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= 004244
(766 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 = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/164 (25%), Positives = 67/164 (40%), Gaps = 44/164 (26%)
Query: 336 KEGNLHQALVLHAEMVRNGLS-----PNVVTYT-SLINSMCKSG---NLNRAMEFFDQMH 386
K+G++ +AL L+ E RNG+ NV+ Y SL + +S L+R + F QM
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 387 VRELRPNEKTYTTLINGFSQHGFLDEAYRLLNEMTKNGFMPSIVTYNALIKGHCTGGRVE 446
V ++ PNE T+T NG ++ + E
Sbjct: 98 VDKVVPNEATFT------------------------NGARLAVAKDDP-----------E 122
Query: 447 DAVGVLHGMARKGLAPDVVSYSTIISGFSRSQELDKAFDTKREM 490
A ++ M G+ P + SY + GF R + DKA++ M
Sbjct: 123 MAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM 166
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 11/111 (9%)
Query: 203 AEEVYNEMGKSRVSPNVYTYNVLIRGFCGVGD----------LEMGLRFFSEMEKNNCLA 252
A +Y+E ++ V + Y YNVL+ C + + L G F +M + +
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103
Query: 253 NVVTYNTLIDGYCKLGRIDDAFKLLRDMGLKGIEPNLISYNVIINGLCKEG 303
N T+ + AF +++ M GI+P L SY + G C++G
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Score = 38.1 bits (87), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 33/156 (21%), Positives = 63/156 (40%), Gaps = 26/156 (16%)
Query: 405 SQHGFLDEAYRLLNEMTKNGFMPSIVTYNALIKGHCTGGRVEDAVGVLHGMARKGLAPDV 464
S+ G + EA RL +E +NG S YN L+ V
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY--------------------------V 70
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQRRITEACELFQE 524
S + + S + L + FD ++M+ V+P+ T+++ + A ++ ++
Sbjct: 71 CSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQ 130
Query: 525 MLSRGMSPDEFTYTTLINAYCTEGDIPQALRLHDEM 560
M + G+ P +Y + +C +GD +A + M
Sbjct: 131 MKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM 166
Score = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 32/146 (21%), Positives = 60/146 (41%), Gaps = 9/146 (6%)
Query: 301 KEGRLKETKGILNEISRKGLVPDEVTYNTLL---------NGYCKEGNLHQALVLHAEMV 351
K+G + E + +E R G+ + YN LL L + + +M+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 352 RNGLSPNVVTYTSLINSMCKSGNLNRAMEFFDQMHVRELRPNEKTYTTLINGFSQHGFLD 411
+ + PN T+T+ + A + QM ++P ++Y + GF + G D
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 412 EAYRLLNEMTKNGFMPSIVTYNALIK 437
+AY + M ++ +P AL+K
Sbjct: 158 KAYEVDAHMVESEVVPEEPELAALLK 183
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 54/135 (40%), Gaps = 25/135 (18%)
Query: 233 GDLEMGLRFFSEMEKNNCLANVVTYNTLIDGYCKLGR----------IDDAFKLLRDMGL 282
GD+ LR + E +N + YN L+ C L + F + + M +
Sbjct: 40 GDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQMIV 98
Query: 283 KGIEPNLISYNVIINGLCKEGRLKETK-------GILNEISRKGLVPDEVTYNTLLNGYC 335
+ PN ++ NG RL K ++ ++ G+ P +Y L G+C
Sbjct: 99 DKVVPNEATF---TNG----ARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151
Query: 336 KEGNLHQALVLHAEM 350
++G+ +A + A M
Sbjct: 152 RKGDADKAYEVDAHM 166
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 53/130 (40%), Gaps = 11/130 (8%)
Query: 261 IDGYCKLGRIDDAFKLLRDMGLKGIEPNLISYNVIINGLCKEGR----------LKETKG 310
+D K G + +A +L + G++ + YNV++ +C L
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFD 91
Query: 311 ILNEISRKGLVPDEVTYNTLLNGYCKEGNLHQALVLHAEMVRNGLSPNVVTYTSLINSMC 370
I ++ +VP+E T+ + + A + +M G+ P + +Y + C
Sbjct: 92 IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151
Query: 371 KSGNLNRAME 380
+ G+ ++A E
Sbjct: 152 RKGDADKAYE 161
>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 = 35.8 bits (81), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 65/164 (39%), Gaps = 44/164 (26%)
