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= 006020
(664 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VRT|A Chain A, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
Fragments - Catalytic Domain
pdb|2VRT|B Chain B, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
Fragments - Catalytic Domain
pdb|2VRT|C Chain C, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
Fragments - Catalytic Domain
pdb|2VRT|D Chain D, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
Fragments - Catalytic Domain
Length = 509
Score = 197 bits (501), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 131/405 (32%), Positives = 208/405 (51%), Gaps = 38/405 (9%)
Query: 237 EADFEDFLEGDHHLDGESNGFFPSKS---EVPDDSHTSHPQGTKDSKHTPGEKTWLQVQK 293
EA F D+ E +GF P K E ++++H + P K L+ +
Sbjct: 54 EAAFVDY-------GAERHGFLPLKEIAREYFPANYSAHGR--------PNIKDVLR--E 96
Query: 294 GTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIG-VSRKITGVERTRLKVIAK 352
G +VIVQ+ KE G KG LT + L + +L+ + R G +SR+I G +RT LK
Sbjct: 97 GQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALA 156
Query: 353 TLQ-PEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPIL 411
+L+ PEG GL +RT G S E LQ DL L W+ I + A+S P L
Sbjct: 157 SLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRP----------APFL 206
Query: 412 LHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIA-PDLCDRVELYDKRIPLF 470
+H+ + +DY + + ++++D+P+ ++ + PD +++LY IPLF
Sbjct: 207 IHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLF 266
Query: 471 DKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNL 530
+ IE +I + + V LP+GGS+VI+ TEAL +ID+N G E+ + NL
Sbjct: 267 SHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARAT--RGGDIEETAFNTNL 324
Query: 531 AAAKQIARELRLRXXXXXXXXXXXXMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGL 590
AA +IAR+LRLR M ++R V +++AV +DR+ +++S +SR GL
Sbjct: 325 EAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGL 384
Query: 591 MEITRKRVRPSVTFMISEPCTCCQGTGRV---EALETSFSKIEQE 632
+E++R+R+ PS+ C C GTG V E+L S ++ +E
Sbjct: 385 LEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEE 429
>pdb|2BX2|L Chain L, Catalytic Domain Of E. Coli Rnase E
pdb|2C0B|L Chain L, Catalytic Domain Of E. Coli Rnase E In Complex With 13-Mer
Rna
pdb|2C4R|L Chain L, Catalytic Domain Of E. Coli Rnase E
Length = 517
Score = 197 bits (501), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 131/405 (32%), Positives = 208/405 (51%), Gaps = 38/405 (9%)
Query: 237 EADFEDFLEGDHHLDGESNGFFPSKS---EVPDDSHTSHPQGTKDSKHTPGEKTWLQVQK 293
EA F D+ E +GF P K E ++++H + P K L+ +
Sbjct: 61 EAAFVDY-------GAERHGFLPLKEIAREYFPANYSAHGR--------PNIKDVLR--E 103
Query: 294 GTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIG-VSRKITGVERTRLKVIAK 352
G +VIVQ+ KE G KG LT + L + +L+ + R G +SR+I G +RT LK
Sbjct: 104 GQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALA 163
Query: 353 TLQ-PEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPIL 411
+L+ PEG GL +RT G S E LQ DL L W+ I + A+S P L
Sbjct: 164 SLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRP----------APFL 213
Query: 412 LHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIA-PDLCDRVELYDKRIPLF 470
+H+ + +DY + + ++++D+P+ ++ + PD +++LY IPLF
Sbjct: 214 IHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLF 273
Query: 471 DKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNL 530
+ IE +I + + V LP+GGS+VI+ TEAL +ID+N G E+ + NL
Sbjct: 274 SHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARAT--RGGDIEETAFNTNL 331
Query: 531 AAAKQIARELRLRXXXXXXXXXXXXMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGL 590
AA +IAR+LRLR M ++R V +++AV +DR+ +++S +SR GL
