GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Sphingomonas koreensis DSMZ 15582

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Ga0059261_2265 Ga0059261_2265 phosphoserine aminotransferase apoenzyme (EC 2.6.1.52)

Query= BRENDA::P52878
         (370 letters)



>FitnessBrowser__Korea:Ga0059261_2265
          Length = 378

 Score =  456 bits (1174), Expect = e-133
 Identities = 219/369 (59%), Positives = 269/369 (72%), Gaps = 2/369 (0%)

Query: 3   PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62
           P   P  P FSSGPCAK PG+S ++L     GRSHRS LGK +L  AI   R+ML LPD 
Sbjct: 8   PATKPARPYFSSGPCAKPPGWSADKLHTEVLGRSHRSKLGKTRLQYAIDLMREMLKLPDT 67

Query: 63  YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122
           + +GIVP SDTGAFEM +W+MLG RGV  L WESF +GW TD  KQLKL D  V  A+YG
Sbjct: 68  HRIGIVPGSDTGAFEMAMWTMLGARGVTTLAWESFGEGWVTDAVKQLKL-DPTVIRADYG 126

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182
           +LPDL +VDF +DV+F WNGTTSGV+VPNGDWIP++REGLT  D+TSA+FA D+P+ K+D
Sbjct: 127 QLPDLSQVDFADDVLFTWNGTTSGVRVPNGDWIPDDREGLTFADSTSAVFAYDLPWDKID 186

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242
           V TFSWQKVLGGEG HG+LIL PRAV+RLE YTPAWPLPK+FRL   GKL + +F+G TI
Sbjct: 187 VATFSWQKVLGGEGGHGVLILGPRAVERLEQYTPAWPLPKVFRLMAKGKLAEGVFKGETI 246

Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSMLA ED +  L+WA+ +GGL  LI R++ N A  +  VA+ +W+  LA  +  RS 
Sbjct: 247 NTPSMLAVEDAIFALEWAKGLGGLDGLIARSDANAAALDKIVAERDWLGHLAADEATRSK 306

Query: 303 TSVCFKVDLSDEK-LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCEW 361
           TSVC  V+ +DE  +K     LEK   AYD+  YRDAP+GLRIWCGATV+  D++ L  W
Sbjct: 307 TSVCLTVEGADEAFIKTFASLLEKADAAYDVAGYRDAPAGLRIWCGATVDTADIEALGPW 366

Query: 362 IEWAYNLVK 370
           ++WAY   K
Sbjct: 367 LDWAYASAK 375


Lambda     K      H
   0.318    0.136    0.429 

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: 489
Number of extensions: 17
Number of successful extensions: 3
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: 370
Length of database: 378
Length adjustment: 30
Effective length of query: 340
Effective length of database: 348
Effective search space:   118320
Effective search space used:   118320
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2265 Ga0059261_2265 (phosphoserine aminotransferase apoenzyme (EC 2.6.1.52))
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))

Software error:

../bin/blast/fastacmd -i /tmp/list.11000.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11000.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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