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= 042717
(474 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DER|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
Trna-Glu In The Initial Trna Binding State
pdb|2DER|B Chain B, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
Trna-Glu In The Initial Trna Binding State
pdb|2DET|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
Trna-Glu In The Pre-Reaction State
pdb|2DEU|A Chain A, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
Trna-Glu In The Adenylated Intermediate State
pdb|2DEU|B Chain B, Cocrystal Structure Of An Rna Sulfuration Enzyme Mnma And
Trna-Glu In The Adenylated Intermediate State
Length = 380
Score = 234 bits (596), Expect = 9e-62, Method: Compositional matrix adjust.
Identities = 142/372 (38%), Positives = 208/372 (55%), Gaps = 29/372 (7%)
Query: 20 KVAVLLSGGVDSSVALRLLHSAGHSCTAFYLKIWFQEDFENFWTECPWEEDMKYAKAVCD 79
KV V +SGGVDSSV+ LL G+ ++K W ++D E + C D+ A+AVCD
Sbjct: 19 KVIVGMSGGVDSSVSAWLLQQQGYQVEGLFMKNWEEDDGEEY---CTAAADLADAQAVCD 75
Query: 80 QVDVPLEVVHLTDEYWKNVVSYIIEEYRCGRTPNPDVLCNTRIKFGAFMD-AISSMEFDY 138
++ + L V+ EYW NV + EY+ GRTPNPD+LCN IKF AF++ A + DY
Sbjct: 76 KLGIELHTVNFAAEYWDNVFELFLAEYKAGRTPNPDILCNKEIKFKAFLEFAAEDLGADY 135
Query: 139 VASGHYAKVVHSSADQEYKPSVLELSKDKVKDQTYFLSHLSQAQLKRLIFPLGCISKEEV 198
+A+GHY + AD + K +L D KDQ+YFL LS Q+ + +FP+G + K +V
Sbjct: 136 IATGHYVR----RADVDGKSRLLR-GLDSNKDQSYFLYTLSHEQIAQSLFPVGELEKPQV 190
Query: 199 RKFATQFDLPNKDRKDSQGICFLGKIKFSEFVARHIGEMEGVILEAETGDFLGKHWGFWF 258
RK A L +KDS GICF+G+ KF EF+ R++ G I+ + GD +G+H G +
Sbjct: 191 RKIAEDLGLVTAKKKDSTGICFIGERKFREFLGRYLPAQPGKIITVD-GDEIGEHQGLMY 249
Query: 259 YTIGQRQGLRLPGG------PWYVVEKDVKNNVVFVSRNYYSFDKKRRLFRVG----SLK 308
+T+GQR+GL + G PWYVV+KDV+NN++ V++ + + RL VG L
Sbjct: 250 HTLGQRKGLGIGGTKEGTEEPWYVVDKDVENNILVVAQGH----EHPRLMSVGLIAQQLH 305
Query: 309 WLSGLPPEEISRLQCKVRHGPGFYNCNLMIEHVEDGGENIAVVQLSEDDQGLAAGQFAAF 368
W+ P R K R+ C ++ ++D + I V+ E + GQ A F
Sbjct: 306 WVDREPFTGTMRCTVKTRYRQTDIPCT--VKALDD--DRIEVI-FDEPVAAVTPGQSAVF 360
Query: 369 YQGTRCIGSGVI 380
Y G C+G G+I
Sbjct: 361 YNGEVCLGGGII 372
>pdb|2HMA|A Chain A, The Crystal Structure Of Trna
(5-Methylaminomethyl-2-Thiouridylate)- Methyltransferase
Trmu From Streptococcus Pneumoniae
Length = 376
Score = 196 bits (499), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 127/356 (35%), Positives = 179/356 (50%), Gaps = 20/356 (5%)
Query: 37 LLHSAGHSCTAFYLKIWFQEDFENFWTECPWEEDMKYAKAVCDQVDVPLEVVHLTDEYWK 96
LL G+ + K W D EN C ED K AV DQ+ +P V+ EYW
Sbjct: 28 LLKEQGYDVIGIFXKNWDDTD-EN--GVCTATEDYKDVVAVADQIGIPYYSVNFEKEYWD 84
Query: 97 NVVSYIIEEYRCGRTPNPDVLCNTRIKFGAFMDAISSMEFDYVASGHYAKVVHSSADQEY 156
V Y + EYR GRTPNPDV CN IKF AF+D ++ DYVA+GHYA+V D++
Sbjct: 85 RVFEYFLAEYRAGRTPNPDVXCNKEIKFKAFLDYAITLGADYVATGHYARVAR---DEDG 141
Query: 157 KPSVLELSKDKVKDQTYFLSHLSQAQLKRLIFPLGCISKEEVRKFATQFDLPNKDRKDSQ 216
L D KDQTYFLS LSQ QL++ FPLG + K EVR+ A + L +KDS
