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= 006396
(647 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 30/74 (40%)
Query: 464 LQEAVQLLEDMYVIGVTPDQITYNTIIRSFCKCKDLRKAFQLLNQMWLHNLEPTSATYNI 523
L + + M V V P++ T+ R D AF ++ QM ++P +Y
Sbjct: 86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 524 LIDGLCVNGDLKNA 537
+ G C GD A
Sbjct: 146 ALFGFCRKGDADKA 159
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 31/152 (20%), Positives = 61/152 (40%), Gaps = 11/152 (7%)
Query: 179 HLLSQISGAWKVIQKLLIKGSDPDIVTYTVLICGYCQIGNVEEGLKLREVMLSQGFKLNV 238
H+ S + +K I+ S ++ + +C + G+V E L+L + G +L+
Sbjct: 4 HMASPSENLSRKAKKKAIQQSPEALLKQKLDMCS--KKGDVLEALRLYDEARRNGVQLSQ 61
Query: 239 IAYSVLL---------SSMCKSGRIDEALGLLYEMEAVGLKPDLVTYSILIRGLCKQDKV 289
Y+VLL + + + + +M + P+ T++ R +D
Sbjct: 62 YHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDP 121
Query: 290 HKAIQLYNEMCSKRISPNSFAHGAILLGLCEK 321
A + +M + I P ++G L G C K
Sbjct: 122 EMAFDMVKQMKAFGIQPRLRSYGPALFGFCRK 153
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 32.3 bits (72), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 38/179 (21%), Positives = 70/179 (39%), Gaps = 12/179 (6%)
Query: 390 KNGKVADARRLLDTIKLHGLEPSAVTYTTFM------NAYCEEG---NIQRLLALLQEME 440
K G V +A RL D + +G++ S Y + A E + R + ++
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 441 TKAIGPTHVTYTVVIKGLCKQWKLQEAVQLLEDMYVIGVTPDQITYNTIIRSFCKCKDLR 500
+ P T+T + + + A ++ G+ P +Y + FC+ D
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 501 KAFQLLNQMWLHNLEPTSATYNILIDGLCVNGDLKNADCLLVSLQEHNISLTKVAYTTI 559
KA+++ + P L L V+ D KNAD + +LQ + +V+ +T
Sbjct: 158 KAYEVDAHXVESEVVPEEPELAAL---LKVSXDTKNADKVYKTLQRLRDLVRQVSKSTF 213
>pdb|3PIH|A Chain A, T. Maritima Uvra In Complex With Fluorescein-Modified Dna
Length = 916
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 52/121 (42%), Gaps = 19/121 (15%)
Query: 45 DIMWDLYDDIKVSETPRN-VYTNSIVIDGLCQQSRLQDAILFLQETA---GKEF------ 94
+I ++Y +V E +N +T +V+D L ++R + IL E A GK F
Sbjct: 179 EIDGEIYRLEEVPELDKNKRHTVKLVVDRLILETRNEHRILDSLELAMREGKGFVEIRNV 238
Query: 95 --GPSVVSLNAIMSRYCKLGFAEVAKGLFCLMLKYGLHPDAFSYNILIHGLCIAGSMEEA 152
G S + +M C +GF E+ LF YG P+ HGL ++ +
Sbjct: 239 DTGESKIFSENLMCPVCGIGFPEITPKLFSFNSPYGACPNC-------HGLGFTFEVDPS 291
Query: 153 L 153
L
Sbjct: 292 L 292
>pdb|1H3D|A Chain A, Structure Of The E.Coli Atp-Phosphoribosyltransferase
pdb|1Q1K|A Chain A, Structure Of Atp-phosphoribosyltransferase From E. Coli
Complexed With Pr-atp
Length = 299
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 340 IQDVVLYNIMIDGYVKLGNIGEAVQLYRQLIEKRI---SPSIVTFNSLIYGFCK 390
++D + +++DG V LG IGE V L +L+ +R P T L +G C+
Sbjct: 53 VRDDDIPGLVMDGVVDLGIIGENV-LEEELLNRRAQGEDPRYFTLRRLDFGGCR 105
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 31/53 (58%)
Query: 236 LNVIAYSVLLSSMCKSGRIDEALGLLYEMEAVGLKPDLVTYSILIRGLCKQDK 288
L + Y+ ++ + G E + +L+ ++ GL PDL++Y+ ++ + +QD+
Sbjct: 163 LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQ 215
>pdb|1CB0|A Chain A, Structure Of Human 5'-deoxy-5'-methylthioadenosine
Phosphorylase At 1.7 A Resolution
pdb|1CG6|A Chain A, Structure Of Human 5'-Deoxy-5'-Methylthioadenosine
Phosphorylase Complexed With
5'-Deoxy-5'-Methylthioadenosine And Sulfate At 1.7 A
Resolution
pdb|1K27|A Chain A, Crystal Structure Of 5'-Deoxy-5'-Methylthioadenosine
Phosphorylase In Complex With A Transition State
Analogue
pdb|1SD1|A Chain A, Structure Of Human 5'-Deoxy-5'-Methylthioadenosine
Phosphorylase Complexed With Formycin A
pdb|1SD2|A Chain A, Structure Of Human 5'-Deoxy-5'-Methylthioadenosine
Phosphorylase Complexed With 5'-Methylthiotubercidin
pdb|3OZC|A Chain A, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase In Complex With Pcl-Phenylthiodadmeimma
pdb|3OZD|A Chain A, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase In Complex With Pcl-Phenylthiodadmeimma
pdb|3OZD|B Chain B, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase In Complex With Pcl-Phenylthiodadmeimma
pdb|3OZE|A Chain A, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
pdb|3OZE|B Chain B, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
pdb|3OZE|C Chain C, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
pdb|3OZE|D Chain D, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
pdb|3OZE|E Chain E, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
pdb|3OZE|F Chain F, Crystal Structure Of Human 5'-Deoxy-5'-Methyladenosine
Phosphorylase
Length = 283
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 532 GDLKNADCLLVSL--QEHNISLTKVAYTTIIKAHCAEGDVHKAMTFFC 577
G +KN DC+L++ ++H I +KV Y I A EG H +T C
Sbjct: 48 GKIKNVDCVLLARHGRQHTIMPSKVNYQANIWALKEEGCTHVIVTTAC 95
>pdb|4DIV|S Chain S, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|T Chain T, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|U Chain U, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|V Chain V, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|W Chain W, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
pdb|4DIV|X Chain X, The Structure Of A 1.8 Mda Viral Genome Injection Device
Suggests Alternative Infection Mechanisms
Length = 253
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 238 VIAYSVLLSSMCKSGRIDEALGLLYEMEAVGLKPDLVTYSILIRGLCKQD 287
+ +++VL S K G+I + E+ +KPD +++ +L GL D
Sbjct: 135 ISSFTVLCSDPFKHGKIQSVKNKVIEVLPYPVKPDKLSFKLLTEGLLATD 184
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 0.139 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,407,543
Number of Sequences: 62578
Number of extensions: 745470
Number of successful extensions: 2157
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2134
Number of HSP's gapped (non-prelim): 31
length of query: 647
length of database: 14,973,337
effective HSP length: 105
effective length of query: 542
effective length of database: 8,402,647
effective search space: 4554234674
effective search space used: 4554234674
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)