GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas putida KT2440

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate PP_5194 PP_5194 aminomethyltransferase

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__Putida:PP_5194
          Length = 360

 Score =  393 bits (1009), Expect = e-114
 Identities = 205/362 (56%), Positives = 256/362 (70%), Gaps = 6/362 (1%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+T LY+ H   GA+ VDF GW MPLHYGSQ++EHH VR+D G+FDVSHMT++D+ G+
Sbjct: 1   MGQRTLLYDLHLALGAKTVDFGGWDMPLHYGSQVEEHHQVRSDCGVFDVSHMTVIDVDGT 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
               +L+ LLANDVA+L   GKALYS +LN  GGVIDDLIVY  TE  +RLV N+ATR K
Sbjct: 61  DATVWLQRLLANDVARLDDPGKALYSPLLNEQGGVIDDLIVYR-TETGYRLVTNAATRAK 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
            L W+      F ++  VR DL+++A+QGP A+ K A L + A+   +  ++PF GV  G
Sbjct: 120 VLDWLQLQRAGFSVDFQVRPDLAILAIQGPRAREKVAALLSPARAALIRELRPFEGVADG 179

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           D FIA TGYTGE G EI  P ++A  F+  LV AG+ P GLGARDTLRLEAGMNLYGQ++
Sbjct: 180 DWFIARTGYTGEDGLEIIFPGDQAVAFFNDLVGAGIAPSGLGARDTLRLEAGMNLYGQDI 239

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGT-EKLVGLVMTEKGVLRNELPVR 299
           DE  +PL +N+GW+IAWEPA+R+FIGR  L  + EHG  EKLVGLV+ E+GVLR    VR
Sbjct: 240 DENHTPLTSNLGWSIAWEPAERNFIGRVGLLAEIEHGVQEKLVGLVLEERGVLRAHQVVR 299

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                    EG ITSG+FSPTL  SIALARVP   G+ A V+IR +  PV+V KP FVR+
Sbjct: 300 VAGI----GEGEITSGSFSPTLSKSIALARVPMATGDRAEVEIRGKWYPVRVVKPTFVRH 355

Query: 360 GK 361
           GK
Sbjct: 356 GK 357


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: 407
Number of extensions: 20
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 PP_5194 PP_5194 (aminomethyltransferase)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.26043.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26043.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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