GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Shewanella sp. ANA-3

Align phosphogluconate dehydratase (characterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__ANA3:7024978
          Length = 608

 Score =  814 bits (2103), Expect = 0.0
 Identities = 406/598 (67%), Positives = 487/598 (81%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           M+  +  VT+RII RS+ +R AYLA +  A+   VHRS L+CGNLAHGFAAC P+DK SL
Sbjct: 1   MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACSPDDKNSL 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           + + + NI IIT++NDMLSAHQPYE YPE+++KA  E  +V QVAGGVPAMCDGVTQGQ 
Sbjct: 61  RQLTKANIGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQP 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAM+ AVGLSHNMFDGAL LG+CDKIVPGL + ALSFGHLP +FVP+GP
Sbjct: 121 GMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M SG+PNKEK RIRQ +A+GKVDR  LLE+EA SYH+ GTCTFYGTAN+NQ+++E MG+Q
Sbjct: 181 MKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFV+PD PLR+AL   AA+QV R+T  G ++ PIG++++EK VVNGIVALLATGGS
Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGGS 300

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TN TMH+VA ARAAGI +NWDDFS+LSD VPL+AR+YPNG ADINHF AAGG+  L++EL
Sbjct: 301 TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL 360

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
           L AGLLHEDVNTVAGFGL RYT EP L +GEL W +G   SLD+ V+ S   PF ++GG 
Sbjct: 361 LDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGL 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           K+L GNLGRAV+K SAV  +++V+EAPAVV + Q+ +   F++G LDRDCVVVV+ QGPK
Sbjct: 421 KLLKGNLGRAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPK 480

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKL P LG L D+ FK+AL+TDGR+SGASGKVP+AIH+TPEA DGGL+AKV+D
Sbjct: 481 ANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD 540

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGA 598
           GD+IRV+  TGEL+LLV +AELAAR     DL  SR G GRELF ALR  LS  E GA
Sbjct: 541 GDLIRVDALTGELSLLVSDAELAARTAAEIDLRHSRYGMGRELFGALRSNLSSPETGA 598


Lambda     K      H
   0.318    0.134    0.392 

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: 1058
Number of extensions: 30
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: 603
Length of database: 608
Length adjustment: 37
Effective length of query: 566
Effective length of database: 571
Effective search space:   323186
Effective search space used:   323186
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate 7024978 Shewana3_2149 (phosphogluconate dehydratase (RefSeq))
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.24452.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24452.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.