Query: 331 LNGYCKEGNLHQALVLHAEMVRNGLS-----PNVVTYT-SLINSMCKSG---NLNRAMEF 381
L+ K+G++ +AL L+ E RNG+ NV+ Y SL + +S L+R +
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 382 FDQMHVRELRPNEKTYTTLINGFSQHGFLDEAYRLLNEMTKNGFMPSIVTYNALIKGHCT 441
F Q V ++ PNE T+T NG ++ +
Sbjct: 93 FKQXIVDKVVPNEATFT------------------------NGARLAVAKDDP------- 121
Query: 442 GGRVEDAVGVLHGMARKGLAPDVVSYSTIISGFSRSQELDKAFD 485
E A + G+ P + SY + GF R + DKA++
Sbjct: 122 ----EXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYE 161
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 44/108 (40%), Gaps = 11/108 (10%)
Query: 206 VYNEMGKSRVSPNVYTYNVLIRGFCGVGD----------LEMGLRFFSEMEKNNCLANVV 255
+Y+E ++ V + Y YNVL+ C + + L G F + + + N
Sbjct: 48 LYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQXIVDKVVPNEA 106
Query: 256 TYNTLIDGYCKLGRIDDAFKLLRDMGLKGIEPNLISYNVIINGLCKEG 303
T+ + AF ++ GI+P L SY + G C++G
Sbjct: 107 TFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 30/149 (20%), Positives = 58/149 (38%), Gaps = 26/149 (17%)
Query: 405 SQHGFLDEAYRLLNEMTKNGFMPSIVTYNALIKGHCTGGRVEDAVGVLHGMARKGLAPDV 464
S+ G + EA RL +E +NG S YN L+ V
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY--------------------------V 70
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQRRITEACELFQE 524
S + + S + L + FD ++ + V+P+ T+++ + A + ++
Sbjct: 71 CSLAEAATESSPNPGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQ 130
Query: 525 MLSRGMSPDEFTYTTLINAYCTEGDIPQA 553
+ G+ P +Y + +C +GD +A
Sbjct: 131 XKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/130 (19%), Positives = 51/130 (39%), Gaps = 9/130 (6%)
Query: 296 INGLCKEGRLKETKGILNEISRKGLVPDEVTYNTLL---------NGYCKEGNLHQALVL 346
++ K+G + E + +E R G+ + YN LL L + +
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 347 HAEMVRNGLSPNVVTYTSLINSMCKSGNLNRAMEFFDQMHVRELRPNEKTYTTLINGFSQ 406
+ + + + PN T+T+ + A + Q ++P ++Y + GF +
Sbjct: 93 FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCR 152
Query: 407 HGFLDEAYRL 416
G D+AY +
Sbjct: 153 KGDADKAYEV 162
>pdb|3C6K|A Chain A, Crystal Structure Of Human Spermine Synthase In Complex
With Spermidine And 5-Methylthioadenosine
pdb|3C6K|B Chain B, Crystal Structure Of Human Spermine Synthase In Complex
With Spermidine And 5-Methylthioadenosine
pdb|3C6K|C Chain C, Crystal Structure Of Human Spermine Synthase In Complex
With Spermidine And 5-Methylthioadenosine
pdb|3C6K|D Chain D, Crystal Structure Of Human Spermine Synthase In Complex
With Spermidine And 5-Methylthioadenosine
pdb|3C6M|A Chain A, Crystal Structure Of Human Spermine Synthase In Complex
With Spermine And 5-Methylthioadenosine
pdb|3C6M|B Chain B, Crystal Structure Of Human Spermine Synthase In Complex
With Spermine And 5-Methylthioadenosine
pdb|3C6M|C Chain C, Crystal Structure Of Human Spermine Synthase In Complex
With Spermine And 5-Methylthioadenosine
pdb|3C6M|D Chain D, Crystal Structure Of Human Spermine Synthase In Complex
With Spermine And 5-Methylthioadenosine
Length = 381
Score = 33.1 bits (74), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 45/103 (43%), Gaps = 6/103 (5%)
Query: 436 IKGHCTGGRVEDAVGVLHGMARKGLAPDVVSYSTIISGFSRSQELDKAFDTKREMVEKG- 494
+KG C +ED + VL A++G D V S S E D ++ R +++
Sbjct: 259 LKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSM 318
Query: 495 -VLPDTITYSSLIHGLCEQRRITEACELFQEMLSRGMSPDEFT 536
VL Y G C +TEA L++E L R P EF+
Sbjct: 319 KVLKQDGKY--FTQGNC--VNLTEALSLYEEQLGRLYCPVEFS 357
>pdb|3U6W|A Chain A, Truncated M. Tuberculosis Leua (1-425) Complexed With Kiv
pdb|3U6W|B Chain B, Truncated M. Tuberculosis Leua (1-425) Complexed With Kiv
Length = 427