Sbjct: 332 EAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGL 391
Query: 591 MEITRKRVRPSVTFMISEPCTCCQGTGRV---EALETSFSKIEQE 632
+E++R+R+ PS+ C C GTG V E+L S ++ +E
Sbjct: 392 LEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEE 436
>pdb|2VMK|A Chain A, Crystal Structure Of E. Coli Rnase E Apoprotein -
Catalytic Domain
pdb|2VMK|B Chain B, Crystal Structure Of E. Coli Rnase E Apoprotein -
Catalytic Domain
pdb|2VMK|C Chain C, Crystal Structure Of E. Coli Rnase E Apoprotein -
Catalytic Domain
pdb|2VMK|D Chain D, Crystal Structure Of E. Coli Rnase E Apoprotein -
Catalytic Domain
Length = 515
Score = 197 bits (500), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 131/405 (32%), Positives = 208/405 (51%), Gaps = 38/405 (9%)
Query: 237 EADFEDFLEGDHHLDGESNGFFPSKS---EVPDDSHTSHPQGTKDSKHTPGEKTWLQVQK 293
EA F D+ E +GF P K E ++++H + P K L+ +
Sbjct: 54 EAAFVDY-------GAERHGFLPLKEIAREYFPANYSAHGR--------PNIKDVLR--E 96
Query: 294 GTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIG-VSRKITGVERTRLKVIAK 352
G +VIVQ+ KE G KG LT + L + +L+ + R G +SR+I G +RT LK
Sbjct: 97 GQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALA 156
Query: 353 TLQ-PEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPIL 411
+L+ PEG GL +RT G S E LQ DL L W+ I + A+S P L
Sbjct: 157 SLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRP----------APFL 206
Query: 412 LHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIA-PDLCDRVELYDKRIPLF 470
+H+ + +DY + + ++++D+P+ ++ + PD +++LY IPLF
Sbjct: 207 IHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLF 266
Query: 471 DKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNL 530
+ IE +I + + V LP+GGS+VI+ TEAL +ID+N G E+ + NL
Sbjct: 267 SHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARAT--RGGDIEETAFNTNL 324
Query: 531 AAAKQIARELRLRXXXXXXXXXXXXMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGL 590
AA +IAR+LRLR M ++R V +++AV +DR+ +++S +SR GL
Sbjct: 325 EAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGL 384
Query: 591 MEITRKRVRPSVTFMISEPCTCCQGTGRV---EALETSFSKIEQE 632
+E++R+R+ PS+ C C GTG V E+L S ++ +E
Sbjct: 385 LEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEE 429
>pdb|3U07|A Chain A, Crystal Structure Of The Vpa0106 Protein From Vibrio
Parahaemolyticus. Northeast Structural Genomics
Consortium Target Vpr106.
pdb|3U07|B Chain B, Crystal Structure Of The Vpa0106 Protein From Vibrio
Parahaemolyticus. Northeast Structural Genomics
Consortium Target Vpr106.
pdb|3U07|C Chain C, Crystal Structure Of The Vpa0106 Protein From Vibrio
Parahaemolyticus. Northeast Structural Genomics
Consortium Target Vpr106
Length = 443
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 39/104 (37%), Gaps = 22/104 (21%)
Query: 258 FPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYP 317
F ++ + DDS+T+HP D+ H G WL V VIV V G
Sbjct: 61 FQNRRALADDSYTAHPTINNDTLHLXG---WLDVA-AEPVIVSVPDXDEG---------- 106
Query: 318 KLRSRFWILITS----CDRIGVSRKITGVERTRLKVIAKTLQPE 357
R+WIL T S + G + + A+ Q E
Sbjct: 107 ----RYWILHTXDXGHYTNAAFSSRTRGTKGGQFXFAAQDWQGE 146
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
0.315 0.132 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,040,825
Number of Sequences: 62578
Number of extensions: 705356
Number of successful extensions: 1706
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1682
Number of HSP's gapped (non-prelim): 15
length of query: 664
length of database: 14,973,337
effective HSP length: 105
effective length of query: 559
effective length of database: 8,402,647
effective search space: 4697079673
effective search space used: 4697079673
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 55 (25.8 bits)