GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Shewanella loihica PV-4

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

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



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  546 bits (1407), Expect = e-160
 Identities = 267/403 (66%), Positives = 323/403 (80%), Gaps = 1/403 (0%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSV H  + RA FD+VMVPNYAP+A IPVRG GSRVWDQ G E +DFAGGIAVN LGH H
Sbjct: 1   MSVNHK-LTRAQFDEVMVPNYAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCH 59

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV AL EQ  K+WH++NV TNEPAL LA KLV+ATFAE+V+F NSGAEANEAA KLAR
Sbjct: 60  PALVGALKEQGEKIWHLANVMTNEPALALATKLVEATFAEKVYFANSGAEANEAALKLAR 119

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R A D+FG EK +I+A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+P+ND+AAL+
Sbjct: 120 RYALDKFGAEKDQIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALE 179

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           A VSDKTCA++LEP+QGEGG++ A+  +L+  R L D HNAL++FDEVQTG+GR G+L+A
Sbjct: 180 AEVSDKTCAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYA 239

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y    VTPDILT+AK+LGGGFPIAAMLTT ++A HL +GTHG+TYGGNPLACA+  AV+D
Sbjct: 240 YMRTEVTPDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLD 299

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVL+GV  +    +  L QI EKY +FTEVRG GLLLG VL++ ++G++KD   A
Sbjct: 300 VVNTPEVLDGVKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVA 359

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
              EGLM L AGP+VIRF PSLV+ +ADI  GL RFERA AK+
Sbjct: 360 GTSEGLMCLIAGPNVIRFTPSLVIPEADIAEGLARFERAVAKV 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: 503
Number of extensions: 10
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: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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 5208066 Shew_0578 (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.4724.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4724.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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