Sbjct: 142 TVHXLR-GVDNGKDQTYFLSQLSQEQLQKTXFPLGHLEKPEVRRLAEEAGLSTAKKKDST 200
Query: 217 GICFLGKIKFSEFVARHIGEMEGVILEAETGDFLGKHWGFWFYT------IGQRQGLRLP 270
GICF+G+ F F++ ++ G + D G+H G +YT +G
Sbjct: 201 GICFIGEKNFKNFLSNYLPAQPGRXXTVDGRD-XGEHAGLXYYTIGQRGGLGIGGQHGGD 259
Query: 271 GGPWYVVEKDVKNNVVFVSRNYYSFDKKRRLFRVGSLKWLSGLPPEEISRLQCKVRHGPG 330
PW+VV KD+ N+++V + +Y D S + PEE + L+C +
Sbjct: 260 NAPWFVVGKDLSKNILYVGQGFYH-DSLXSTSLEASQVHFTREXPEEFT-LECTAKFRYR 317
Query: 331 FYNCNLMIEHVEDGGENIAVVQLSEDDQGLAAGQFAAFYQGTRCIGSGVILESWDD 386
+ + + HV+ GE V+ +E + + GQ FY G C+G G+I ++ D
Sbjct: 318 QPDSKVTV-HVK--GEKTEVI-FAEPQRAITPGQAVVFYDGEECLGGGLIDNAYRD 369
>pdb|3VF1|A Chain A, Structure Of A Calcium-Dependent 11r-Lipoxygenase
Suggests A Mechanism For Ca-Regulation
pdb|3VF1|B Chain B, Structure Of A Calcium-Dependent 11r-Lipoxygenase
Suggests A Mechanism For Ca-Regulation
Length = 698
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 13 MPHQKGLKVAVLLSGGVDSSVALRLLHSAGHSCTAFYLKIWFQEDFENFWTEC 65
M ++ ++ L G D+SV+++L G +AF L +F DFE+ T+
Sbjct: 20 MKYKITVETGDLRGAGTDASVSIKLTGKDGAETSAFSLDKYFHNDFESGGTDT 72
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
Length = 1193
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 31/101 (30%), Positives = 41/101 (40%), Gaps = 12/101 (11%)
Query: 293 YSFDKKRRLFRVGSLKWLSGLPPEEISRLQCKVRHGPGFYNCNLMIEHVEDGGENIAVVQ 352
Y +R + RVGS G P SRL V H P +N + + HV D EN+
Sbjct: 64 YCGGDERDVLRVGS----GGFWPRR-SRLWGGVDHAPAGFNPTVTVFHVYDILENV---- 114
Query: 353 LSEDDQGLAAGQF-AAFYQGTRCIGSGVILESWDDQGFPVC 392
E G+ A QF A F G+ + L +G V
Sbjct: 115 --EHAYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVA 153
>pdb|2C5S|A Chain A, Crystal Structure Of Bacillus Anthracis Thii, A Trna-
Modifying Enzyme Containing The Predicted Rna-Binding
Thump Domain
Length = 413
Score = 32.3 bits (72), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 23/44 (52%)
Query: 7 RYLSCSMPHQKGLKVAVLLSGGVDSSVALRLLHSAGHSCTAFYL 50
R + +P G KV VLLSGG+DS VA L G S A +
Sbjct: 176 RMGAGGLPVGVGGKVMVLLSGGIDSPVAAYLTMKRGVSVEAVHF 219
>pdb|2VXO|A Chain A, Human Gmp Synthetase In Complex With Xmp
pdb|2VXO|B Chain B, Human Gmp Synthetase In Complex With Xmp
Length = 697
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/22 (68%), Positives = 17/22 (77%)
Query: 20 KVAVLLSGGVDSSVALRLLHSA 41
KV VLLSGGVDS+V LL+ A
Sbjct: 242 KVLVLLSGGVDSTVCTALLNRA 263
>pdb|1CT9|A Chain A, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|B Chain B, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|C Chain C, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
pdb|1CT9|D Chain D, Crystal Structure Of Asparagine Synthetase B From
Escherichia Coli
Length = 553
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 54/129 (41%), Gaps = 8/129 (6%)
Query: 22 AVLLSGGVDSSV--ALRLLHSAGHSCTAFYLKIWFQEDFENFWTECPWEEDMKYAKAVCD 79
VLLSGG+DSS+ A+ ++A + W+ + +F P D+K A+ V +
Sbjct: 230 GVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQ-LHSFAVGLPGSPDLKAAQEVAN 288
