GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas fluorescens GW456-L13

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971
          Length = 406

 Score =  775 bits (2001), Expect = 0.0
 Identities = 386/406 (95%), Positives = 397/406 (97%)

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

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAER FFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVA DR+G+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK
Sbjct: 121 RVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AAVSDKTCAVVLEPIQGEGGVLPAEL+YLQGARELC+ HNALLVFDEVQTGMGR+G LFA
Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDEVQTGMGRTGHLFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGV PDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVA AVID
Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           VINTPEVL GVNAKHDKFK RLEQIGEKYGLFT+VRGLGLL+GCVLSDAWKGKAKDIFNA
Sbjct: 301 VINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+EGLMILQAGPDV+RFAPSLVVEDADIDAGLDRFERAAAKLTQA
Sbjct: 361 AEQEGLMILQAGPDVVRFAPSLVVEDADIDAGLDRFERAAAKLTQA 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: 657
Number of extensions: 7
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 PfGW456L13_1971 (Succinylornithine transaminase (EC 2.6.1.81))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.15843.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15843.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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