GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Pedobacter sp. GW460-11-11-14-LB5

Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate CA265_RS18930 CA265_RS18930 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::BAA22834.1
         (378 letters)



>FitnessBrowser__Pedo557:CA265_RS18930
          Length = 363

 Score =  239 bits (609), Expect = 1e-67
 Identities = 136/372 (36%), Positives = 209/372 (56%), Gaps = 16/372 (4%)

Query: 4   LTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGC 63
           +TN   +  N++     ++I G  I  +   E+  +  ++         PGFIDLQ+ G 
Sbjct: 5   ITNTSYFQDNEIKSNQDILIEGSTISIINSSENKETSQSLT-------IPGFIDLQIYGA 57

Query: 64  GGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSL 123
            G +F+ + T E++ IM    LK G T FL  + T+S E     I AA+E+++   N  L
Sbjct: 58  AGRLFSADPTVESLTIMEDDLLKKGTTGFLACMATNSSEVFNACIKAAKEHRSAAKN-CL 116

Query: 124 GLHLEGPYLNVMKKGIHSVDFIRPSD-DTMIDTICANSDVIAKVTLAPENNKPEHIEKLV 182
           GLHLEGP+LN  + G H   F+R +  D + + I     VI  +T+APE    E I+ L+
Sbjct: 117 GLHLEGPFLNPKRLGAHVPAFVRKASLDEIKELIDFGDGVIKMMTIAPEIQDDEVIQYLL 176

Query: 183 KAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGI 242
             G+VVS+GH+NAT+ EA  ++  GI   THLFNAM+P+  REPG+  A+++  +  A I
Sbjct: 177 DHGVVVSLGHSNATFDEATAAYNKGIQTTTHLFNAMSPIHHREPGIPTAVFNHNKAMASI 236

Query: 243 IADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGT 302
           IADG HVD+  ++ A K+  E+L L+TDA           +        ++ K V  +GT
Sbjct: 237 IADGQHVDFEVLKFAQKLLKERLFLITDAVTACSTGPYQHV-------EKENKYVMPDGT 289

Query: 303 LGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDR 362
           L GS++TM++AV+N V H  I+L + ++M TLYPA+ IG++     I  G  ANL V D 
Sbjct: 290 LSGSSITMLQAVKNCVTHCAISLSDGVKMGTLYPAQLIGIENLTATIATGHQANLLVLDD 349

Query: 363 DFNVKATVVNGQ 374
           + ++K  +  G+
Sbjct: 350 ELSLKEVIFRGE 361


Lambda     K      H
   0.318    0.135    0.388 

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: 326
Number of extensions: 11
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: 378
Length of database: 363
Length adjustment: 30
Effective length of query: 348
Effective length of database: 333
Effective search space:   115884
Effective search space used:   115884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS18930 CA265_RS18930 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.30112.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30112.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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