GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Shewanella loihica PV-4

Align phosphogluconate dehydratase (characterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__PV4:5209582
          Length = 608

 Score =  805 bits (2079), Expect = 0.0
 Identities = 399/602 (66%), Positives = 486/602 (80%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           M+  +  VT+RII RS+ TR+ YLA + +AK + VHRS L+CGNLAHGFAAC P DK ++
Sbjct: 1   MHSVVQSVTDRIIARSQATRAKYLAALGEAKANGVHRSSLSCGNLAHGFAACSPADKNAI 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           K+  + NI I+T++NDMLSAHQPYEHYP++++ A HE  +V QVA GVPAMCDGVTQGQ 
Sbjct: 61  KAFNKANIGIVTAFNDMLSAHQPYEHYPQLLKDACHEVGSVAQVAAGVPAMCDGVTQGQP 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAMS AVGLSHNMFDGAL LG+CDKIVPGL + ALSFGHLP +FVP+GP
Sbjct: 121 GMELSLLSREVIAMSTAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M SG+PNKEK R+RQ +A+G+VDR ALLE+E+ SYH+ GTCTFYGTAN+NQ+++E MG+Q
Sbjct: 181 MKSGIPNKEKARVRQKFAQGQVDRAALLEAESKSYHSAGTCTFYGTANSNQLMLEVMGLQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFV+PD PLR+AL   AA+QV R+T  G ++ PIG++++EK VVNGIVALLATGGS
Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGS 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 AGLLHEDV TVAG GL RYT EP L + EL W EG  +SLD  V+ +   PF  +GG 
Sbjct: 361 LDAGLLHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPNESLDKEVLTAVASPFQANGGL 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           K+L GNLGRAV+K SAV   ++ +EAPAVV + Q+ +   F+AG LDRDCVVVV+ QGPK
Sbjct: 421 KLLKGNLGRAVIKVSAVAESHRFVEAPAVVIDDQNKLEGLFKAGELDRDCVVVVKGQGPK 480

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

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600
           GD+IRV+  TGE++LLVDEA LA+RE    DL ++  G GRELF+ALR  LS  E GA C
Sbjct: 541 GDLIRVDANTGEVSLLVDEAVLASREVEKVDLRSTSFGMGRELFAALRSNLSSPETGARC 600

Query: 601 IT 602
            T
Sbjct: 601 TT 602


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: 1067
Number of extensions: 34
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 5209582 Shew_2046 (phosphogluconate dehydratase (RefSeq))
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.5657.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5657.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.