GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas stutzeri RCH2

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate GFF180 Psest_0181 glycine cleavage system T protein

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__psRCH2:GFF180
          Length = 360

 Score =  425 bits (1092), Expect = e-123
 Identities = 215/364 (59%), Positives = 270/364 (74%), Gaps = 6/364 (1%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+TPLY+QH   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT+VD+ G 
Sbjct: 1   MGQRTPLYDQHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVVDVAGE 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           +   +L++LLANDV +L  +G+ALY+ MLN  GGVIDDLIVY  +E  +RLVVN++TREK
Sbjct: 61  QATAYLQHLLANDVTRLKGTGRALYTAMLNERGGVIDDLIVY-LSEWGYRLVVNASTREK 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+W+ Q A  F +E+  R +L+M+A+QGP+A+ + A L + A+   ++ +KPF G+  G
Sbjct: 120 DLAWMQQQAAGFAVEVKERPELAMLAIQGPHARTRTAELVSQARATLIQELKPFQGLAEG 179

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           D FI  TGYTGE G EI LP E+A DF   LV AG+ P GLGARDTLRLEAG+NLYGQ+M
Sbjct: 180 DWFIGRTGYTGEDGLEIILPAEQAPDFLSELVGAGIPPIGLGARDTLRLEAGLNLYGQDM 239

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHG-TEKLVGLVMTEKGVLRNELPVR 299
            E +SPLAANMGWT+AWEP +RDF+GR ALE QR  G   KLVGLV+ E+GVLR    VR
Sbjct: 240 TEDVSPLAANMGWTVAWEPTERDFVGRAALEQQRAQGDLPKLVGLVLEERGVLRAHQVVR 299

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                    +G ITSG+FSPTLG SIALARVP G GE A V+IR +  PV+V +P FVR+
Sbjct: 300 VNGV----GDGEITSGSFSPTLGKSIALARVPAGTGERAEVEIRGKWYPVRVVQPTFVRH 355

Query: 360 GKAV 363
           GK +
Sbjct: 356 GKVL 359


Lambda     K      H
   0.320    0.136    0.402 

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: 413
Number of extensions: 9
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: 364
Length of database: 360
Length adjustment: 29
Effective length of query: 335
Effective length of database: 331
Effective search space:   110885
Effective search space used:   110885
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate GFF180 Psest_0181 (glycine cleavage system T protein)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.10354.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10354.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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