GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella oneidensis MR-1

Align 3-deoxy-7-phosphoheptulonate synthase, Tyr-sensitive (EC 2.5.1.54) (characterized)
to candidate 200536 SO1361 phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (NCBI ptt file)

Query= ecocyc::AROF-MONOMER
         (356 letters)



>FitnessBrowser__MR1:200536
          Length = 363

 Score =  463 bits (1192), Expect = e-135
 Identities = 223/354 (62%), Positives = 281/354 (79%)

Query: 1   MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60
           MQ+D +NNVHI+ E VL+TP++LKAA PLS      I ++RK+++DI+  RD R+L++ G
Sbjct: 1   MQQDTINNVHISSENVLITPQELKAALPLSEHAYRYILNARKTVADIVHKRDNRVLIITG 60

Query: 61  PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120
           PCSIHD + A EYA + K L  E+SD  Y++MRVYFEKPRTTVGWKG+INDP MDGSFDV
Sbjct: 61  PCSIHDIDAAKEYALKLKKLHDELSDEFYILMRVYFEKPRTTVGWKGMINDPDMDGSFDV 120

Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180
           E GL++AR+L++ L  + LP+ATEALDP SPQY+ +L +WSAIGARTTESQTHREMASGL
Sbjct: 121 EKGLKLARELMIWLAELELPVATEALDPISPQYISELVTWSAIGARTTESQTHREMASGL 180

Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAP 240
           SMPVGFKNGTDG L  AINA+++AA  HRF+GINQ GQVALLQT GNPDGHVILRGG  P
Sbjct: 181 SMPVGFKNGTDGKLDVAINALKSAASSHRFMGINQQGQVALLQTAGNPDGHVILRGGVTP 240

Query: 241 NYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL 300
           NY  A VA+CE ++ +A L   L++DCSHGNS+KDY RQ  V E V AQI +GN+SIIG+
Sbjct: 241 NYDAASVAECEAQLHKAKLNARLIIDCSHGNSSKDYARQVPVCEDVFAQIYNGNKSIIGV 300

Query: 301 MIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           M+ES+++EGNQS ++P  E+ YGVSVTD+CI+WE T+++LR     L+  L  R
Sbjct: 301 MLESHLNEGNQSCDKPSGELAYGVSVTDSCINWEKTESVLRAGASKLSSVLPTR 354


Lambda     K      H
   0.316    0.131    0.378 

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: 426
Number of extensions: 6
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: 356
Length of database: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 200536 SO1361 (phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (NCBI ptt file))
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

Software error:

../bin/blast/fastacmd -i /tmp/list.10551.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10551.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.