GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas stutzeri RCH2

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF39 Psest_0039 phosphoglucomutase, alpha-D-glucose phosphate-specific

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__psRCH2:GFF39
          Length = 554

 Score =  686 bits (1771), Expect = 0.0
 Identities = 353/550 (64%), Positives = 410/550 (74%), Gaps = 14/550 (2%)

Query: 7   AGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAITQ 66
           AG+   P  L  LP LV  YYS  PDP D AQQVAFGTSGHRGS+L G+FNE HILA TQ
Sbjct: 7   AGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQ 66

Query: 67  AIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDS-------RDRYTP 119
           AI +YR  +G  GPLF+G DTH LSEPA++SALEVLAAN +   +D+          YTP
Sbjct: 67  AICDYRRQEGIDGPLFMGMDTHALSEPAFISALEVLAANGIETRIDAGCAETGGEPGYTP 126

Query: 120 TPAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRAN 179
           TPAIS+AIL+YNRGRT  LADGIV+TPSHNPP DGG KYNP NGGPADT  T  I +RAN
Sbjct: 127 TPAISNAILSYNRGRTSGLADGIVITPSHNPPGDGGFKYNPTNGGPADTGVTKWIQERAN 186

Query: 180 EILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGG 236
            +L+A    VKR+   +AL+  T QR D++  YV  L  V+D+ AIR +G++   DPLGG
Sbjct: 187 ALLVAGLEGVKRMDYRQALKATTTQRFDFIDAYVGGLERVIDLDAIRGSGLKFAVDPLGG 246

Query: 237 ASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNR 296
           A V YW  IA R GL L V++ +VD T+RFM LD DGKIRMDCSSP AMAGLI     N+
Sbjct: 247 AGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGKIRMDCSSPHAMAGLIE----NK 302

Query: 297 ERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSS 356
           +R+ +A   D D DRHGIVT   GL+NPNHYLAVAIEYL+THRP W A   +GKT+VSSS
Sbjct: 303 DRFDVAFACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVSSS 362

Query: 357 IIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGII 416
           +IDRV AGI R+LVEVPVGFKWFVDGL+  +LGFGGEESAGASFL + G  W+TDKDG+I
Sbjct: 363 MIDRVAAGIERRLVEVPVGFKWFVDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDGLI 422

Query: 417 MALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATEL 476
           + LLAAEI AVTG  PS+RY AL   +G P Y RIDA A+REQKARL +LSA QVSA EL
Sbjct: 423 LGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAANREQKARLGKLSASQVSAKEL 482

Query: 477 AGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQ 536
           AG+PIT  LT APGNGAA+GGLKV TAN WFAARPSGTEDVYKIYAESF G  HL  +Q 
Sbjct: 483 AGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLKRIQA 542

Query: 537 TAREVVDRVI 546
            A+ +VD V+
Sbjct: 543 EAKALVDSVL 552


Lambda     K      H
   0.318    0.135    0.401 

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: 1048
Number of extensions: 44
Number of successful extensions: 4
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: 547
Length of database: 554
Length adjustment: 36
Effective length of query: 511
Effective length of database: 518
Effective search space:   264698
Effective search space used:   264698
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 GFF39 Psest_0039 (phosphoglucomutase, alpha-D-glucose phosphate-specific)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.15947.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15947.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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