GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Pseudomonas fluorescens FW300-N1B4

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Pf1N1B4_1024 Fumarylacetoacetase (EC 3.7.1.2)

Query= BRENDA::Q8RW90
         (421 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1024
          Length = 434

 Score =  372 bits (955), Expect = e-107
 Identities = 196/416 (47%), Positives = 261/416 (62%), Gaps = 14/416 (3%)

Query: 16  FPIQNLPYGVFKPESNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLNKF 75
           FP+QNLP GVF  +  S PR  VAIGD + DL A  +AGLFDG+  K  +      LN F
Sbjct: 20  FPLQNLPLGVFSVKG-SAPRSGVAIGDHIFDLEAALDAGLFDGVAKKAVEATRGGQLNAF 78

Query: 76  LAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFFAS 135
             +GR A    R  L  +      +    +    K     +  EM +P  I DYTDF+  
Sbjct: 79  FELGREARVALRERLIELFKEGSTLHGKIEAQGAKLLPLAADCEMHLPAKINDYTDFYVG 138

Query: 136 MHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEPYF 195
           + HA+N G +FR P+N + PN+  +PI YHGRAS+I  SGTD+ RP+GQ  P G +EP F
Sbjct: 139 IEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRPSGTDVRRPKGQTLPAGQTEPTF 197

Query: 196 GPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLGPF 255
           GP  +LD+ELE+   +G GN +G  I + +AADHI G  L+NDWSARDIQAWEY PLGPF
Sbjct: 198 GPCARLDYELELGIWIGQGNAMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPLGPF 257

Query: 256 LGKSFGTTISPWIVTLDALEPFGCQAPKQ---DPPPLPYLAEKE---SVNYDISLEVQLK 309
           L KSF T+ISPW+VT +ALEPF    P +   DP PLPYL +K    +  +DI LEV L 
Sbjct: 258 LSKSFITSISPWVVTAEALEPFRRAQPARPEGDPQPLPYLFDKRDQAAGAFDIELEVLLL 317

Query: 310 PSGRDDSCV----ITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDSYG 365
                +  +    +T SN Q++YWT+ Q +AHH+VNGC L+ GDL G+GT+SGPE   +G
Sbjct: 318 TESMREQNLPAHRLTLSNTQHMYWTVAQMVAHHSVNGCQLQAGDLFGSGTLSGPENGQFG 377

Query: 366 CLLELTWNGQKPLSL-NGTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIVPS 419
            LLE+T  G+KP+ L +G  + FLEDGD++     C  +G+ ++GFG C GK++P+
Sbjct: 378 SLLEITEGGKKPIELASGEVRKFLEDGDEIILRARCSREGFASIGFGECRGKVLPA 433


Lambda     K      H
   0.319    0.139    0.434 

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: 588
Number of extensions: 35
Number of successful extensions: 7
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: 421
Length of database: 434
Length adjustment: 32
Effective length of query: 389
Effective length of database: 402
Effective search space:   156378
Effective search space used:   156378
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Pf1N1B4_1024 (Fumarylacetoacetase (EC 3.7.1.2))
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.15127.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15127.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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