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_0986 PP_0986 aminomethyltransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5556
         (374 letters)



>FitnessBrowser__Putida:PP_0986
          Length = 373

 Score =  602 bits (1553), Expect = e-177
 Identities = 300/372 (80%), Positives = 330/372 (88%)

Query: 3   TEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQIRL 62
           +E LLKTPLHALHLELGARMVPFAGYDMPVQYPLGV+KEH HTR+QAGLFDVSHMGQI L
Sbjct: 2   SETLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVLKEHLHTREQAGLFDVSHMGQIIL 61

Query: 63  TGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAACK 122
            GA AAKALE+LVPVDIIDLPVGMQRYAMFTNE GGILDDLMVANLG D LFLVVNAACK
Sbjct: 62  RGADAAKALESLVPVDIIDLPVGMQRYAMFTNEQGGILDDLMVANLGEDTLFLVVNAACK 121

Query: 123 DQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTLLG 182
           +QDLAHL+ HIG++C ++PLFE RALLALQGPAAV VL RLAP+VA MTFMQF+RV LLG
Sbjct: 122 EQDLAHLQTHIGSRCEVQPLFEERALLALQGPAAVKVLERLAPEVAGMTFMQFRRVKLLG 181

Query: 183 MDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLYGH 242
           +DC+VSRSGYTGEDG+EISVP   A+ LAR L+AEPEV  IGLGARDSLRLEAGLCLYGH
Sbjct: 182 VDCFVSRSGYTGEDGYEISVPVNAADALARRLMAEPEVQPIGLGARDSLRLEAGLCLYGH 241

Query: 243 DMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERTPV 302
           DMN+ETTPIEASLLWAISKVRRADGARA GFPGAE +FA  + GV RKRVGLLPQERTPV
Sbjct: 242 DMNSETTPIEASLLWAISKVRRADGARAAGFPGAEAIFAHVRDGVARKRVGLLPQERTPV 301

Query: 303 REGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLLVS 362
           REGA+IV+   + +G VCSGGFGPTL  P+AMGY+DS + ALDT ++A+VRGKKV L VS
Sbjct: 302 REGADIVDANDKPVGKVCSGGFGPTLAAPVAMGYIDSEHAALDTALFAVVRGKKVALKVS 361

Query: 363 KMPFVPQRYYRG 374
           KMPFV  RYYRG
Sbjct: 362 KMPFVTPRYYRG 373


Lambda     K      H
   0.321    0.138    0.406 

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: 589
Number of extensions: 22
Number of successful extensions: 1
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: 373
Length adjustment: 30
Effective length of query: 344
Effective length of database: 343
Effective search space:   117992
Effective search space used:   117992
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 PP_0986 PP_0986 (aminomethyltransferase)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.1700.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1700.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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