GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella amazonensis SB2B

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 6937550 Sama_1706 phosphoglucomutase (RefSeq)

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__SB2B:6937550
          Length = 560

 Score =  648 bits (1671), Expect = 0.0
 Identities = 322/549 (58%), Positives = 401/549 (73%), Gaps = 5/549 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           MAIH+RAG+ AQQ DL+N+ +L + YY L P+A +    V FGTSGHRG A   SFNE H
Sbjct: 1   MAIHDRAGKQAQQGDLVNIPKLMSHYYRLLPDASDPAQKVSFGTSGHRGCAFHRSFNEQH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAIAQA+ + R +  ITGP Y+G DTHALS+ A++SV+EVL AN V V+ Q ++ +TPT
Sbjct: 61  ILAIAQAVVDWRTQADITGPLYLGMDTHALSQAAYLSVIEVLIANKVQVLAQRDDAYTPT 120

Query: 121 PAVSNAILVHNK----KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176
           P VS AI+  N+    +   L+DGI+ITPSHNPP+DGGIKYNPP+GGPA+ ++T  +E R
Sbjct: 121 PVVSQAIVAANRHQTGEDALLSDGIIITPSHNPPQDGGIKYNPPHGGPAEGDITSWIETR 180

Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
           AN  LA GL GV+R++   A     +K VDL+ P+V+ LA+++DMAAI KAG+ +GVDPL
Sbjct: 181 ANHYLAHGLDGVRRVNYGIASGLSLLKHVDLISPYVQSLAEVIDMAAIAKAGVRMGVDPL 240

Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296
           GGSGI YW+ IAEHY LN+ +VN  +D TF FM LDKDG IRMDCSS  AMAGLL  +D+
Sbjct: 241 GGSGIHYWQPIAEHYGLNIEVVNQAIDPTFDFMPLDKDGKIRMDCSSPYAMAGLLVHKDE 300

Query: 297 FDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355
           FD+   NDPDYDRHGIV P +GLM+PNHYLAVAI+YL  HRP W K +AVGKTLVSSA+I
Sbjct: 301 FDICVGNDPDYDRHGIVCPGSGLMDPNHYLAVAIDYLLGHRPNWAKTLAVGKTLVSSALI 360

Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415
           D+V    G  L+EVPVGFKWFVDGL D S  FGGEESAGA+FL+ DG+ W TDKDG I+ 
Sbjct: 361 DKVCMAHGVPLMEVPVGFKWFVDGLADSSVCFGGEESAGAAFLKMDGSTWCTDKDGFILA 420

Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475
           LLAAEI AVTGK P E Y EL A  G   Y R+ +      KA    L+ + + A+++AG
Sbjct: 421 LLAAEILAVTGKTPAERYEELVAEHGRSFYKRIDSPLNPKMKAKFGALNAQTLGATSVAG 480

Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535
           D ITA LT APGNGA+IGG+KV TD GWFAARPSGTE  +K+Y ESF+ E H  ++  +A
Sbjct: 481 DAITAVLTKAPGNGAAIGGIKVCTDKGWFAARPSGTEPLFKLYAESFVSEAHLGELISDA 540

Query: 536 VEIVSEVLK 544
             ++   LK
Sbjct: 541 QSLLGTALK 549


Lambda     K      H
   0.316    0.134    0.395 

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: 913
Number of extensions: 31
Number of successful extensions: 3
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: 546
Length of database: 560
Length adjustment: 36
Effective length of query: 510
Effective length of database: 524
Effective search space:   267240
Effective search space used:   267240
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate 6937550 Sama_1706 (phosphoglucomutase (RefSeq))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.12684.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12684.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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