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= 026701
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XB3|A Chain A, The Structure Of Cyanobacterial Psbp
Length = 165
Score = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 45/155 (29%), Positives = 67/155 (43%), Gaps = 9/155 (5%)
Query: 87 AFVDRIDGYSYVYPSDWTEFEFTGH-DSGFKDRYLQLQNVRVRF-IPTDKKDVHDLGPME 144
A+VD DGY ++YP W + + D F D +NV V K + +LG E
Sbjct: 10 AYVDSYDGYEFLYPRGWVQVQVEDPVDVVFHDIIETTENVSVVVNTVASTKSLEELGSPE 69
Query: 145 EVVSNLARHVYAAP--NQVADILDMQEKSVDGKNYYTFEYILTSPN-----YXXXXXXXX 197
EV L R++ A + + ++ + D K YY EY +T P
Sbjct: 70 EVGDRLLRNIIAPSESGRSSALIAATSQKADDKTYYILEYAVTLPGDGNTAQQRHNLSSI 129
Query: 198 XXXNGRYYTLIVGANERRWKRVRNKLKVVADSFRI 232
G+ YTL V A E RW +V ++ K + SF +
Sbjct: 130 AVSRGKVYTLSVSAPEERWPKVEDQFKTIVSSFTV 164
>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
Synechocystis Sp. Pcc 6803
Length = 170
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 43/154 (27%), Positives = 71/154 (46%), Gaps = 10/154 (6%)
Query: 88 FVDRIDGYSYVYPSDWTEFEFTGHDSG----FKDRYLQLQNVRVRF--IPTDKKDVHDLG 141
+ D DGY ++YP+ W + G G F+D + +N+ V IP+DK + DLG
Sbjct: 17 YSDTKDGYEFLYPNGWIGVDVKGASPGVDVVFRDLIERDENLSVIISEIPSDKT-LTDLG 75
Query: 142 PMEEVVSNLARHVYAAP--NQVADILDMQEKSVDGKNYYTFEY-ILTSPNYXXXXXXXXX 198
+V + V A ++ A++++ + + DG+ YYT EY +L N
Sbjct: 76 TATDVGYRFMKTVNDASQGDRQAELINAEARDEDGQVYYTLEYRVLVGDNVERHDLASVT 135
Query: 199 XXNGRYYTLIVGANERRWKRVRNKLKVVADSFRI 232
G+ T + E RW V++ VA SF +
Sbjct: 136 TNRGKLITFDLSTAEDRWDTVKSLFDTVASSFHV 169
>pdb|1V2B|A Chain A, Crystal Structure Of Psbp Protein In The Oxygen-Evolving
Complex Of Photosystem Ii From Higher Plants
pdb|1V2B|B Chain B, Crystal Structure Of Psbp Protein In The Oxygen-Evolving
Complex Of Photosystem Ii From Higher Plants
Length = 177
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 64/162 (39%), Gaps = 22/162 (13%)
Query: 93 DGYSYVYPSDWT---EFEFTGHDSGFKDRYLQLQNVRVRFIPTDKKDVHDLGPMEEVVSN 149
DG+ PS W E E+ G F+D + NV V PTDKK + D G E+ +S
Sbjct: 15 DGFKLQIPSKWNPNKEVEYPGQVLRFEDNFDATSNVIVAITPTDKKSITDFGSPEQFLSQ 74
Query: 150 ----LARHVYAAPNQ-----------VADILDMQEKSVDGKNYYTFEYILTSPNYXXXXX 194
L R Y+ +A++L+ V GK YY + + +
Sbjct: 75 VDYLLGRQAYSGKTDSEGGFESDAVAIANVLETSTAEVGGKQYYYLSILTRTADGNEGGK 134
Query: 195 X---XXXXXNGRYYTLIVGANERRW-KRVRNKLKVVADSFRI 232
+G+ Y A ++RW K + ++ A SF +
Sbjct: 135 HQLVTATVNDGKLYICKAQAGDKRWFKGAKKFVENTATSFSL 176
>pdb|2VU4|A Chain A, Structure Of Psbp Protein From Spinacia Oleracea At 1.98 A
Resolution
Length = 190
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 39/162 (24%), Positives = 64/162 (39%), Gaps = 22/162 (13%)
