GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Shewanella amazonensis SB2B

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

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



>FitnessBrowser__SB2B:6938908
          Length = 404

 Score =  536 bits (1381), Expect = e-157
 Identities = 258/394 (65%), Positives = 315/394 (79%)

Query: 10  RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTE 69
           RA FD+VMVPNYAPAA IPVRG GSRVWDQ G E +DFAGGIAVN LGH HPALV AL E
Sbjct: 9   RAQFDEVMVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKE 68

Query: 70  QANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGT 129
           Q  KLWH+SN  TNEPAL LA KLV+ATFA+RV+F NSGAEANEAA KLARR A ++FG 
Sbjct: 69  QGEKLWHLSNTMTNEPALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGE 128

Query: 130 EKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCA 189
            K E++A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+P+ND+AAL+AAVSD TCA
Sbjct: 129 HKVEVIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPAAITHLPFNDIAALEAAVSDNTCA 188

Query: 190 VVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPD 249
           ++LEP+QGEGG++  +  +L+  R L D HNAL++FDEVQTG+GR+G L+AY    + PD
Sbjct: 189 IMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPD 248

Query: 250 ILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLN 309
           ILT+AK+LGGGFPIAAMLTT D+A HL VGTHG+TYGGNPLACA+  AV+DV+NTPEVL+
Sbjct: 249 ILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLD 308

Query: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMIL 369
           GV  +   F+  L QI EKY +F+E+RG GLLLG VL++ + G+++D  NA+  EGL+ L
Sbjct: 309 GVKHREQLFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTL 368

Query: 370 QAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
            AG +V+RF PSLV+ +ADI  GL RFERA AK+
Sbjct: 369 MAGANVVRFTPSLVIPEADIVEGLARFERAVAKV 402


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: 501
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: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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 6938908 Sama_3011 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.7449.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7449.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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