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= 044044
(508 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 = 0.069, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 35/81 (43%)
Query: 158 VSHGFVVLGRILRSCFTPNAVTFTSLIKGLCAESRIMEAAALFTKHRVFACEPDVFTYNT 217
+S GF + +++ PN TFT+ + A+ A + + + F +P + +Y
Sbjct: 86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 218 LINGLCRTGHTIVALNLFEEM 238
+ G CR G A + M
Sbjct: 146 ALFGFCRKGDADKAYEVDAHM 166
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 37/153 (24%), Positives = 65/153 (42%), Gaps = 20/153 (13%)
Query: 201 TKHRVFACEPDVFTYNTLINGLC-RTGHTIVALNLFEEMANGNG------EFGV---VCK 250
K + P+ L +C + G + AL L++E A NG + V VC
Sbjct: 16 AKKKAIQQSPEALLKQKL--DMCSKKGDVLEALRLYDE-ARRNGVQLSQYHYNVLLYVCS 72
Query: 251 -PNTVTYNTIIDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSVIRGFCYANDWNEAKR 309
T ++ GL + GF ++F +M + + P+ T+T+ R +D A
Sbjct: 73 LAEAATESSPNPGLSR-GF-----DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFD 126
Query: 310 LFIEMMDQGVQPDVVTFSVIMDELCKNGKMDKA 342
+ +M G+QP + ++ + C+ G DKA
Sbjct: 127 MVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 27/123 (21%), Positives = 49/123 (39%), Gaps = 9/123 (7%)
Query: 306 EAKRLFIEMMDQGVQPDVVTFSVIM---------DELCKNGKMDKASRLLELMIWRGVNP 356
EA RL+ E GVQ ++V++ E N + + + + MI V P
Sbjct: 44 EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103
Query: 357 NTYTYNTLIDGYCLTDKIDHARKLFVSMESNGCMHDVVSYNTLINWYCKNKDVEEALSLY 416
N T+ D + A + M++ G + SY + +C+ D ++A +
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD 163
Query: 417 SEM 419
+ M
Sbjct: 164 AHM 166
>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 = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 30/69 (43%)
Query: 158 VSHGFVVLGRILRSCFTPNAVTFTSLIKGLCAESRIMEAAALFTKHRVFACEPDVFTYNT 217
+S GF + + + PN TFT+ + A+ A + + F +P + +Y
Sbjct: 86 LSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGP 145
Query: 218 LINGLCRTG 226
+ G CR G
Sbjct: 146 ALFGFCRKG 154
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 32.0 bits (71), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 256 YNTIIDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSVIRGFCYAN-DWNEAKRLFIEM 314
YN ++ G ++G + + +KD + PD+++Y + ++ + D +R +M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 315 MDQGVQPDVVTFSVIMDE 332
+G++ + +V++ E
Sbjct: 228 SQEGLKLQALFTAVLLSE 245
>pdb|2UY1|A Chain A, Crystal Structure Of Cstf-77
Length = 493
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 11/116 (9%)
Query: 378 RKLFVSMESNGCMHDVVSYNTLINWYCKNKDVEEALSLYSEMLSKGIKPTVVTYNTLFLG 437
RKLF+ + + G V Y I +Y +++S L K T++ FL
Sbjct: 306 RKLFIELGNEGVGPHVFIYCAFIEYYATGSRAT-PYNIFSSGLLKHPDSTLLK-EEFFLF 363
Query: 438 LFEIHQVERALKLFDEMRRNHVAADTYTYNNFIDGLCKSGFVLEALELFRAIRDSK 493
L I E A LF + + + D + + F++ ++ELFR + D K
Sbjct: 364 LLRIGDEENARALFKRLEKT---------SRMWDSMIEYEFMVGSMELFRELVDQK 410
>pdb|2UY1|B Chain B, Crystal Structure Of Cstf-77
Length = 493
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 48/116 (41%), Gaps = 11/116 (9%)
Query: 378 RKLFVSMESNGCMHDVVSYNTLINWYCKNKDVEEALSLYSEMLSKGIKPTVVTYNTLFLG 437
RKLF+ + + G V Y I +Y +++S L K T++ FL
Sbjct: 306 RKLFIELGNEGVGPHVFIYCAFIEYYATGSRAT-PYNIFSSGLLKHPDSTLLK-EEFFLF 363
Query: 438 LFEIHQVERALKLFDEMRRNHVAADTYTYNNFIDGLCKSGFVLEALELFRAIRDSK 493
L I E A LF + + + D + + F++ ++ELFR + D K
Sbjct: 364 LLRIGDEENARALFKRLEKT---------SRMWDSMIEYEFMVGSMELFRELVDQK 410
>pdb|4HRT|A Chain A, Scapharca Tetrameric Hemoglobin, Unliganded
pdb|4HRT|C Chain C, Scapharca Tetrameric Hemoglobin, Unliganded
pdb|4HRT|E Chain E, Scapharca Tetrameric Hemoglobin, Unliganded
pdb|4HRT|G Chain G, Scapharca Tetrameric Hemoglobin, Unliganded
pdb|1SCT|A Chain A, Scapharca Tetrameric Hemoglobin, Co-state
pdb|1SCT|C Chain C, Scapharca Tetrameric Hemoglobin, Co-state
pdb|1SCT|E Chain E, Scapharca Tetrameric Hemoglobin, Co-state
pdb|1SCT|G Chain G, Scapharca Tetrameric Hemoglobin, Co-state
Length = 150
Score = 30.0 bits (66), Expect = 3.0, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 389 CMHDVVSYNTLINWYCKNKDVEE-ALSLYSEMLSKGIKPTVVTYNTLFLGLFEIHQVERA 447
C + + N +W + D+E L L S + + ++P TY F L ++ + +
Sbjct: 10 CGSEAIKANLRRSWGVLSADIEATGLMLMSNLFT--LRPDTKTY---FTRLGDVQKGKAN 64
Query: 448 LKLFDEMRRNHVAADTYTYNNFIDGL 473
KL R H TY NNF+D L
Sbjct: 65 SKL-----RGHAITLTYALNNFVDSL 85
>pdb|4A1F|A Chain A, Crystal Structure Of C-Terminal Domain Of Helicobacter
Pylori Dnab Helicase
pdb|4A1F|B Chain B, Crystal Structure Of C-Terminal Domain Of Helicobacter
Pylori Dnab Helicase
Length = 338
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 19/23 (82%)
Query: 260 IDGLCKEGFVDKAKELFLKMKDE 282
ID L KEG +++A+EL+LK+ +E
Sbjct: 253 IDKLKKEGKIEEAQELYLKVNEE 275
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
0.323 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,520,122
Number of Sequences: 62578
Number of extensions: 585448
Number of successful extensions: 1639
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1617
Number of HSP's gapped (non-prelim): 27
length of query: 508
length of database: 14,973,337
effective HSP length: 103
effective length of query: 405
effective length of database: 8,527,803
effective search space: 3453760215
effective search space used: 3453760215
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)