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= 020620
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 59/191 (30%), Positives = 96/191 (50%), Gaps = 12/191 (6%)
Query: 11 LKDILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDIS 70
+KD + ++P RE+ E R + IS +RE V+ + A + FGS+ ++L+ D+D
Sbjct: 25 IKDFVAYISPSREEIEIRNQTISTIREAVKQL--WPDADLHVFGSYSTDLYLPGSDIDCV 82
Query: 71 IELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCD 130
+ S G K ++ L L L++K ++ VA ARVPI+KF H I
Sbjct: 83 V-------TSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIA 135
Query: 131 ISIDNLCGQIKSKFLF-WISQIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVL 189
+S + G +K + W+ G R++VL+VK++ A +NN TG +S+ LV
Sbjct: 136 VSFERTNGIEAAKLIREWLDDTPG-LRELVLIVKQFLHARRLNNVHTGGLGGFSIICLV- 193
Query: 190 FHFQTCVPAIL 200
F F P I+
Sbjct: 194 FSFLHMHPRII 204
>pdb|4EP7|A Chain A, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
pdb|4EP7|B Chain B, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
Length = 340
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 49/174 (28%), Positives = 82/174 (47%), Gaps = 21/174 (12%)
Query: 48 ATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL 107
A + FGS S L + D+D+ + + + + + + L+ +
Sbjct: 46 AELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEG---------- 95
Query: 108 QFVAHARVPILKFETIHQN-----ISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLV 162
+F+ AR+PI+K + +N CDI +N + L +++D R + MVLLV
Sbjct: 96 KFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLV 155
Query: 163 KEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLK 216
K WAK IN+P GT +SY L+VL++ + I PP ++P L+ LK
Sbjct: 156 KHWAKRKQINSPYFGTLSSYGYVLMVLYYL---IHVIKPP---VFPNLLLSPLK 203
>pdb|4FHX|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - H336n Mutant Bound
To Mgatp
Length = 349
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/174 (28%), Positives = 82/174 (47%), Gaps = 21/174 (12%)
Query: 48 ATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL 107
A + FGS S L + D+D+ + + + + + + L+ +
Sbjct: 55 AELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEG---------- 104
Query: 108 QFVAHARVPILKFETIHQN-----ISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLV 162
+F+ AR+PI+K + +N CDI +N + L +++D R + MVLLV
Sbjct: 105 KFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLV 164
Query: 163 KEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLK 216
K WAK IN+P GT +SY L+VL++ + I PP ++P L+ LK
Sbjct: 165 KHWAKRKQINSPYFGTLSSYGYVLMVLYYL---IHVIKPP---VFPNLLLSPLK 212
>pdb|4FH3|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity
pdb|4FH5|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgutp Bound
pdb|4FHP|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Cautp Bound
pdb|4FHV|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgctp Bound
pdb|4FHW|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mggtp Bound
pdb|4FHY|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mg 3'-Datp Bound
Length = 349
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/174 (28%), Positives = 82/174 (47%), Gaps = 21/174 (12%)
Query: 48 ATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL 107
A + FGS S L + D+D+ + + + + + + L+ +
Sbjct: 55 AELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEG---------- 104
Query: 108 QFVAHARVPILKFETIHQN-----ISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLV 162
