GapMind for catabolism of small carbon sources

 

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

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate AO356_16825 AO356_16825 homogentisate 1,2-dioxygenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_16825
          Length = 434

 Score =  869 bits (2245), Expect = 0.0
 Identities = 415/434 (95%), Positives = 423/434 (97%)

Query: 1   MNLVSPASDLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEA 60
           MNL S  SDLAYQSG GNEFASEALPGALP+GQNSPQK PYGLYAELFSGTAFTMARSEA
Sbjct: 1   MNLDSTMSDLAYQSGLGNEFASEALPGALPIGQNSPQKAPYGLYAELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAA 120
           RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPL+IPAEPTDF+DGLVCMAA
Sbjct: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLDIPAEPTDFLDGLVCMAA 120

Query: 121 NAGADKPAGISLYQYQANRSMERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVL 180
           NAGADKPAG+SLY Y+ANRSMERVFFNADGEWLIVPQLGRLRI TELGVLELAPLEI VL
Sbjct: 121 NAGADKPAGVSLYHYRANRSMERVFFNADGEWLIVPQLGRLRIATELGVLELAPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPT 240
           PRGLKFR+ELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YENLAQPT
Sbjct: 181 PRGLKFRVELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYENLAQPT 240

Query: 241 SLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           +LVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGG S
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGTS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420
           LHSCMSAHGPDGETCTKAINA+LQP KIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINADLQPAKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420

Query: 421 CWASLPVTFDPTRR 434
           CWASLPVTFDPTRR
Sbjct: 421 CWASLPVTFDPTRR 434


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: 915
Number of extensions: 24
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 AO356_16825 AO356_16825 (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.2727.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2727.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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