GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2E3

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate AO353_15550 AO353_15550 homogentisate 1,2-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_15550
         (434 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15550
          Length = 434

 Score =  902 bits (2330), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60
           MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA
Sbjct: 1   MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA 120
           RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA
Sbjct: 61  RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA 120

Query: 121 NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL 180
           NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL
Sbjct: 121 NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT 240
           PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT
Sbjct: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT 240

Query: 241 TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 420
           LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 420

Query: 421 CWASLPVTFNPNRR 434
           CWASLPVTFNPNRR
Sbjct: 421 CWASLPVTFNPNRR 434


Lambda     K      H
   0.320    0.137    0.433 

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: 912
Number of extensions: 25
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 AO353_15550 AO353_15550 (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.24304.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24304.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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