+F+ AR+PI+K + +N CDI +N + L +++D R + MVLLV
Sbjct: 105 KFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLV 164
Query: 163 KEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLK 216
K WAK IN+P GT +SY L+VL++ + I PP ++P L+ LK
Sbjct: 165 KHWAKRKQINSPYFGTLSSYGYVLMVLYYL---IHVIKPP---VFPNLLLSPLK 212
>pdb|4E7X|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
Length = 405
Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/174 (28%), Positives = 82/174 (47%), Gaps = 21/174 (12%)
Query: 48 ATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL 107
A + FGS S L + D+D+ + + + + + + L+ +
Sbjct: 83 AELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEG---------- 132
Query: 108 QFVAHARVPILKFETIHQN-----ISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLV 162
+F+ AR+PI+K + +N CDI +N + L +++D R + MVLLV
Sbjct: 133 KFLQRARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLV 192
Query: 163 KEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLK 216
K WAK IN+P GT +SY L+VL++ + I PP ++P L+ LK
Sbjct: 193 KHWAKRKQINSPYFGTLSSYGYVLMVLYYL---IHVIKPP---VFPNLLLSPLK 240
>pdb|3HJ1|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp
pdb|3HJ1|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp
Length = 387
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 47/153 (30%), Positives = 77/153 (50%), Gaps = 4/153 (2%)
Query: 44 SLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKG- 102
++ A VE FGS VS + D DIS+ N S ++V + + R ++
Sbjct: 45 AVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKRMTRFGKEASA 104
Query: 103 -GYRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVL- 160
G ++++ AR+P+++F I CD+SI N+ G SK L I Q+ F +
Sbjct: 105 MGMEDVRYI-RARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIH 163
Query: 161 LVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQ 193
LVK W KA ++ P+ TFNS++++ + L Q
Sbjct: 164 LVKAWGKAREVIAPERSTFNSFTVTTMALMVLQ 196
>pdb|3HIY|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HIY|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HJ4|A Chain A, Minor Editosome-Associated Tutase 1
pdb|3HJ4|B Chain B, Minor Editosome-Associated Tutase 1
Length = 384
Score = 65.5 bits (158), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/149 (30%), Positives = 74/149 (49%), Gaps = 4/149 (2%)
Query: 44 SLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKG- 102
++ A VE FGS VS + D DIS+ N S ++V + R ++
Sbjct: 42 AVNKAHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGXERVDEQNNKRXTRFGKEASA 101
Query: 103 -GYRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVL- 160
G ++++ AR+P+++F I CD+SI N+ G SK L I Q+ F +
Sbjct: 102 XGXEDVRYI-RARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIH 160
Query: 161 LVKEWAKAHDINNPKTGTFNSYSLSLLVL 189
LVK W KA ++ P+ TFNS++++ L
Sbjct: 161 LVKAWGKAREVIAPERSTFNSFTVTTXAL 189
>pdb|3PQ1|A Chain A, Crystal Structure Of Human Mitochondrial Poly(A)
Polymerase (Papd1)
pdb|3PQ1|B Chain B, Crystal Structure Of Human Mitochondrial Poly(A)
Polymerase (Papd1)
Length = 464
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 76/178 (42%), Gaps = 12/178 (6%)
Query: 89 SLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWI 148
S+LG+ L G +Q + +AR P+++F C ++ +N S+ L+
Sbjct: 234 SVLGECLDHF--GPGCVGVQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIY 291
Query: 149 SQIDGRFRDMVLLVKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTCVPAILPPLKDIY 207
+D R R +V V+ WA+AH + + G + ++SL+ V+F Q P ILP L
Sbjct: 292 GALDSRVRALVFSVRCWARAHSLTSSIPGAWITNFSLTXXVIFFLQRRSPPILPTL---- 347
Query: 208 PGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLS 265
D LK + ++ + E R S N +L L F E F +
Sbjct: 348 -----DSLKTLADAEDKCVIEGNNCTFVRDLSRIKPSQNTETLELLLKEFFEYFGNFA 400
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 53/210 (25%), Positives = 91/210 (43%), Gaps = 44/210 (20%)
Query: 14 ILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIEL 73
ILG LN L ++W ++ IS+ + + +SV G + FGS+ + ++ D+D
Sbjct: 64 ILGKLNNLVKEW---IREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADID----- 115
Query: 74 SNGSCISSAGKKVKQS-LLGDLLRALRQKGGYRRLQFVAHARVPILK--FETIHQNI--- 127
C+ A + V +S L+ + + L+ V A VP++K F+ I +I
Sbjct: 116 --ALCV--APRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFA 171
Query: 128 --------------------SCDI-SIDNLCG-QIKSKFLFWISQIDGRFRDMVLLVKEW 165
+ DI I +L G ++ + L + ID FR + +K W
Sbjct: 172 RLALQTIPEDLDLRDDSLLKNLDIRXIRSLNGCRVTDEILHLVPNIDN-FRLTLRAIKLW 230
Query: 166 AKAHDINNPKTGTFNSYSLSLLVLFHFQTC 195
AK H+I + G S ++LV +TC
Sbjct: 231 AKRHNIYSNILGFLGGVSWAMLVA---RTC 257
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 53/210 (25%), Positives = 91/210 (43%), Gaps = 44/210 (20%)
Query: 14 ILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIEL 73
ILG LN L ++W ++ IS+ + + +SV G + FGS+ + ++ D+D
Sbjct: 64 ILGKLNNLVKEW---IREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADID----- 115
Query: 74 SNGSCISSAGKKVKQS-LLGDLLRALRQKGGYRRLQFVAHARVPILK--FETIHQNI--- 127
C+ A + V +S L+ + + L+ V A VP++K F+ I +I
Sbjct: 116 --ALCV--APRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLXFDGIEIDILFA 171
Query: 128 --------------------SCDI-SIDNLCG-QIKSKFLFWISQIDGRFRDMVLLVKEW 165
+ DI I +L G ++ + L + ID FR + +K W
Sbjct: 172 RLALQTIPEDLDLRDDSLLKNLDIRXIRSLNGCRVTDEILHLVPNIDN-FRLTLRAIKLW 230
Query: 166 AKAHDINNPKTGTFNSYSLSLLVLFHFQTC 195
AK H+I + G S ++LV +TC
Sbjct: 231 AKRHNIYSNILGFLGGVSWAMLVA---RTC 257
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 87/203 (42%), Gaps = 41/203 (20%)
Query: 14 ILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIEL 73
ILG LN L ++W ++ IS+ + + +SV G + FGS+ + ++ D+D
Sbjct: 64 ILGKLNNLVKEW---IREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADID----- 115
Query: 74 SNGSCISSAGKKVKQS-LLGDLLRALRQKGGYRRLQFVAHARVPILK--FETIHQNI--- 127
C+ A + V +S L+ + + L+ V A VP++K F+ I +I
Sbjct: 116 --ALCV--APRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFA 171
Query: 128 --------------------SCDIS-IDNLCG-QIKSKFLFWISQIDGRFRDMVLLVKEW 165
+ DI I +L G ++ + L + ID FR + +K W
Sbjct: 172 RLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDN-FRLTLRAIKLW 230
Query: 166 AKAHDINNPKTGTFNSYSLSLLV 188
AK H+I + G S + LV
Sbjct: 231 AKRHNIYSNILGFLGGVSWAXLV 253
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 24/121 (19%)
Query: 112 HARVPILKFETIHQNISCDISID-NLCGQI---------KSKFLFWISQIDGRFRDMVLL 161
+A+V ++K ETI ++ D ++D N G+I +S+ L +IDGR +DM+
Sbjct: 273 YAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMI-- 330
Query: 162 VKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRA 220
+ D+ +TG ++ +L Q V A L +D ++D+L G R
Sbjct: 331 -----RGLDV---RTGVLPRTHGSALFTRGETQALVTATLGTARD---AQVLDELMGERT 379
Query: 221 N 221
+
Sbjct: 380 D 380
