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= 010342
(512 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 = 35.4 bits (80), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 13 AHKLFFDMKSRGHVPNVVSYTTLIHGYCRTGEMDVAYKVFDEMRHCGVLPNSLTYSVLVR 72
A + MK+ G P + SY + G+CR G+ D AY+V M V+P + L++
Sbjct: 124 AFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLK 183
Query: 73 GVLRTRDVERANVLMFKLWERMKE 96
+ T++ ++ ++K +R+++
Sbjct: 184 VSMDTKNADK----VYKTLQRLRD 203
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 161 VVYVMRKRGLTPSLVSYNSIVHGLCKHGGCMRAYQL 196
+V M+ G+ P L SY + G C+ G +AY++
Sbjct: 127 MVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 423 VYAAMIKGLCRSGKIHEAVHFLYELVDSGVTPNIVCYNVVIDGACKLSMKREAYQI---L 479
+Y A++ G R G E V+ L+ + D+G+TP+++ Y + C ++A I L
Sbjct: 167 MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ--CMGRQDQDAGTIERCL 224
Query: 480 REMRKNGLNPDAV 492
+M + GL A+
Sbjct: 225 EQMSQEGLKLQAL 237
>pdb|2UY1|B Chain B, Crystal Structure Of Cstf-77
Length = 493
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 45/108 (41%), Gaps = 14/108 (12%)
Query: 15 KLFFDMKSRGHVPNVVSYTTLIHGYCRTGEMDVAYKVFDEMRHCGVL--PNS-LTYSVLV 71
KLF ++ + G P+V Y I Y TG Y +F G+L P+S L
Sbjct: 307 KLFIELGNEGVGPHVFIYCAFIEYYA-TGSRATPYNIFS----SGLLKHPDSTLLKEEFF 361
Query: 72 RGVLRTRDVERANVLMFKL------WERMKEEEDLSVNNAAFANLVDS 113
+LR D E A L +L W+ M E E + + F LVD
Sbjct: 362 LFLLRIGDEENARALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQ 409
>pdb|2UY1|A Chain A, Crystal Structure Of Cstf-77
Length = 493
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 45/108 (41%), Gaps = 14/108 (12%)
Query: 15 KLFFDMKSRGHVPNVVSYTTLIHGYCRTGEMDVAYKVFDEMRHCGVL--PNS-LTYSVLV 71
KLF ++ + G P+V Y I Y TG Y +F G+L P+S L
Sbjct: 307 KLFIELGNEGVGPHVFIYCAFIEYYA-TGSRATPYNIFS----SGLLKHPDSTLLKEEFF 361
Query: 72 RGVLRTRDVERANVLMFKL------WERMKEEEDLSVNNAAFANLVDS 113
+LR D E A L +L W+ M E E + + F LVD
Sbjct: 362 LFLLRIGDEENARALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQ 409
>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 = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 21 KSRGHVPNVVSYTTLIHGYCRTGEMDVAYKV 51
K+ G P + SY + G+CR G+ D AY+V
Sbjct: 132 KAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Score = 28.5 bits (62), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 169 GLTPSLVSYNSIVHGLCKHGGCMRAYQL 196
G+ P L SY + G C+ G +AY++
Sbjct: 135 GIQPRLRSYGPALFGFCRKGDADKAYEV 162
>pdb|2YQ4|A Chain A, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus
pdb|2YQ4|B Chain B, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus
pdb|2YQ4|C Chain C, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus
pdb|2YQ4|D Chain D, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus
pdb|2YQ5|A Chain A, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus: Nad Complexed Form
pdb|2YQ5|B Chain B, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus: Nad Complexed Form
pdb|2YQ5|C Chain C, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus: Nad Complexed Form
pdb|2YQ5|D Chain D, Crystal Structure Of D-isomer Specific 2-hydroxyacid
Dehydrogenase From Lactobacillus Delbrueckii Ssp.
Bulgaricus: Nad Complexed Form
Length = 343
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 411 DIVWPSNIHDNYVYAAMIKGLCRSGKIHEAVHFLYELVDSGVTPNIVCYN 460
D WPSN+ N +Y + GL G I AV ++ + + V V YN
Sbjct: 134 DFTWPSNLISNEIYNLTV-GLIGVGHIGSAVAEIFSAMGAKVIAYDVAYN 182
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
0.325 0.140 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,129,141
Number of Sequences: 62578
Number of extensions: 620107
Number of successful extensions: 1719
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1701
Number of HSP's gapped (non-prelim): 23
length of query: 512
length of database: 14,973,337
effective HSP length: 103
effective length of query: 409
effective length of database: 8,527,803
effective search space: 3487871427
effective search space used: 3487871427
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: 54 (25.4 bits)