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= 020206
(329 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1G8S|A Chain A, Methanococcus Jannaschii Fibrillarin Pre-Rrna Processing
Protein
Length = 230
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 84 KKVLIVFDDVNHPRQIEFLIGNLDWF-ASGSRILITARDKQALINCGVNKIY-QIKELVH 141
+KV ++++DV P Q E LI N WF G +I + + + +I+ + KE++
Sbjct: 142 EKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILE 201
Query: 142 VDALKLLNQC---AFGRDH 157
K++++ F +DH
Sbjct: 202 AGGFKIVDEVDIEPFEKDH 220
>pdb|1FBN|A Chain A, Crystal Structure Of A Fibrillarin Homologue From
Methanococcus Jannaschii, A Hyperthermophile, At 1.6 A
Length = 230
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 84 KKVLIVFDDVNHPRQIEFLIGNLDWF-ASGSRILITARDKQALINCGVNKIY-QIKELVH 141
+KV ++++DV P Q E LI N WF G I + + + +I+ + KE++
Sbjct: 142 EKVDVIYEDVAQPNQAEILIKNAKWFLKKGGYGXIAIKARSIDVTKDPKEIFKEQKEILE 201
Query: 142 VDALKLLNQC---AFGRDH 157
K++++ F +DH
Sbjct: 202 AGGFKIVDEVDIEPFEKDH 220
>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
Bound To Origin Dna (From S. Solfataricus)
Length = 386
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 20/98 (20%)
Query: 8 IWGIGGVGKTAIAGAFFSKISRRFEGSYFAH---NVREAEETGKLADLRKELLSTLLNDG 64
I+G+ G GKTA+ SK+ ++F G F H N R+ D +L+ LL
Sbjct: 50 IYGLTGTGKTAVVKFVLSKLHKKFLGK-FKHVYINTRQ-------IDTPYRVLADLLESL 101
Query: 65 NMNKFPNIGLNFQS--KRLTR------KKVLIVFDDVN 94
++ K P GL+ +RL + +V+IV D+++
Sbjct: 102 DV-KVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEID 138
>pdb|3A4Y|A Chain A, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|B Chain B, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|C Chain C, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|D Chain D, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 58/123 (47%), Gaps = 25/123 (20%)
Query: 111 SGSRILITARDKQALINCGVNKIYQIKELVHVDALKLLNQCAFGRDHPDASYIELTHEAI 170
+GS L+ A ++ L++CG ++Q KE + N FG D + + LTH A+
Sbjct: 13 TGSAHLLLAGGRRVLLDCG---MFQGKE-------EARNHAPFGFDPKEVDAVLLTHAAL 62
Query: 171 KYAQGVPIALKILGRFLFRK--RKEVWENAISKLEMVPQMEIQEVLKI---SYDGLDDKE 225
+ +P LFR+ R V+ + L M ++ +++ LK+ + G +D E
Sbjct: 63 DHVGRLPK--------LFREGYRGPVYATRATVLLM--EIVLEDALKVMDEPFFGPEDVE 112
Query: 226 KNI 228
+ +
Sbjct: 113 EAL 115
>pdb|1JCJ|A Chain A, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1JCJ|B Chain B, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
Length = 260
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 9/105 (8%)
Query: 144 ALKLLNQCAFGRDHPDASYIELTHEAIKYAQGVPIALKILGRFLFRKRKEVWENAISKLE 203
ALKL++ D D I L H+A K G A+ I RF+ RK + E
Sbjct: 12 ALKLMDLTTLNDDDTDEKVIALCHQA-KTPVGNTAAICIYPRFIPIARKTLKEQG----- 65
Query: 204 MVPQMEIQEVLKISYDGLDDKEKNIFLDIACFLVGEDR-DIVTKY 247
P++ I V + G DD + + A G D D+V Y
Sbjct: 66 -TPEIRIATVTNFPH-GNDDIDIALAETRAAIAYGADEVDVVFPY 108
>pdb|1KTN|A Chain A, Structural Genomics, Protein Ec1535