Query: 93 DGYSYVYPSDWT---EFEFTGHDSGFKDRYLQLQNVRVRFIPTDKKDVHDLGPMEEVVSN 149
DG+ + PS W E EF G ++D + N+ V PTDKK + D G E+ +S
Sbjct: 28 DGFKLLVPSKWNPSKEKEFPGQVLRYEDNFDATSNLSVLVQPTDKKSITDFGSPEDFLSQ 87
Query: 150 ----LARHVYAAPNQ-----------VADILDMQEKSVDGKNYYTFEYILTSPNYXXXXX 194
L + Y A++L+ VDGK YY+ + + +
Sbjct: 88 VDYLLGKQAYFGKTDSEGGFDSGVVASANVLESSTPVVDGKQYYSITVLTRTADGDEGGK 147
Query: 195 X---XXXXXNGRYYTLIVGANERRW-KRVRNKLKVVADSFRI 232
+G+ Y A ++RW K + ++ SF +
Sbjct: 148 HQVIAATVKDGKLYICKAQAGDKRWFKGAKKFVESATSSFSV 189
>pdb|1ECX|A Chain A, Nifs-Like Protein
pdb|1ECX|B Chain B, Nifs-Like Protein
Length = 384
Score = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 118 RYLQLQNVRVRFIPTDKKDVHDLGPMEEVV--SNLARHVYAAPNQVADILDMQE--KSVD 173
+YL ++ +V+++P D + V L +E++V + AA N+V I +++ + V
Sbjct: 107 KYLSMKGFKVKYVPVDSRGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTRIVK 166
Query: 174 GKNYYTFEYI 183
KN T ++
Sbjct: 167 KKNKETLVHV 176
>pdb|3K2Q|A Chain A, Crystal Structure Of Pyrophosphate-Dependent
Phosphofructokinase From Marinobacter Aquaeolei,
Northeast Structural Genomics Consortium Target Mqr88
pdb|3K2Q|B Chain B, Crystal Structure Of Pyrophosphate-Dependent
Phosphofructokinase From Marinobacter Aquaeolei,
Northeast Structural Genomics Consortium Target Mqr88
pdb|3K2Q|C Chain C, Crystal Structure Of Pyrophosphate-Dependent
Phosphofructokinase From Marinobacter Aquaeolei,
Northeast Structural Genomics Consortium Target Mqr88
Length = 420
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 72 PANSLFAQEIPKNYDAFVDRID------GYSYVYPSDWTEFE---FTGHDSGFKDRYLQL 122
P + + EIP N + F++R+D GY V S+ ++E F D+G KD +
Sbjct: 211 PPHVILFPEIPFNREKFLERVDQCVRDYGYCVVVASEGAQYEDGRFVA-DAGAKDAFGHT 269
Query: 123 Q 123
Q
Sbjct: 270 Q 270
>pdb|1EG5|A Chain A, Nifs-like Protein
pdb|1EG5|B Chain B, Nifs-like Protein
Length = 384
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 118 RYLQLQNVRVRFIPTDKKDVHDLGPMEEVV--SNLARHVYAAPNQVADILDMQE--KSVD 173
+YL + +V+++P D + V L +E++V + AA N+V I +++ + V
Sbjct: 107 KYLSXKGFKVKYVPVDSRGVVKLEELEKLVDEDTFLVSIXAANNEVGTIQPVEDVTRIVK 166
Query: 174 GKNYYTFEYI 183
KN T ++
Sbjct: 167 KKNKETLVHV 176
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
0.319 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,720,322
Number of Sequences: 62578
Number of extensions: 268467
Number of successful extensions: 505
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 494
Number of HSP's gapped (non-prelim): 13
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)