GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Shewanella amazonensis SB2B

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= CharProtDB::CH_024084
         (386 letters)



>FitnessBrowser__SB2B:6936711
          Length = 659

 Score =  409 bits (1051), Expect = e-118
 Identities = 213/386 (55%), Positives = 275/386 (71%), Gaps = 7/386 (1%)

Query: 1   MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60
           M    PL   RE+I+ +D  +L LLA RREL++EV ++K +  RPVRD  RER+LL RL+
Sbjct: 1   MEKPQPLSETREQITDIDNTVLQLLARRRELSLEVARSKEVDVRPVRDTQRERELLSRLV 60

Query: 61  TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSAR----IAFLGPKGSYS 116
             G+   LD H++ +L+Q IIEDSVL QQA L     + NP + +    IA+LG +GSYS
Sbjct: 61  QKGREQGLDPHFVMQLYQSIIEDSVLNQQAYLH---GRANPETQKQQYCIAYLGARGSYS 117

Query: 117 HLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHT 176
           +LAA +Y  R     ++ GC  F +I + VE+G ADY  +PIENTSSG+IN+VYD+LQHT
Sbjct: 118 YLAANRYCQRRQVDMVDLGCQSFDEIVHAVESGHADYGFLPIENTSSGSINEVYDVLQHT 177

Query: 177 SLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSA 236
           SL+IVGE T+ + HCLL    T  S I T+Y+HPQP  QCS++L R+P  ++EY  S++ 
Sbjct: 178 SLAIVGETTIEVGHCLLAKPGTKASDIKTLYAHPQPISQCSRYLARHPGLRLEYCASSAE 237

Query: 237 AMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPA 296
           AMEKV  A S  VAA+GS  GG LY L+ +E+  ANQ+ N +RF+V+ARKA+ V +Q+PA
Sbjct: 238 AMEKVQAADSKDVAAIGSAEGGGLYQLEAIEKGLANQKVNQSRFIVVARKAVAVPEQLPA 297

Query: 297 KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQ 356
           K TL+MATGQ+ GALVEALLVL+ +NL M++LESRPI G PWEEMFYLDI ANL S  MQ
Sbjct: 298 KCTLIMATGQKPGALVEALLVLKANNLNMSKLESRPIPGTPWEEMFYLDIDANLASVPMQ 357

Query: 357 KALKELGEITRSMKVLGCYPSENVVP 382
            ALKEL  ITR +KVLGCYP E V P
Sbjct: 358 LALKELERITRFIKVLGCYPCETVAP 383


Lambda     K      H
   0.318    0.132    0.374 

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: 499
Number of extensions: 13
Number of successful extensions: 2
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: 386
Length of database: 659
Length adjustment: 34
Effective length of query: 352
Effective length of database: 625
Effective search space:   220000
Effective search space used:   220000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 6936711 Sama_0898 (prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
to HMM TIGR01797 (chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.3753.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3753.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.