pdb|1KTN|B Chain B, Structural Genomics, Protein Ec1535
Length = 250
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 9/105 (8%)
Query: 144 ALKLLNQCAFGRDHPDASYIELTHEAIKYAQGVPIALKILGRFLFRKRKEVWENAISKLE 203
ALKL++ D D I L H+A K G A+ I RF+ RK + E
Sbjct: 11 ALKLMDLTTLNDDDTDEKVIALCHQA-KTPVGNTAAICIYPRFIPIARKTLKEQG----- 64
Query: 204 MVPQMEIQEVLKISYDGLDDKEKNIFLDIACFLVGEDR-DIVTKY 247
P++ I V + G DD + + A G D D+V Y
Sbjct: 65 -TPEIRIATVTNFPH-GNDDIDIALAETRAAIAYGADEVDVVFPY 107
>pdb|1JCL|A Chain A, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1JCL|B Chain B, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1P1X|A Chain A, Comparison Of Class I Aldolase Binding Site Architecture
Based On The Crystal Structure Of
2-Deoxyribose-5-Phosphate Aldolase Determined At 0.99
Angstrom Resolution
pdb|1P1X|B Chain B, Comparison Of Class I Aldolase Binding Site Architecture
Based On The Crystal Structure Of
2-Deoxyribose-5-Phosphate Aldolase Determined At 0.99
Angstrom Resolution
Length = 260
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 9/105 (8%)
Query: 144 ALKLLNQCAFGRDHPDASYIELTHEAIKYAQGVPIALKILGRFLFRKRKEVWENAISKLE 203
ALKL++ D D I L H+A K G A+ I RF+ RK + E
Sbjct: 12 ALKLMDLTTLNDDDTDEKVIALCHQA-KTPVGNTAAICIYPRFIPIARKTLKEQG----- 65
Query: 204 MVPQMEIQEVLKISYDGLDDKEKNIFLDIACFLVGEDR-DIVTKY 247
P++ I V + G DD + + A G D D+V Y
Sbjct: 66 -TPEIRIATVTNFPH-GNDDIDIALAETRAAIAYGADEVDVVFPY 108
>pdb|2J6I|A Chain A, Candida Boidinii Formate Dehydrogenase (Fdh) C-Terminal
Mutant
pdb|2J6I|B Chain B, Candida Boidinii Formate Dehydrogenase (Fdh) C-Terminal
Mutant
pdb|2J6I|C Chain C, Candida Boidinii Formate Dehydrogenase (Fdh) C-Terminal
Mutant
pdb|2J6I|D Chain D, Candida Boidinii Formate Dehydrogenase (Fdh) C-Terminal
Mutant
Length = 364
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 40/109 (36%), Gaps = 22/109 (20%)
Query: 84 KKVLIVFDDVNHPRQIEFL-------IGNLDWFASGSRILITARDKQA------------ 124
K VL+++D H E L +G +W LIT DK+
Sbjct: 2 KIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDA 61
Query: 125 --LINCGVNKIYQIKELV-HVDALKLLNQCAFGRDHPDASYIELTHEAI 170
+I + Y KE + LKL+ G DH D YI T + I
Sbjct: 62 DIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKI 110
>pdb|2WQM|A Chain A, Structure Of Apo Human Nek7
pdb|2WQN|A Chain A, Structure Of Adp-Bound Human Nek7
Length = 310
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 175 GVPIALKILGRFLFRKRKEVWENAISKLEMVPQMEIQEVLKISYDGLDDKEKNIFLDIA 233
GVP+ALK + F K + I +++++ Q+ V+K ++D E NI L++A
Sbjct: 57 GVPVALKKVQIFDLMDAK-ARADCIKEIDLLKQLNHPNVIKYYASFIEDNELNIVLELA 114
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
0.323 0.139 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,490,461
Number of Sequences: 62578
Number of extensions: 376009
Number of successful extensions: 1030
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 1021
Number of HSP's gapped (non-prelim): 28
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)