GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas putida KT2440

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PP_3578 PP_3578 phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__Putida:PP_3578
          Length = 545

 Score =  647 bits (1670), Expect = 0.0
 Identities = 341/549 (62%), Positives = 400/549 (72%), Gaps = 8/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA    LVD+P L+TAYY+  PD    AQ+VAFGTSGHRGS+L  +FNE H
Sbjct: 1   MTLSPLAGKPAPASVLVDIPRLLTAYYTGRPDATVAAQRVAFGTSGHRGSSLELSFNEYH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           +LAI+QAI  YR  +G  GPLFIG DTH LS PA  SALEVLAAN V  ++   D YTPT
Sbjct: 61  VLAISQAICLYRQEKGIDGPLFIGADTHALSAPATASALEVLAANGVQVMLSKDDEYTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PA+SHAIL +NRGRT+ LADGIV+TPSHNPP  GG KYNPPNGGPAD+  T  I  +ANE
Sbjct: 121 PAVSHAILCHNRGRTQGLADGIVITPSHNPPQSGGFKYNPPNGGPADSDVTKWIEGKANE 180

Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L A  + VKR+  A+AL+  T  RHDY+ +YV DL NV+D   IR AG+R+G DPLGGA
Sbjct: 181 LLAANLAGVKRMDHAQALQAPTTHRHDYVSNYVADLENVIDFDVIRGAGLRLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA  + LDL VVN  VD T+RFMT+D DG+IRMD SSP AM GLI    G RE
Sbjct: 241 GVRYWSAIAKHYQLDLEVVNTEVDPTFRFMTVDWDGQIRMDPSSPYAMQGLI----GLRE 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ +A   D D DRHGIVTPD GLL PN+YLAVAI+YL+ HRP W +  AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPD-GLLQPNNYLAVAIDYLFRHRPQWRSDAAVGKTVVSSGL 355

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV   +GR L EVPVGFK+F  GL   +LGFGGEESAGASFLRRDGSVW TDKDG+I 
Sbjct: 356 IDRVTQRLGRDLYEVPVGFKFFAQGLFDGSLGFGGEESAGASFLRRDGSVWATDKDGLIP 415

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ A TG  PSQ Y  L    G P   R++A AD  QKA L++L+ +QV +TELA
Sbjct: 416 ALLAAEMTARTGRNPSQAYADLTEALGKPFATRVEAKADARQKALLSKLAPEQVKSTELA 475

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GEPI   L+ APGNG A+GGLKV TAN WFAARPSGTED+YKIYAESF    HL  + + 
Sbjct: 476 GEPIVQILSHAPGNGQAIGGLKVMTANGWFAARPSGTEDIYKIYAESFIDEAHLQRLVEE 535

Query: 538 AREVVDRVI 546
           A+ +VD  I
Sbjct: 536 AQVLVDEAI 544


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: 961
Number of extensions: 31
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: 545
Length adjustment: 35
Effective length of query: 512
Effective length of database: 510
Effective search space:   261120
Effective search space used:   261120
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 PP_3578 PP_3578 (phosphoglucomutase)
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.22645.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22645.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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