GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Dyella japonica UNC79MFTsu3.2

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate N515DRAFT_0589 N515DRAFT_0589 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::Caulo:CCNA_00452
         (378 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0589
          Length = 386

 Score =  378 bits (971), Expect = e-109
 Identities = 202/373 (54%), Positives = 253/373 (67%), Gaps = 1/373 (0%)

Query: 4   ALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPR-DLKGGLLVPGFIDTQVN 62
           AL+NGRVL + G     AVLV+ G I  ++ A     D   R DL+G LL+PGFID QVN
Sbjct: 9   ALVNGRVLADHGPRNDLAVLVRGGRIEALVPAGDPSLDKATRHDLQGRLLLPGFIDVQVN 68

Query: 63  GGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPG 122
           GGGG+LFN APTV+T+  I AAHRRFGTTG LPTLI+D   V+  A+ A + AIA GVPG
Sbjct: 69  GGGGLLFNAAPTVDTLRGIAAAHRRFGTTGMLPTLITDTADVMHAALEAVDAAIAEGVPG 128

Query: 123 VLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIRRL 182
           +LG+H+EGPFL P RKGIHDA  FR+ D   +A +    RG  ++TLAPER   + IR+L
Sbjct: 129 ILGIHLEGPFLAPARKGIHDANLFRLPDAADIADIARKHRGVVMMTLAPERVPLETIRQL 188

Query: 183 ADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCG 242
           + AGVIV AGHT A YATMR AL+ G++GFTHL+NAM+PL SR+PG VGAAL+ P +WCG
Sbjct: 189 SAAGVIVVAGHTAADYATMRAALDAGVSGFTHLYNAMTPLGSRDPGVVGAALDDPHSWCG 248

Query: 243 IIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVDDH 302
           +IVD  HV P  L++A+  +A  + +LVTDAMP VG  D  + L G+ I   DGVC  D 
Sbjct: 249 LIVDLHHVHPASLRVAIAAKARGKSVLVTDAMPPVGADDPTYVLNGQTIVARDGVCQSDD 308

Query: 303 GTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLL 362
           G LAGS LDM   VR+ ++ + L L +A  MAS  PA++LGL    G I  G  AD  +L
Sbjct: 309 GVLAGSALDMATGVRHLVNAVGLPLAEASRMASAYPAAWLGLERELGRIVAGQRADFAVL 368

Query: 363 NDRLEVAATWIDG 375
           +D L V  TWI G
Sbjct: 369 DDALVVQETWIGG 381


Lambda     K      H
   0.321    0.140    0.410 

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: 525
Number of extensions: 25
Number of successful extensions: 2
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: 386
Length adjustment: 30
Effective length of query: 348
Effective length of database: 356
Effective search space:   123888
Effective search space used:   123888
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 N515DRAFT_0589 N515DRAFT_0589 (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.1567.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1567.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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