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= 041094
(523 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ID6|A Chain A, Crystal Structure Of Sulfolobus Solfataricus Nop5 (1-262)
And Fibrillarin Complex
Length = 268
Score = 32.3 bits (72), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 221 VAQAIGYKRLEKRYYDFIMRSGGWYYKDRLGRTRGPLELITLKTAWGAGIIDKDTFIWGE 280
VA I + E+ YY+F+ Y + +L +L+ ++ IDK ++ E
Sbjct: 100 VAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSE 159
Query: 281 DMDEWVPIH 289
+ EW IH
Sbjct: 160 RLREWYSIH 168
>pdb|3ID5|A Chain A, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3ID5|E Chain E, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3PLA|A Chain A, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|B Chain B, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|K Chain K, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
Length = 388
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%)
Query: 221 VAQAIGYKRLEKRYYDFIMRSGGWYYKDRLGRTRGPLELITLKTAWGAGIIDKDTFIWGE 280
VA I + E+ YY+F+ Y + +L +L+ ++ IDK ++ E
Sbjct: 100 VAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSE 159
Query: 281 DMDEWVPIH 289
+ EW IH
Sbjct: 160 RLREWYSIH 168
>pdb|3B8X|A Chain A, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
pdb|3B8X|B Chain B, Crystal Structure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase (Cold) H188n
Mutant With Bound Gdp-Perosamine
Length = 390
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 177 RPMPRKAIKTKEESDDKFWDFMKQFQFGLWGFRQRPYPPGRPIDVAQAIGYKRLEK--RY 234
R +P+K T +SDD+F + F+F L G+ RP ++++ AIG ++L+K R+
Sbjct: 221 RNLPKKNKVTGVKSDDQFEE---SFKFVLPGYNVRP------LEMSGAIGIEQLKKLPRF 271
Query: 235 YDFIMRSGGWYYKDRL 250
+ R Y+ D+
Sbjct: 272 IS-VRRKNAEYFLDKF 286
>pdb|2GMS|A Chain A, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMS|B Chain B, E Coli Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase With
Bound Hydrated Plp
pdb|2GMU|A Chain A, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
pdb|2GMU|B Chain B, Crystal Structure Of E Coli
Gdp-4-Keto-6-Deoxy-D-Mannose-3- Dehydratase Complexed
With Plp-Glutamate Ketimine Intermediate
Length = 390
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 177 RPMPRKAIKTKEESDDKFWDFMKQFQFGLWGFRQRPYPPGRPIDVAQAIGYKRLEK--RY 234
R +P+K T +SDD+F + F+F L G+ RP ++++ AIG ++L+K R+
Sbjct: 221 RNLPKKNKVTGVKSDDQFEE---SFKFVLPGYNVRP------LEMSGAIGIEQLKKLPRF 271
Query: 235 YDFIMRSGGWYYKDRL 250
+ R Y+ D+
Sbjct: 272 IS-VRRKNAEYFLDKF 286
>pdb|3GR9|A Chain A, Crystal Structure Of Cold H188k S187n
pdb|3GR9|B Chain B, Crystal Structure Of Cold H188k S187n
pdb|3GR9|C Chain C, Crystal Structure Of Cold H188k S187n
pdb|3GR9|D Chain D, Crystal Structure Of Cold H188k S187n
pdb|3GR9|E Chain E, Crystal Structure Of Cold H188k S187n
pdb|3GR9|F Chain F, Crystal Structure Of Cold H188k S187n
pdb|3GR9|G Chain G, Crystal Structure Of Cold H188k S187n
pdb|3GR9|H Chain H, Crystal Structure Of Cold H188k S187n
Length = 390
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 177 RPMPRKAIKTKEESDDKFWDFMKQFQFGLWGFRQRPYPPGRPIDVAQAIGYKRLEK--RY 234
R +P+K T +SDD+F + F+F L G+ RP ++++ AIG ++L+K R+
Sbjct: 221 RNLPKKNKVTGVKSDDQFEE---SFKFVLPGYNVRP------LEMSGAIGIEQLKKLPRF 271
Query: 235 YDFIMRSGGWYYKDRL 250
+ R Y+ D+
Sbjct: 272 IS-VRRKNAEYFLDKF 286
>pdb|2R0T|A Chain A, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
pdb|2R0T|B Chain B, Crystal Sructure Of
Gdp-4-Keto-6-Deoxymannose-3-Dehydratase With A Trapped
Plp-Glutamate Geminal Diamine
Length = 390
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 177 RPMPRKAIKTKEESDDKFWDFMKQFQFGLWGFRQRPYPPGRPIDVAQAIGYKRLEK--RY 234
R +P+K T +SDD+F + F+F L G+ RP ++++ AIG ++L+K R+
Sbjct: 221 RNLPKKNKVTGVKSDDQFEE---SFKFVLPGYNVRP------LEMSGAIGIEQLKKLPRF 271
Query: 235 YDFIMRSGGWYYKDRL 250
+ R Y+ D+
Sbjct: 272 IS-VRRKNAEYFLDKF 286
>pdb|1WH2|A Chain A, Solution Structure Of The Gyf Domain Of A Hypothetical
Protein From Arabidopsis Thaliana
Length = 78
Score = 28.5 bits (62), Expect = 8.7, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 244 WYYKDRLGRTRGPLELITLKTAWGAGIIDKDTFIW--GEDMDEWV 286
W YKD G +GP L LK A K +W GE M+ V
Sbjct: 20 WLYKDPQGLVQGPFSLTQLKAWSDAEYFTKQFRVWMTGESMESAV 64
>pdb|2D4W|A Chain A, Crystal Structure Of Glycerol Kinase From Cellulomonas Sp.
Nt3060
pdb|2D4W|B Chain B, Crystal Structure Of Glycerol Kinase From Cellulomonas Sp.
Nt3060
Length = 504
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 23/108 (21%), Positives = 46/108 (42%), Gaps = 17/108 (15%)
Query: 244 WYYKDRLGRTRGPLELITLKTAWGAGIIDKDTFIWGEDM--DEWVPIHMVYGLEKAIATW 301
W + G T G + + + A ++D DT W ED+ D +P+ M+ +
Sbjct: 166 WVLWNMTGGTEGGVHVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIR------ 219
Query: 302 EVRLGAAATAFLHKLQKGIPPWVPLKG----HEKKTYKQLQEEAMESR 345
+++ + H +G+ P VP+ G + T+ Q E +++
Sbjct: 220 -----SSSEVYGHGRPRGLVPGVPIAGILGDQQAATFGQACFEVGQAK 262
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 0.138 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,775,880
Number of Sequences: 62578
Number of extensions: 651062
Number of successful extensions: 1251
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1244
Number of HSP's gapped (non-prelim): 14
length of query: 523
length of database: 14,973,337
effective HSP length: 103
effective length of query: 420
effective length of database: 8,527,803
effective search space: 3581677260
effective search space used: 3581677260
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: 54 (25.4 bits)