GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas simiae WCS417

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate GFF5324 PS417_27255 glycine cleavage system protein T

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__WCS417:GFF5324
          Length = 360

 Score =  402 bits (1032), Expect = e-116
 Identities = 203/364 (55%), Positives = 265/364 (72%), 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   MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVTGP 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           + +E+L+YLLANDV +L   G+ALYS MLN  GGV+DD+IVY  TE  +RLVVN++TR++
Sbjct: 61  QAKEWLQYLLANDVERLHDCGRALYSAMLNEKGGVVDDMIVYR-TESAYRLVVNASTRDQ 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           D++W+      + +++  R +L+M+A+QGP+A+ K A L   ++   +  +KPF G   G
Sbjct: 120 DMTWMHAQLGNYQVQLHERPELAMLAIQGPHARQKIAELVTQSRSTLIHQLKPFEGQADG 179

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

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

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                 N  EG ITSG+FSPTL  SIALARVP    + A V+IR +  PV+V KP FVR+
Sbjct: 300 I----ANIGEGEITSGSFSPTLSKSIALARVPTATADRAEVEIRGKWYPVRVVKPTFVRH 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: 406
Number of extensions: 13
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 GFF5324 PS417_27255 (glycine cleavage system protein T)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.15150.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15150.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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