GapMind for catabolism of small carbon sources

 

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

Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 5209451 Shew_1922 phosphoglucomutase (RefSeq)

Query= CharProtDB::CH_002452
         (546 letters)



>FitnessBrowser__PV4:5209451
          Length = 559

 Score =  636 bits (1641), Expect = 0.0
 Identities = 317/558 (56%), Positives = 400/558 (71%), Gaps = 15/558 (2%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60
           MA+H RAG+PAQQ DL+N+ +L + YY L P+  N    V FGTSGHRG A   SFNE H
Sbjct: 1   MALHERAGKPAQQRDLVNIPKLMSHYYRLSPDVTNDAQKVTFGTSGHRGCAFNKSFNEKH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           ILAI QA+ + R + GI GP  VG DTHALS+ A+++ LEVL ANGV VIV +N+ +TPT
Sbjct: 61  ILAIVQAVVDHRIEAGIKGPMIVGIDTHALSQAAYVTALEVLTANGVQVIVAKNDEYTPT 120

Query: 121 PAVSNAILVHNKKGGP---------LADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTK 171
           P VS+AI+  N+  G          L DG++ITPSHNPP+DGGIKYNPP+GGPA+  +T 
Sbjct: 121 PVVSHAIIAANRVQGAGLTYGLNYGLTDGLIITPSHNPPQDGGIKYNPPHGGPAEGGITA 180

Query: 172 VVEDRANALLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTL 231
            VE RAN  LA  L+GVKR++   A+ +  ++E+DL+  +VE L  ++DM AI++AG+ +
Sbjct: 181 WVEQRANEYLAKQLEGVKRLTYSVAVTTSLIQERDLMAAYVEDLEQVIDMQAIKQAGIRI 240

Query: 232 GVDPLGGSGIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLL 291
           GVDPLGGSGI YW +I E Y L++T+VND++D  F FM LDKDG IRMDCSS  AMAGLL
Sbjct: 241 GVDPLGGSGIHYWAKIAERYGLDITLVNDRIDPAFGFMPLDKDGKIRMDCSSPYAMAGLL 300

Query: 292 ALRDKFDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLV 350
             +D FD+ F NDPDYDRHGIV P +GLMNPNHYLAVAI YL  HRPQW  D+ +GKTLV
Sbjct: 301 VHQDAFDICFGNDPDYDRHGIVCPGSGLMNPNHYLAVAIEYLLSHRPQWSADLKIGKTLV 360

Query: 351 SSAMIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKD 410
           SSAMID+V  +  R L EVPVGFKWFV+GL D SF FGGEESAGA+FLR DG  W TDKD
Sbjct: 361 SSAMIDKVCREQSRSLCEVPVGFKWFVEGLADASFAFGGEESAGAAFLRRDGGSWCTDKD 420

Query: 411 GIIMCLLAAEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSA 470
           G I+ LLAAEI AVTGK P + Y E+ +R G   Y R+ +     +KA  ++L  E ++ 
Sbjct: 421 GFILALLAAEILAVTGKTPAKLYAEMVERHGESFYKRIDSPVNPKRKAKFNQLVSEPLNV 480

Query: 471 STL-----AGDPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGE 525
           S L     AGD I   LT APGNGA+IGG+KV+T+  WFAARPSGTE  +K+Y ESF+ E
Sbjct: 481 SDLGCEAMAGDAILEVLTHAPGNGAAIGGIKVVTEKAWFAARPSGTEALFKLYGESFVSE 540

Query: 526 EHRKQIEKEAVEIVSEVL 543
            H +Q+ ++A +++  +L
Sbjct: 541 AHLEQVLEQAQQMIERLL 558


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: 925
Number of extensions: 36
Number of successful extensions: 5
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: 559
Length adjustment: 36
Effective length of query: 510
Effective length of database: 523
Effective search space:   266730
Effective search space used:   266730
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 5209451 Shew_1922 (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.4654.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4654.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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