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= 003397
(823 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 59/127 (46%), Gaps = 1/127 (0%)
Query: 209 LDVRAYTSILHAYSKAGKYEKAISLFEKVKEMGLSPTLVTYNVMLDVYGKMGRSWDRILG 268
L + Y +++ +++ G +++ + + VK+ GL+P L++Y L G+ + I
Sbjct: 163 LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIER 222
Query: 269 LLDEMRSRGLEFDEFTCSTVISACGREGLLNEAKEFFAGLKLEGYVPGTVTYNSLLQ-VF 327
L++M GL+ + ++S R +L + L +P V + LL+ V+
Sbjct: 223 CLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVY 282
Query: 328 GKAGVYS 334
K G S
Sbjct: 283 AKDGRVS 289
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 666 NLVTYNNLMDMYARAGKCWKAEEILKGILKSGGTPDLVSYNTVIKGFCRQGLMQEA---M 722
L YN +M +AR G + +L + +G TPDL+SY ++ RQ Q+A
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQD--QDAGTIE 221
Query: 723 RMLYEMTNRGIR 734
R L +M+ G++
Sbjct: 222 RCLEQMSQEGLK 233
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 705 YNTVIKGFCRQGLMQEAMRMLYEMTNRGIRPCIFTYNTFVS--GYAGQGMFTEIDEVIKH 762
YN V+ G+ RQG +E + +L+ + + G+ P + +Y + G Q T I+ ++
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGT-IERCLEQ 226
Query: 763 MFQHNCK 769
M Q K
Sbjct: 227 MSQEGLK 233
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 30/127 (23%), Positives = 55/127 (43%), Gaps = 16/127 (12%)
Query: 320 YNSLLQVFGKAGVYSEALSILKEMEDNNCPPDSVTYNEVVGAYVR----AGFYEEGAALI 375
YN+++ + + G + E + +L ++D PD ++Y + R AG E +
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIER---CL 224
Query: 376 DTMSSKGLMPNAVTYTTLIDAYGRAGKVNKALRLLNKMKES-----GCAPNVCTYNAVLG 430
+ MS +GL A+ L+ RA L+ ++K+K + P V T +
Sbjct: 225 EQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKVKPTFSLPPQLPPPVNTSKLLRD 280
Query: 431 MLGKKGR 437
+ K GR
Sbjct: 281 VYAKDGR 287
>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 = 0.15, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 10/143 (6%)
Query: 595 PSWMLLRTLILVNFKCRALQGMERAFQELQKHGYKPDLVIFNSMLSICA---------KN 645
P +L + L + + K L+ + R + E +++G + +N +L +C+ N
Sbjct: 25 PEALLKQKLDMCSKKGDVLEAL-RLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPN 83
Query: 646 SMYDRANEMLHLILESGMQPNLVTYNNLMDMYARAGKCWKAEEILKGILKSGGTPDLVSY 705
R ++ ++ + PN T+ N + A +++K + G P L SY
Sbjct: 84 PGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSY 143
Query: 706 NTVIKGFCRQGLMQEAMRMLYEM 728
+ GFCR+G +A + M
Sbjct: 144 GPALFGFCRKGDADKAYEVDAHM 166
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 34/139 (24%), Positives = 56/139 (40%), Gaps = 19/139 (13%)
Query: 429 LGMLGKKGRSEEMMKILCDMKSSGCSPNRITWNTMLTMCG----------NKGLDKYVNQ 478
L M KKG E +++ + + +G ++ +N +L +C N GL + +
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFD- 91
Query: 479 VFREMKSCGFEPDRDTFNTLISAYGRCGSGVDATKMFEDMMKT----GFTPCVTTYNAFL 534
+F++M P+ TF R D +M DM+K G P + +Y L
Sbjct: 92 IFKQMIVDKVVPNEATFTN----GARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPAL 147
Query: 535 NALARRGDWKAAESVILDM 553
R+GD A V M
Sbjct: 148 FGFCRKGDADKAYEVDAHM 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 = 32.7 bits (73), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 10/139 (7%)
Query: 595 PSWMLLRTLILVNFKCRALQGMERAFQELQKHGYKPDLVIFNSMLSICA---------KN 645
P +L + L + K L+ + R + E +++G + +N +L +C+ N
Sbjct: 25 PEALLKQKLDXCSKKGDVLEAL-RLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPN 83
Query: 646 SMYDRANEMLHLILESGMQPNLVTYNNLMDMYARAGKCWKAEEILKGILKSGGTPDLVSY 705
R ++ + + PN T+ N + A + +K G P L SY
Sbjct: 84 PGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSY 143
Query: 706 NTVIKGFCRQGLMQEAMRM 724
+ GFCR+G +A +
Sbjct: 144 GPALFGFCRKGDADKAYEV 162
>pdb|3L7O|A Chain A, Crystal Structure Of Ribose-5-Phosphate Isomerase A From
Streptococcus Mutans Ua159
pdb|3L7O|B Chain B, Crystal Structure Of Ribose-5-Phosphate Isomerase A From
Streptococcus Mutans Ua159
Length = 225
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 615 GMERAFQELQKHGYKPDLVIFNSMLSIC-AKNSMYDRANEMLHLILESGMQPNLVTYNNL 673
G ER F+E +K GYKP ++ + + KN + D L+ G P+ + + N+
