GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas simiae WCS417

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF2629 PS417_13395 phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__WCS417:GFF2629
          Length = 547

 Score =  639 bits (1648), Expect = 0.0
 Identities = 337/549 (61%), Positives = 399/549 (72%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA  + LVD+P LVTAYY+ +PD     Q+VAFGTSGHRG++   +FNE H
Sbjct: 1   MTISPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGNSFELSFNEWH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           +LAI+QAI  YR AQG  GPLF+G DTH LS PA  SALEVLAAN V  ++   D YTPT
Sbjct: 61  VLAISQAICLYREAQGINGPLFVGLDTHALSTPAGASALEVLAANGVHVMLAEGDEYTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PAISHAI+ YNRGRT  LADGIV+TPSHNPP  GG KYNPPNGGPADT  T  I  +ANE
Sbjct: 121 PAISHAIICYNRGRTSGLADGIVITPSHNPPQSGGYKYNPPNGGPADTHVTKWIEAKANE 180

Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L  + + VKR+  A+AL+  T  RHDYL  YV DL NV+D+ AIR A +R+G DPLGGA
Sbjct: 181 LLAKKLAGVKRITHAQALKADTTHRHDYLNTYVADLVNVIDMDAIRSADLRLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA  + L+L VVN  VDAT+RFM +D DG+IRMD SS  AM GLI    G +E
Sbjct: 241 GVRYWSAIAEHYRLNLEVVNTEVDATFRFMCVDWDGQIRMDPSSSYAMQGLI----GLKE 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ +A   D D DRHGIVTP  GLL PN+YLAV+I+YL+ +RP W A  AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPDWRADAAVGKTVVSSGL 356

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV A IGR+L EVPVGFKWF DGL   +LGFGGEESAGASFLR+DG+VW+TDKDG+I 
Sbjct: 357 IDRVAARIGRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGTVWSTDKDGLIP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ +  G  PSQ Y  L    G P   R+DA A   QKA L +LS DQV++TELA
Sbjct: 417 ALLAAEMTSRKGQDPSQIYRGLTDALGEPFAIRVDAKATPAQKALLGKLSPDQVTSTELA 476

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GE I   L+ APGN  A+GGLKV T N WFAARPSGTED+YKIYAESF G  HL ++ + 
Sbjct: 477 GESIQQILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFIGEDHLKQLVEE 536

Query: 538 AREVVDRVI 546
           A+ +VD  I
Sbjct: 537 AQVLVDGAI 545


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: 972
Number of extensions: 36
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: 547
Length of database: 547
Length adjustment: 36
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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: 52 (24.6 bits)

Align candidate GFF2629 PS417_13395 (phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.15041.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15041.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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