GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Shewanella sp. ANA-3

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

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



>FitnessBrowser__ANA3:7023380
          Length = 405

 Score =  541 bits (1394), Expect = e-158
 Identities = 266/406 (65%), Positives = 326/406 (80%), Gaps = 1/406 (0%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSV+   + RA FD VMVPNYAPAA IPVRG GSRVWDQ G E IDFAGGIAVN LGH H
Sbjct: 1   MSVD-MKLNRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCH 59

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV AL  Q  KLWH+SNV TNEPAL LA KLV++TFAERV+F NSGAEANEAA KLAR
Sbjct: 60  PALVNALKTQGEKLWHLSNVMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLAR 119

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R A ++FG EK EI+A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+PYND+AAL+
Sbjct: 120 RYALEKFGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALE 179

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AAVSDKTCA++LEP+QGEGG++ A+ ++L+  REL + HNAL++FDEVQTG+GR+G+L+A
Sbjct: 180 AAVSDKTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYA 239

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y    + PDILT+AK+LGGGFPIAAMLTT ++A+HL VGTHG+TYGGNPLACA+  AV+D
Sbjct: 240 YMGTDIVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLD 299

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVLNGV  +    +  L +I EKY +F+E+RG GLLLG VL++ ++G+++D   A
Sbjct: 300 VVNTPEVLNGVKHREQLLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVA 359

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           +  EGLM L AG +V+RFAPSLV+ +ADI  GL RFERA A +  A
Sbjct: 360 SVAEGLMSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASIAAA 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: 509
Number of extensions: 11
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 7023380 Shewana3_0610 (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.3092.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3092.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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