GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2E2

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate Pf6N2E2_4485 Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4485
          Length = 360

 Score =  392 bits (1006), Expect = e-113
 Identities = 198/364 (54%), Positives = 260/364 (71%), Gaps = 6/364 (1%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+TPLY+ H   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT++D+ G 
Sbjct: 1   MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVDGP 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           + + +L+ LLANDV +L  +G ALYS MLN  GG++DD+I+Y   ED +RLV N++TR++
Sbjct: 61  QAKVWLQRLLANDVDRLQDTGSALYSAMLNERGGIVDDMIIYR-VEDGYRLVFNASTRDQ 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+W+      + +++  R +L+M+A+QGP A+ K A L    + Q ++ +KPF G   G
Sbjct: 120 DLAWMQAQLGGYDVQLHERPELAMLAIQGPQARQKIAELVTQPRGQIIQQLKPFEGRADG 179

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

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTE-KLVGLVMTEKGVLRNELPVR 299
           ++ +SPLA+NM W+IAWEPA R FIGR ALE +   G + KLVGLV+ E+GVLR    VR
Sbjct: 240 NQDVSPLASNMAWSIAWEPASRPFIGRSALEAELASGVQHKLVGLVLEERGVLRAHQVVR 299

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                 N  EG ITSG+FSPTL  SIALARVP    + A V+IR +  PV+V KP FVR+
Sbjct: 300 I----ANVGEGEITSGSFSPTLSKSIALARVPMATADRAEVEIRGKWYPVRVVKPTFVRH 355

Query: 360 GKAV 363
           GK +
Sbjct: 356 GKTL 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: 415
Number of extensions: 18
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 Pf6N2E2_4485 (Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10))
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.21245.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21245.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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