Sbjct: 140 GAERLFREFEKKGYKPSFREYDGVRFVTDMKNFIID---------LDLGSIPDPIAFGNM 190
Query: 674 MD 675
+D
Sbjct: 191 LD 192
>pdb|3EQN|A Chain A, Crystal Structure Of Beta-1,3-Glucanase From Phanerochaete
Chrysosporium (Lam55a)
pdb|3EQN|B Chain B, Crystal Structure Of Beta-1,3-Glucanase From Phanerochaete
Chrysosporium (Lam55a)
pdb|3EQO|A Chain A, Crystal Structure Of Beta-1,3-Glucanase From Phanerochaete
Chrysosporium (Lam55a) Gluconolactone Complex
pdb|3EQO|B Chain B, Crystal Structure Of Beta-1,3-Glucanase From Phanerochaete
Chrysosporium (Lam55a) Gluconolactone Complex
Length = 758
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 5/39 (12%)
Query: 479 VFREMKSCGFEPDRDTFNTL-----ISAYGRCGSGVDAT 512
VFR +K+ G + D +T +T I+A GRCG G D+T
Sbjct: 48 VFRNVKNYGAKGDGNTDDTAAIQAAINAGGRCGQGCDST 86
>pdb|3AS8|A Chain A, Mama Msr-1 P41212
pdb|3ASF|A Chain A, Mama Msr-1 C2
pdb|3ASF|B Chain B, Mama Msr-1 C2
Length = 186
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 328 GKAGVYSEALSILKEMEDNNCPPDSVTYNEVVGAYVRAGFYEEGAALIDTMSSKGLMPNA 387
KAG YSEA+ +L+++ D + V + + AYV+ G + G L++ S P+
Sbjct: 19 AKAGRYSEAVVMLEQVYDADAFDVEVALHLGI-AYVKTGAVDRGTELLE--RSIADAPDN 75
Query: 388 VTYTTLID-AYGRAGKVNKALRLLNKMKES 416
+ T++ Y + K + A+ LL K+ E+
Sbjct: 76 IKVATVLGLTYVQVQKYDLAVPLLVKVAEA 105
>pdb|3ASG|A Chain A, Mama D159k Mutant 2
pdb|3ASG|B Chain B, Mama D159k Mutant 2
pdb|3ASH|A Chain A, Mama D159k Mutant 1
pdb|3ASH|B Chain B, Mama D159k Mutant 1
Length = 186
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 328 GKAGVYSEALSILKEMEDNNCPPDSVTYNEVVGAYVRAGFYEEGAALIDTMSSKGLMPNA 387
KAG YS+A+ +L+++ D + V + + AYV+ G + G L++ S P+
Sbjct: 19 AKAGRYSQAVMLLEQVYDADAFDVDVALHLGI-AYVKTGAVDRGTELLE--RSLADAPDN 75
Query: 388 VTYTTLID-AYGRAGKVNKALRLLNKMKES 416
V T++ Y + K + A+ LL K+ E+
Sbjct: 76 VKVATVLGLTYVQVQKYDLAVPLLIKVAEA 105
>pdb|3ASD|A Chain A, Mama R50e Mutant
Length = 200
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 328 GKAGVYSEALSILKEMEDNNCPPDSVTYNEVVGAYVRAGFYEEGAALIDTMSSKGLMPNA 387
KAG YS+A+ +L+++ D + V + + AYV+ G + G L++ S P+
Sbjct: 19 AKAGRYSQAVMLLEQVYDADAFDVDVALHLGI-AYVKTGAVDRGTELLE--RSLADAPDN 75
Query: 388 VTYTTLID-AYGRAGKVNKALRLLNKMKES 416
V T++ Y + K + A+ LL K+ E+
Sbjct: 76 VKVATVLGLTYVQVQKYDLAVPLLIKVAEA 105
>pdb|3AS4|A Chain A, Mama Amb-1 C2221
pdb|3AS5|A Chain A, Mama Amb-1 P212121
pdb|3AS5|B Chain B, Mama Amb-1 P212121
Length = 186
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 328 GKAGVYSEALSILKEMEDNNCPPDSVTYNEVVGAYVRAGFYEEGAALIDTMSSKGLMPNA 387
KAG YS+A+ +L+++ D + V + + AYV+ G + G L++ S P+
Sbjct: 19 AKAGRYSQAVMLLEQVYDADAFDVDVALHLGI-AYVKTGAVDRGTELLE--RSLADAPDN 75
Query: 388 VTYTTLID-AYGRAGKVNKALRLLNKMKES 416
V T++ Y + K + A+ LL K+ E+
Sbjct: 76 VKVATVLGLTYVQVQKYDLAVPLLIKVAEA 105
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Orthorombic Crystal Form)
Length = 136
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 33/128 (25%), Positives = 59/128 (46%), Gaps = 10/128 (7%)
Query: 213 AYTSILHAYSKAGKYEKAISLFEKVKEMGLSPTLVTYNVMLDVYGKMGRSWDRILGLLDE 272
A+ ++ +AY K G Y++AI ++K E+ YN + + Y K G +D + E
Sbjct: 3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYN-LGNAYYKQG-DYDEAI----E 56
Query: 273 MRSRGLEFDEFTCS---TVISACGREGLLNEAKEFFAGLKLEGYVPGTVTYNSLLQVFGK 329
+ LE D + + +A ++G +EA E++ LE + +L + K
Sbjct: 57 YYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQK-ALELDPRSAEAWYNLGNAYYK 115
Query: 330 AGVYSEAL 337
G Y EA+
Sbjct: 116 QGDYDEAI 123
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
0.320 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,032,984
Number of Sequences: 62578
Number of extensions: 958445
Number of successful extensions: 2484
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2458
Number of HSP's gapped (non-prelim): 38
length of query: 823
length of database: 14,973,337
effective HSP length: 107
effective length of query: 716
effective length of database: 8,277,491
effective search space: 5926683556
effective search space used: 5926683556
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)