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 24/121 (19%)
Query: 112 HARVPILKFETIHQNISCDISID-NLCGQI---------KSKFLFWISQIDGRFRDMVLL 161
+A+V ++K ETI ++ D ++D N G+I +S+ L +IDGR +DM+
Sbjct: 267 YAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMI-- 324
Query: 162 VKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRA 220
+ D+ +TG ++ +L Q V A L +D ++D+L G R
Sbjct: 325 -----RGLDV---RTGVLPRTHGSALFTRGETQALVTATLGTARD---AQVLDELMGERT 373
Query: 221 N 221
+
Sbjct: 374 D 374
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 24/121 (19%)
Query: 112 HARVPILKFETIHQNISCDISID-NLCGQI---------KSKFLFWISQIDGRFRDMVLL 161
+A+V ++K ETI ++ D ++D N G+I +S+ L +IDGR +DM+
Sbjct: 267 YAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMI-- 324
Query: 162 VKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRA 220
+ D+ +TG ++ +L Q V A L +D ++D+L G R
Sbjct: 325 -----RGLDV---RTGVLPRTHGSALFTRGETQALVTATLGTARD---AQVLDELMGERT 373
Query: 221 N 221
+
Sbjct: 374 D 374
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 24/121 (19%)
Query: 112 HARVPILKFETIHQNISCDISID-NLCGQI---------KSKFLFWISQIDGRFRDMVLL 161
+A+V ++K ETI ++ D ++D N G+I +S+ L +IDGR +DM+
Sbjct: 273 YAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGREKDMI-- 330
Query: 162 VKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRA 220
+ D+ +TG ++ +L Q V A L +D ++D+L G R
Sbjct: 331 -----RGLDV---RTGVLPRTHGSALFTRGETQALVTATLGTARD---AQVLDELMGERT 379
Query: 221 N 221
+
Sbjct: 380 D 380
>pdb|2HAF|A Chain A, Crystal Structure Of A Putative Translation Repressor From
Vibrio Cholerae
Length = 211
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 9 PILKDILGMLNPLREDWETRMKVISDLR-EVVESVESLRGATVEPFGSFVSNLFSRWGDL 67
P+ +D +L+ R+ +E+ MK+ D+ + + ++ G EP G V+ +S W
Sbjct: 92 PVSEDRGFILHRPRDHYESSMKMTDDIAVTTSKDILTVLGTEAEPEGYIVALGYSGWSAG 151
Query: 68 DISIELSNGSCIS 80
+ +EL+ S ++
Sbjct: 152 QLEVELTENSWLT 164
>pdb|2AJ2|A Chain A, X-Ray Crystal Structure Of Protein Vc0467 From Vibrio
Cholerae. Northeast Structural Genomics Consortium
Target Vcr8
Length = 208
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 9 PILKDILGMLNPLREDWETRMKVISDLR-EVVESVESLRGATVEPFGSFVSNLFSRWGDL 67
P+ +D +L+ R+ +E+ K D+ + + ++ G EP G V+ +S W
Sbjct: 90 PVSEDRGFILHRPRDHYESSXKXTDDIAVTTSKDILTVLGTEAEPEGYIVALGYSGWSAG 149
Query: 68 DISIELSNGSCIS 80
+ +EL+ S ++
Sbjct: 150 QLEVELTENSWLT 162
>pdb|1I6U|A Chain A, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
pdb|1I6U|B Chain B, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
Length = 130
Score = 27.7 bits (60), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 19/101 (18%)
Query: 73 LSNGSCISSAGKKV-----KQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNI 127
L++ S GKKV L+G +L+ + G +F+ R I K E I +
Sbjct: 11 LNHISNCERVGKKVVYIKPASKLIGRVLKVXQDNGYIGEFEFIEDGRAGIFKVELIGK-- 68
Query: 128 SCDISIDNLCGQIKSKF---LFWISQIDGRF---RDMVLLV 162
N CG IK +F F + + R+ RD +L+
Sbjct: 69 ------INKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILI 103
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
0.324 0.140 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,334,706
Number of Sequences: 62578
Number of extensions: 359658
Number of successful extensions: 1034
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1008
Number of HSP's gapped (non-prelim): 26
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)