GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Caulobacter crescentus NA1000

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate CCNA_02615 CCNA_02615 homogentisate 1,2-dioxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5290
         (434 letters)



>FitnessBrowser__Caulo:CCNA_02615
          Length = 425

 Score =  560 bits (1442), Expect = e-164
 Identities = 272/420 (64%), Positives = 321/420 (76%), Gaps = 3/420 (0%)

Query: 9   DLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEARRTWMYRI 68
           DL YQ+GFG+ F +EA PGALPVG+NSPQKVP+GLYAE  SG+AFT  R E RRTW+YR+
Sbjct: 2   DLRYQTGFGSYFETEAHPGALPVGRNSPQKVPFGLYAEQLSGSAFTAPRHENRRTWLYRL 61

Query: 69  RPSANHPAFTRLER-QLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAANAGADKP 127
           RPSA H A+    + +L     G  TPNRLRW+PLEIPA PTDF+DGLV +A NA A   
Sbjct: 62  RPSAGHEAYQPYAQDKLVSAFPGPATPNRLRWSPLEIPAAPTDFVDGLVSLAGNADAATL 121

Query: 128 AGISLYQYQANRSME-RVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVLPRGLKF 186
            GI+ + Y  N SM+ RVF+NADGE LIVPQ+G L + TE+GVL+  P  I V+PRG++F
Sbjct: 122 GGIAAHVYLVNVSMKNRVFYNADGEMLIVPQMGELTLVTEMGVLKAGPGHIAVIPRGVRF 181

Query: 187 RIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPTSLVQKF 246
           R+E+  P ARGY+ EN+GA  RLP+LGPIG+NGLANPRDF  PVA +E++  PT ++QKF
Sbjct: 182 RVEVEGP-ARGYVCENYGAAFRLPELGPIGANGLANPRDFEAPVAAFEDIDTPTQVIQKF 240

Query: 247 LGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHG 306
            G LW    DHSPLDVVAWHGN  PY+YDL RFNTI TVS+DHPDPSIFTVLTSP+   G
Sbjct: 241 QGALWAATWDHSPLDVVAWHGNLTPYRYDLSRFNTINTVSYDHPDPSIFTVLTSPSDTPG 300

Query: 307 LANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGASLHSCMS 366
            AN DFVIFPPRWMVAE+TFRPPWFHRN+M+EFMGLI GAYDAKA GF+PGGASLH+CMS
Sbjct: 301 TANCDFVIFPPRWMVAEDTFRPPWFHRNVMSEFMGLIHGAYDAKAGGFVPGGASLHNCMS 360

Query: 367 AHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDACWASLP 426
            HGPD  +  KA    L P KID TMAFMFE+  V RP+  AL+   LQ+DYDACW   P
Sbjct: 361 DHGPDVASHKKATEVVLAPHKIDGTMAFMFESRWVFRPTHLALESAALQSDYDACWTGFP 420


Lambda     K      H
   0.321    0.138    0.435 

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: 746
Number of extensions: 28
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: 434
Length of database: 425
Length adjustment: 32
Effective length of query: 402
Effective length of database: 393
Effective search space:   157986
Effective search space used:   157986
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: 51 (24.3 bits)

Align candidate CCNA_02615 CCNA_02615 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.17065.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17065.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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