GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas putida KT2440

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase

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



>FitnessBrowser__Putida:PP_4481
          Length = 406

 Score =  698 bits (1802), Expect = 0.0
 Identities = 334/405 (82%), Positives = 374/405 (92%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVE A V+RADFDQVMVPNY+PAAFIPVRG GSRVWDQSGRELIDFAGGIAVN LGH H
Sbjct: 1   MSVEQAPVQRADFDQVMVPNYSPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVNALGHCH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQAN LWHVSNVFTNEPALRLAHKLVDATFA+R FFCNSGAE+NEAAFKLAR
Sbjct: 61  PALVKALTEQANTLWHVSNVFTNEPALRLAHKLVDATFADRAFFCNSGAESNEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVAHDRFG +K+EI+A +NSFHGRTLFTV+VGGQ KYSDGFGPKITGI+HVPYNDL ALK
Sbjct: 121 RVAHDRFGPQKHEIIATVNSFHGRTLFTVSVGGQPKYSDGFGPKITGISHVPYNDLEALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           A +SDKTCAVV+EPIQGE GV+PA+ +YL+GAR+LCD HNALL+FDEVQTG+GR+G L+A
Sbjct: 181 AQISDKTCAVVIEPIQGESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRTGSLYA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGV PDILTSAKSLGGGFPI AMLTT +LAKHL VGTHGTTYGGNPL CAVA AV+D
Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAVACAVLD 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPE L G+ AKH++FKTRLEQIG++Y LF++VRG+GLLLGCVL++AWKGKAKD+ NA
Sbjct: 301 VVNTPETLAGIKAKHERFKTRLEQIGQQYNLFSQVRGVGLLLGCVLTEAWKGKAKDVLNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQ 405
           AE+EG+M+LQAGPDV+RFAPSLVVEDADID GLDRFERA A LT+
Sbjct: 361 AEKEGVMVLQAGPDVVRFAPSLVVEDADIDEGLDRFERAVATLTK 405


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: 595
Number of extensions: 9
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 PP_4481 PP_4481 (Succinylornithine transaminase/acetylornithine aminotransferase)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.32006.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32006.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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