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= 029058
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 36/87 (41%), Gaps = 7/87 (8%)
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 ----LARHVYAAPNQVADILDMQEVCI 172
L R Y+ + V I
Sbjct: 75 VDYLLGRQAYSGKTDSEGGFESDAVAI 101
>pdb|2VU4|A Chain A, Structure Of Psbp Protein From Spinacia Oleracea At 1.98 A
Resolution
Length = 190
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
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 L 150
+
Sbjct: 88 V 88
>pdb|2XB3|A Chain A, The Structure Of Cyanobacterial Psbp
Length = 165
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
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 EVVSNLARHVYA 156
EV L R++ A
Sbjct: 70 EVGDRLLRNIIA 81
>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
Synechocystis Sp. Pcc 6803
Length = 170
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
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 PMEEV 146
+V
Sbjct: 76 TATDV 80
>pdb|1ECX|A Chain A, Nifs-Like Protein
pdb|1ECX|B Chain B, Nifs-Like Protein
Length = 384
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 118 RYLQLQNVRVRFIPTDKKDVHDLGPMEEVV--SNLARHVYAAPNQVADILDMQEVC 171
+YL ++ +V+++P D + V L +E++V + AA N+V I +++V
Sbjct: 107 KYLSMKGFKVKYVPVDSRGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVT 162
>pdb|1EG5|A Chain A, Nifs-like Protein
pdb|1EG5|B Chain B, Nifs-like Protein
Length = 384
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 118 RYLQLQNVRVRFIPTDKKDVHDLGPMEEVV--SNLARHVYAAPNQVADILDMQEVC 171
+YL + +V+++P D + V L +E++V + AA N+V I +++V
Sbjct: 107 KYLSXKGFKVKYVPVDSRGVVKLEELEKLVDEDTFLVSIXAANNEVGTIQPVEDVT 162
>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 = 28.5 bits (62), Expect = 2.6, 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|3I0Z|A Chain A, Crystal Structure Of Putative Putative
Tagatose-6-Phosphate KetoseALDOSE ISOMERASE
(NP_344614.1) FROM STREPTOCOCCUS PNEUMONIAE Tigr4 At
1.70 A Resolution
pdb|3I0Z|B Chain B, Crystal Structure Of Putative Putative
Tagatose-6-Phosphate KetoseALDOSE ISOMERASE
(NP_344614.1) FROM STREPTOCOCCUS PNEUMONIAE Tigr4 At
1.70 A Resolution
Length = 389
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 145 EVVSNLARHVYAAPNQVADILDMQEVCIFY----PGFGYDMAASL-LLQLPTGKV 194
EVVS+LAR V V +++D+ + Y P FG A L +L+L G+V
Sbjct: 206 EVVSSLARKVLDKAEDVKELVDLDFNRVIYLGAGPFFGLAHEAQLKILELTAGQV 260
>pdb|2WS2|A Chain A, The 2 Angstrom Structure Of A Nu-Class Gst From Haemonchus
Contortus
pdb|2WS2|B Chain B, The 2 Angstrom Structure Of A Nu-Class Gst From Haemonchus
Contortus
Length = 204
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 37 QNFFTCPEDISSDEENKSKRRLLLMGAGLLTANLLPANSLFAQEIPKNYDAF 88
Q FFT I +ENK+ L+G L A+L A F + PK YD F
Sbjct: 130 QKFFTIVTKIL--KENKTG---YLVGDSLTFADLYVAEMGFTEHYPKLYDGF 176
>pdb|1WMD|A Chain A, Crystal Structure Of Alkaline Serine Protease Kp-43 From
Bacillus Sp. Ksm-Kp43 (1.30 Angstrom, 100 K)
pdb|1WME|A Chain A, Crystal Structure Of Alkaline Serine Protease Kp-43 From
Bacillus Sp. Ksm-kp43 (1.50 Angstrom, 293 K)
Length = 434
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 10 WVSTTLSKKLNVAYPNELTRSATAFSCQNFFTC 42
W TL K LNVAY NE + +T+ FT
Sbjct: 307 WGRVTLDKSLNVAYVNESSSLSTSQKATYSFTA 339
>pdb|3B0Y|A Chain A, K263d Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 151 ARHVYAAPNQVADILDM-QEVCIFYPGFGYDMAASLLLQLPTGKVK 195
AR +Y + +I + +E + PG G D+A +L L TGKV+
Sbjct: 34 ARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVR 79
>pdb|3B0X|A Chain A, K263a Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 151 ARHVYAAPNQVADILDM-QEVCIFYPGFGYDMAASLLLQLPTGKVK 195
AR +Y + +I + +E + PG G D+A +L L TGKV+
Sbjct: 34 ARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVR 79
>pdb|3AU2|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Complexed
With Ca-Dgtp
pdb|3AU6|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With PrimerTEMPLATE DNA AND DDGTP
pdb|3AUO|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
pdb|3AUO|B Chain B, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
Length = 575
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 151 ARHVYAAPNQVADILDM-QEVCIFYPGFGYDMAASLLLQLPTGKVK 195
AR +Y + +I + +E + PG G D+A +L L TGKV+
Sbjct: 34 ARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVR 79
>pdb|1WMF|A Chain A, Crystal Structure Of Alkaline Serine Protease Kp-43 From
Bacillus Sp. Ksm-kp43 (oxidized Form, 1.73 Angstrom)
Length = 434
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 10 WVSTTLSKKLNVAYPNELTRSATAFSCQNFFTC 42
W TL K LNVAY NE + +T+ FT
Sbjct: 307 WGRVTLDKSLNVAYVNESSSLSTSQKATYSFTA 339
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
0.320 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,881,380
Number of Sequences: 62578
Number of extensions: 239450
Number of successful extensions: 474
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 467
Number of HSP's gapped (non-prelim): 19
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)