Score = 32.3 bits (72), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQ-RRITEAC 519
+ Y I GF + + D FD RE++E+G +PD +T L E R +AC
Sbjct: 107 MGYKEIEVGFPSASQTD--FDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQAC 160
>pdb|3HPX|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Leua
Active Site Domain 1-425 (Truncation Mutant
Delta:426-644)
pdb|3HPX|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Leua
Active Site Domain 1-425 (Truncation Mutant
Delta:426-644)
Length = 425
Score = 32.3 bits (72), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQ-RRITEAC 519
+ Y I GF + + D FD RE++E+G +PD +T L E R +AC
Sbjct: 105 MGYKEIEVGFPSASQTD--FDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQAC 158
>pdb|3FIG|A Chain A, Crystal Structure Of Leucine-bound Leua From Mycobacterium
Tuberculosis
pdb|3FIG|B Chain B, Crystal Structure Of Leucine-bound Leua From Mycobacterium
Tuberculosis
Length = 646
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQ-RRITEAC 519
+ Y I GF + + D FD RE++E+G +PD +T L E R +AC
Sbjct: 107 MGYKEIEVGFPSASQTD--FDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQAC 160
>pdb|3HPS|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Ketoisocaproate (Kic)
pdb|3HPS|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Ketoisocaproate (Kic)
pdb|3HPZ|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Bromopyruvate
pdb|3HPZ|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Bromopyruvate
pdb|3HQ1|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Citrate And Mn2+
pdb|3HQ1|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Leua
Complexed With Citrate And Mn2+
Length = 644
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 465 VSYSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQ-RRITEAC 519
+ Y I GF + + D FD RE++E+G +PD +T L E R +AC
Sbjct: 105 MGYKEIEVGFPSASQTD--FDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQAC 158
>pdb|1SR9|A Chain A, Crystal Structure Of Leua From Mycobacterium Tuberculosis
pdb|1SR9|B Chain B, Crystal Structure Of Leua From Mycobacterium Tuberculosis
Length = 644
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 467 YSTIISGFSRSQELDKAFDTKREMVEKGVLPDTITYSSLIHGLCEQ-RRITEAC 519
Y I GF + + D FD RE++E+G +PD +T L E R +AC
Sbjct: 107 YKEIEVGFPSASQTD--FDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQAC 158
>pdb|4ACO|A Chain A, Structure Of The Budding Yeast Ndc10 N-Terminal Domain
Length = 956
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 139 LCDSTSSSAVIDLVVKSYSHLN--MIDKAVNIVNLAKVHGFMPGVLSYNAILDSVIRSGR 196
+ + S S D KSY+ M+DK+++ + + F P N + S+ +SG
Sbjct: 820 MSTTASPSPEQDQEAKSYTDEQEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGN 879
Query: 197 NNWVKFAEEVYNEMGKSRVSPNVYTYN 223
+W E +Y E KS V +Y N
Sbjct: 880 KSWRANCEALYKER-KSIVEFYIYLVN 905
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 432 YNALIKGHCTGGRVEDAVGVLHGMARKGLAPDVVSYSTIISGFSRSQE 479
YNA++ G G ++ V VL + GL PD++SY+ + R +
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQ 215
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 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,132,061
Number of Sequences: 62578
Number of extensions: 911134
Number of successful extensions: 2265
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2218
Number of HSP's gapped (non-prelim): 39
length of query: 766
length of database: 14,973,337
effective HSP length: 106
effective length of query: 660
effective length of database: 8,340,069
effective search space: 5504445540
effective search space used: 5504445540
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: 55 (25.8 bits)