BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 028581
         (207 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2WSC|D Chain D, Improved Model Of Plant Photosystem I
 pdb|2WSE|D Chain D, Improved Model Of Plant Photosystem I
 pdb|2WSF|D Chain D, Improved Model Of Plant Photosystem I
          Length = 212

 Score =  290 bits (743), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 155/216 (71%), Positives = 172/216 (79%), Gaps = 15/216 (6%)

Query: 3   MAATTQASLFAPANFST-----TKSSAPWKQSS--SFSVRPLKHNAPRTNTIKAMAEGKT 55
           MA  T A+LF+ ++ S+     T+ +  +KQ S  +F+ +P    A R +TI+A A  + 
Sbjct: 1   MAMGTPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFASKP----ASRLHTIRAAAAAEG 56

Query: 56  ETPTKEAPVG----FTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEM 111
           +             FTPPELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEM
Sbjct: 57  KAAAATETKEATKAFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEM 116

Query: 112 PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP 171
           PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYP
Sbjct: 117 PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYP 176

Query: 172 EKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           EKVNPGR+GVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 177 EKVNPGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL 212


>pdb|3LW5|D Chain D, Improved Model Of Plant Photosystem I
          Length = 138

 Score =  278 bits (711), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 133/138 (96%), Positives = 136/138 (98%)

Query: 70  ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 129
           ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAIMREGPNLLKLA
Sbjct: 1   ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLA 60

Query: 130 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN GR+GVGQN+RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIG 120

Query: 190 KNVSPIEVKFTGKQVYDL 207
           KNVSPIEVKFTGKQ YDL
Sbjct: 121 KNVSPIEVKFTGKQPYDL 138


>pdb|2O01|D Chain D, The Structure Of A Plant Photosystem I Supercomplex At 3.4
           Angstrom Resolution
          Length = 138

 Score =  274 bits (700), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 132/138 (95%), Positives = 134/138 (97%)

Query: 70  ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 129
           ELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA
Sbjct: 1   ELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 60

Query: 130 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           RKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNPGR+GVG N RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGLNMRSIG 120

Query: 190 KNVSPIEVKFTGKQVYDL 207
           KNVSPIEVKFTGKQ YDL
Sbjct: 121 KNVSPIEVKFTGKQPYDL 138


>pdb|1JB0|D Chain D, Crystal Structure Of Photosystem I: A Photosynthetic
           Reaction Center And Core Antenna System From
           Cyanobacteria
 pdb|3PCQ|D Chain D, Femtosecond X-Ray Protein Nanocrystallography
 pdb|4FE1|D Chain D, Improving The Accuracy Of Macromolecular Structure
           Refinement At 7 A Resolution
          Length = 138

 Score =  169 bits (427), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 81/130 (62%), Positives = 98/130 (75%), Gaps = 1/130 (0%)

Query: 78  PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLAL 137
           P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MREG NL+  ARKEQCLAL
Sbjct: 8   PLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLAL 67

Query: 138 GT-RLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIE 196
              +LR +    Y+ YR+FP+GE   +HPKDGV+PEKVN GRE V    RSIG+N +P +
Sbjct: 68  AAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQ 127

Query: 197 VKFTGKQVYD 206
           +KFTGK+ YD
Sbjct: 128 LKFTGKKPYD 137


>pdb|1O8P|A Chain A, Unbound Structure Of Cscbm6-3 From Clostridium
           Stercorarium
          Length = 151

 Score = 26.9 bits (58), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 67  TPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
           TP  ++    SP+  G T       Q E++   +   P  QIF +P GG+AI
Sbjct: 7   TPANVNSGPTSPV--GGTRSAFSNIQAEDY--DSSYGPNLQIFSLPGGGSAI 54


>pdb|1NAE|A Chain A, Structure Of Cscbm6-3 From Clostridium Stercorarium In
           Complex With Xylotriose
 pdb|1O8S|A Chain A, Structure Of Cscbm6-3 From Clostridium Stercorarium In
           Complex With Cellobiose
 pdb|1OD3|A Chain A, Structure Of Cscbm6-3 From Clostridium Stercorarium In
           Complex With Laminaribiose
          Length = 168

 Score = 26.9 bits (58), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 67  TPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
           TP  ++    SP+  G T       Q E++   +   P  QIF +P GG+AI
Sbjct: 24  TPANVNSGPTSPV--GGTRSAFSNIQAEDY--DSSYGPNLQIFSLPGGGSAI 71


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.314    0.131    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,769,268
Number of Sequences: 62578
Number of extensions: 305546
Number of successful extensions: 363
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 8
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)