GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2C3

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO356_18160 AO356_18160 glycine cleavage system protein T

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_18160
          Length = 374

 Score =  723 bits (1866), Expect = 0.0
 Identities = 361/374 (96%), Positives = 371/374 (99%)

Query: 1   MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60
           MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI
Sbjct: 1   MSTEQLLKTPLHALHLELGARMVPFAGYDMPVQYPLGVMKEHQHTRDQAGLFDVSHMGQI 60

Query: 61  RLTGAGAAKALETLVPVDIIDLPVGMQRYAMFTNENGGILDDLMVANLGNDELFLVVNAA 120
           RL+GAGAAKALETLVPVDIIDLPVGMQRYAMFTN+NGGILDDLMVANLGNDELFLVVNAA
Sbjct: 61  RLSGAGAAKALETLVPVDIIDLPVGMQRYAMFTNDNGGILDDLMVANLGNDELFLVVNAA 120

Query: 121 CKDQDLAHLRAHIGAQCSIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180
           CKDQDLAHLRAHIG QC+IEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL
Sbjct: 121 CKDQDLAHLRAHIGDQCNIEPLFEARALLALQGPAAVTVLARLAPDVAKMTFMQFQRVTL 180

Query: 181 LGMDCYVSRSGYTGEDGFEISVPAAEAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240
           LG+DC+VSRSGYTGEDGFEISVPAA+AEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY
Sbjct: 181 LGVDCFVSRSGYTGEDGFEISVPAADAEKLARALLAEPEVAAIGLGARDSLRLEAGLCLY 240

Query: 241 GHDMNTETTPIEASLLWAISKVRRADGARAGGFPGAETVFAQQQGGVKRKRVGLLPQERT 300
           GHDMNTETTPIEASLLWAISKVRRADG RAGGFPGAE+VFAQQQGGVKRKRVGLLPQERT
Sbjct: 241 GHDMNTETTPIEASLLWAISKVRRADGGRAGGFPGAESVFAQQQGGVKRKRVGLLPQERT 300

Query: 301 PVREGAEIVNEAGEIIGTVCSGGFGPTLGGPLAMGYLDSAYVALDTPVWAIVRGKKVPLL 360
           PVREGAEIVN+AGEIIG+VCSGGFGPTLG PLAMGYLDSAYVALDTPVWAIVRGK+VPLL
Sbjct: 301 PVREGAEIVNDAGEIIGSVCSGGFGPTLGAPLAMGYLDSAYVALDTPVWAIVRGKRVPLL 360

Query: 361 VSKMPFVPQRYYRG 374
           VSKMPFVPQRYYRG
Sbjct: 361 VSKMPFVPQRYYRG 374


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: 669
Number of extensions: 29
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: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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 AO356_18160 AO356_18160 (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.16061.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16061.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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