GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Shewanella oneidensis MR-1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 201480 SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)

Query= BRENDA::A0A0H3NJ17
         (546 letters)



>FitnessBrowser__MR1:201480
          Length = 550

 Score =  645 bits (1665), Expect = 0.0
 Identities = 321/548 (58%), Positives = 405/548 (73%), Gaps = 5/548 (0%)

Query: 1   MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60
           MAIH RAGQ A Q DL+N+ +L + YY +KP    AE  V FGTSGHRG+A + SFN+ H
Sbjct: 1   MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDH 60

Query: 61  ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120
           I AI QA+ + R    I GP ++G DTHALS  A++S +EVLAAN V V +Q+N+GFTPT
Sbjct: 61  IWAITQAVVDYRQSVNIEGPLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPT 120

Query: 121 PAVSNAILVHN----KKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176
           P VS+AI+  N    + G  L+DG++ITPSHNPP+DGGIKYNPP+GGPA+ N+T  +E R
Sbjct: 121 PVVSHAIICANHAAAQNGALLSDGLIITPSHNPPQDGGIKYNPPHGGPAEGNITAWIESR 180

Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236
           AN  L   L+GV +++   A+ASG+V A+DL+ P+V  L ++VDM AI KA L LGVDPL
Sbjct: 181 ANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGVDPL 240

Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296
           GGSGI YW  IA+HY +++TLVND+VD +F FM LDKDG IRMDCSS  AMAGLLA ++ 
Sbjct: 241 GGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKES 300

Query: 297 FDLAFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355
           FDL   NDPDYDRHGIV P  GLM+PNHYLAVAI+YL  HRP W   +A+GKTLVSSA+I
Sbjct: 301 FDLCVGNDPDYDRHGIVCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALI 360

Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415
           D++    G+KL+EVPVGFKWFVDGL + +  FGGEESAGA+FLR DGT W TDKDG I+ 
Sbjct: 361 DKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGEESAGAAFLRRDGTTWCTDKDGFILV 420

Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475
           LLAAE+ AVTGK P + + EL A+FG   Y R+ +  +   KA  +KL+ + ++A+ LAG
Sbjct: 421 LLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLNATMLAG 480

Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535
           + I A LT APGN ASIGG+KV T NGWFAARPSGTE  +KIY ESF+ E+H  +I K+A
Sbjct: 481 EKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDA 540

Query: 536 VEIVSEVL 543
             ++ + L
Sbjct: 541 QALIDKAL 548


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: 885
Number of extensions: 35
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: 550
Length adjustment: 36
Effective length of query: 510
Effective length of database: 514
Effective search space:   262140
Effective search space used:   262140
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 201480 SO2336 (phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.4666.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4666.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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