GapMind for catabolism of small carbon sources

 

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

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03025
          Length = 406

 Score =  768 bits (1984), Expect = 0.0
 Identities = 379/406 (93%), Positives = 396/406 (97%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVEHAAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKL+DATFA+RVFFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVAHDRFG+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHV +NDL ALK
Sbjct: 121 RVAHDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AA+SDKTCAVVLEPIQGEGGVLPA+L+YLQGARELC  HNALL+FDEVQTGMGRSG+LFA
Sbjct: 181 AAISDKTCAVVLEPIQGEGGVLPADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID
Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVLNGV AKHD FKTRLEQIG KYGLFT+VRGLGLLLGCVLS+AWKGKAKD+FNA
Sbjct: 301 VVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AEREGLMILQAGPDVIRFAPSLVVEDADI+ GL+RFERA AKLTQA
Sbjct: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFERAVAKLTQA 406


Lambda     K      H
   0.320    0.136    0.400 

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: 666
Number of extensions: 8
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 AO353_03025 AO353_03025 (acetylornithine aminotransferase)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.4109.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4109.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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