GapMind for catabolism of small carbon sources

 

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

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate 5211050 Shew_3466 glycerol kinase (RefSeq)

Query= CharProtDB::CH_121461
         (502 letters)



>FitnessBrowser__PV4:5211050
          Length = 498

 Score =  724 bits (1870), Expect = 0.0
 Identities = 338/489 (69%), Positives = 414/489 (84%), Gaps = 1/489 (0%)

Query: 3   EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLV 62
           ++KY++ALDQGTTSSR ++ DHDAN++++SQREF QIYPK GWVEHDPMEIWA+QSSTL+
Sbjct: 2   QQKYVIALDQGTTSSRTIIFDHDANVVAISQREFSQIYPKVGWVEHDPMEIWASQSSTLI 61

Query: 63  EVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLE 122
           E LA+A I SD++A+IGITNQRETT++W+K TGKPIYNAIVWQCRR+  +CE L+ +G E
Sbjct: 62  EALARAGIHSDEVASIGITNQRETTVLWDKATGKPIYNAIVWQCRRSQPLCESLRAEGYE 121

Query: 123 DYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVT 182
           DYIR NTGLV+DPYFS TK++WILD+VEG+RE+A  GELLFGT+DTWL+WK+T+G+VHVT
Sbjct: 122 DYIRQNTGLVLDPYFSATKIRWILDNVEGAREKAEAGELLFGTIDTWLVWKLTEGKVHVT 181

Query: 183 DYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISG 242
           D TNASRTML+NIH   WD  +LE L+IP  +LPEV+ S  VYG+T I G+GG  IP++G
Sbjct: 182 DPTNASRTMLYNIHQQAWDPVLLEALEIPASILPEVKPSCAVYGKTRIAGEGG-EIPVAG 240

Query: 243 IAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYA 302
           +AGDQQ+ALFGQLC+ EGMAKNTYGTGCF+LMNTG +AV+S +GLLTTIA GP GEVNYA
Sbjct: 241 MAGDQQSALFGQLCIDEGMAKNTYGTGCFLLMNTGLQAVQSNHGLLTTIAVGPKGEVNYA 300

Query: 303 LEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYAR 362
           LEG+VFM GA+IQWLRDE+ LI DA D+EYFA KV + NGVY+VPAF GLGAPYWD  AR
Sbjct: 301 LEGSVFMGGATIQWLRDELGLIRDAQDTEYFALKVSDNNGVYLVPAFVGLGAPYWDASAR 360

Query: 363 GAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQF 422
           GA+ GL+RG N NHIIRA LE+IAYQ+RD+L+AM  DSG++L  L+VDGGAVAN+FLMQF
Sbjct: 361 GALVGLSRGANRNHIIRAALEAIAYQSRDLLDAMTKDSGVQLKQLKVDGGAVANDFLMQF 420

Query: 423 QSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNY 482
           Q+DI    V+RP+V E TA+GAA+LAGLAVGFWQ+  EL+ KA +ER F+P I   ER  
Sbjct: 421 QADITDVEVQRPKVTETTAMGAAFLAGLAVGFWQSTAELKHKAGVERCFKPAIADDEREA 480

Query: 483 RYAGWKKAV 491
            Y GWK+AV
Sbjct: 481 LYLGWKRAV 489


Lambda     K      H
   0.318    0.134    0.404 

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: 814
Number of extensions: 22
Number of successful extensions: 2
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: 502
Length of database: 498
Length adjustment: 34
Effective length of query: 468
Effective length of database: 464
Effective search space:   217152
Effective search space used:   217152
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 5211050 Shew_3466 (glycerol kinase (RefSeq))
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.18164.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18164.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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