct: 246 AVASIVVASTFITTGQRCSCARRLIVPEGAAGDAIVDAVAALSDRLRIGRWDETPEPFMG 305

Query: 320 GLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTS--LLTPGIIELTGVADVPDEEVF 377
            L+S  AA+           LG R  + P    EG S   + P I+++TG+ +VPDEE+F
Sbjct: 306 PLVSTGAAERAAAQVAALVGLGARE-IRPFGGVEGRSGAFVRPAILDVTGL-EVPDEEIF 363

Query: 378 GPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQLLLEARAGIVNWNKPLTGAA 437
            P+L V R A FD A+  AN TRFGL+ GL+S D A + +   +ARAG+VN N+P TGAA
Sbjct: 364 APVLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNRNRPTTGAA 423

Query: 438 STAPFGGVGASGNHRPSAWYAADYCAWPMASLESPEL 474
           S+ PFGG+G SGNHRPSA+YAADYCA+P+ASLE+  +
Sbjct: 424 SSMPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERI 460


Lambda     K      H
   0.319    0.134    0.411 

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: 711
Number of extensions: 32
Number of successful extensions: 4
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: 492
Length of database: 471
Length adjustment: 34
Effective length of query: 458
Effective length of database: 437
Effective search space:   200146
Effective search space used:   200146
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: 52 (24.6 bits)

Align candidate Ga0059261_4132 Ga0059261_4132 (succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

Software error:

../bin/blast/fastacmd -i /tmp/list.12569.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12569.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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