GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Sinorhizobium meliloti 1021

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate SMc02047 SMc02047 glycine cleavage system aminomethyltransferase T

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1866
         (374 letters)



>FitnessBrowser__Smeli:SMc02047
          Length = 379

 Score =  416 bits (1068), Expect = e-121
 Identities = 221/375 (58%), Positives = 265/375 (70%), Gaps = 9/375 (2%)

Query: 6   LLKTPLHALHIELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRLTGA 65
           L  TPLHALH+ LGARMVPFAGYDMPVQYP GV+KEH HTR  AGLFDVSHMGQI +   
Sbjct: 7   LKHTPLHALHLSLGARMVPFAGYDMPVQYPEGVLKEHLHTRAAAGLFDVSHMGQIVVRPK 66

Query: 66  N-----AAKALETLVPVDIIDLPVGMQRYAMFTNATGGILDDLMVANLGNDELFLVVNAA 120
           +     AA ALE LVP D++ L  G QRY +FTNA GGILDDLM+ N G D LFLVVNAA
Sbjct: 67  SGKIEDAALALEKLVPADVLGLAEGRQRYGLFTNAAGGILDDLMIVNRG-DHLFLVVNAA 125

Query: 121 CKDQDLAHLRKHIGDQCTIEPLFEERALLALQGPAAVTVLARLAPEVAKMTFMQFARVKL 180
           CKD DLAHL+  +G  C +  L  +RAL+ALQGP A  VL  L  +V+ M FM      L
Sbjct: 126 CKDADLAHLKDGLGSVCDVTML-TDRALIALQGPRAGAVLCELWADVSSMRFMDVTEADL 184

Query: 181 LGVDCFVSRSGYTGEDGFEISVPATNAEALARALLAEAEVAAIGLGARDSLRLEAGLCLY 240
             V C +SRSGYTGEDGFEIS+PA  A  + + LL   +V  IGLGARDSLRLEAGLCLY
Sbjct: 185 HDVSCIISRSGYTGEDGFEISIPAEAAVDVTQRLLEHPDVLPIGLGARDSLRLEAGLCLY 244

Query: 241 GHDMNTDTTPIEASLLWAISKPRRADGARAGGFPGAETVFAQQQAGVSRKRVGLLPQERT 300
           G+D++T+T+PIEA L WAI K RRA G RAGGFPGA  + A+   GVSR+RVGL P+ R 
Sbjct: 245 GNDIDTNTSPIEAGLEWAIQKSRRAGGERAGGFPGAGRILAELTDGVSRRRVGLRPEGRA 304

Query: 301 PVREGAEIV--NEAGDIIGSVCSGGFGPTLGGPLAMGYVDSAYIALDTPVWAIVRGKKVP 358
           PVR  A +    E     G+V SGGFGP++ GP+AMGYVD+ +  + T ++A VRGK +P
Sbjct: 305 PVRGNANLFADEEGRTAAGTVTSGGFGPSVDGPVAMGYVDAEHAEVGTRLFAEVRGKYLP 364

Query: 359 LLVSKMPFVPQRYYR 373
           + V+ +PF+ Q Y R
Sbjct: 365 IAVTALPFIKQTYKR 379


Lambda     K      H
   0.321    0.138    0.405 

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: 484
Number of extensions: 25
Number of successful extensions: 5
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: 374
Length of database: 379
Length adjustment: 30
Effective length of query: 344
Effective length of database: 349
Effective search space:   120056
Effective search space used:   120056
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: 50 (23.9 bits)

Align candidate SMc02047 SMc02047 (glycine cleavage system aminomethyltransferase T)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.27589.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27589.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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