Query: 80 QVDVPLEVVHLTDEYWKNVVS---YIIEEYRCG--RTPNPDVLCNTRIKFGAFMDAISSM 134
+ +H T + + + Y IE Y R P L + +IK +S
Sbjct: 289 HLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGE 348
Query: 135 EFDYVASGH 143
D V G+
Sbjct: 349 GSDEVFGGY 357
>pdb|1GPM|A Chain A, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|B Chain B, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|C Chain C, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|D Chain D, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
Length = 525
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/32 (53%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 20 KVAVLLSGGVDSSVALRLLHSA-GHSCTAFYL 50
KV + LSGGVDSSV LLH A G + T ++
Sbjct: 229 KVILGLSGGVDSSVTAMLLHRAIGKNLTCVFV 260
>pdb|2NZ2|A Chain A, Crystal Structure Of Human Argininosuccinate Synthase In
Complex With Aspartate And Citrulline
Length = 413
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 21 VAVLLSGGVDSSVALRLLHSAGHSCTAFYLKIWFQEDFE 59
V + SGG+D+S L L G+ A+ I +EDFE
Sbjct: 8 VVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFE 46
>pdb|4EQ9|A Chain A, 1.4 Angstrom Crystal Structure Of Putative Abc Transporter
Substrate- Binding Protein From Streptococcus Pneumoniae
Strain Canada Mdr_19a In Complex With Glutathione
Length = 246
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 103 IEEYRCGRTPNPDVLCNTRIKFGAFMDAISSMEFDY 138
+E Y T NP +L T+ F M +S +FDY
Sbjct: 130 LEAYNAEHTDNPTILNYTKADFQQIMVRLSDGQFDY 165
>pdb|1VL2|A Chain A, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|B Chain B, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|C Chain C, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
pdb|1VL2|D Chain D, Crystal Structure Of Argininosuccinate Synthase (Tm1780)
From Thermotoga Maritima At 1.65 A Resolution
Length = 421
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 20 KVAVLLSGGVDSSVALRLLHSAGHSCTAFYLKIWFQEDF 58
KV + SGG+D+SV L+ L G A+ + ++DF
Sbjct: 16 KVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDF 54
>pdb|3KYC|B Chain B, Human Sumo E1 Complex With A Sumo1-Amp Mimic
Length = 660
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 28/47 (59%)
Query: 407 LGKPIKIKVKPETPEEFNSNKGVQSSRNLVNAQNSIAEKSNTTSQEE 453
LGK ++ +V + PE+ + +++++ N + A+ S +T+QE+
Sbjct: 558 LGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQ 604
>pdb|1Y8Q|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8Q|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8R|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|1Y8R|E Chain E, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
Length = 640
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 28/47 (59%)
Query: 407 LGKPIKIKVKPETPEEFNSNKGVQSSRNLVNAQNSIAEKSNTTSQEE 453
LGK ++ +V + PE+ + +++++ N + A+ S +T+QE+
Sbjct: 538 LGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQ 584
>pdb|2L1W|A Chain A, The Solution Structure Of Soybean Calmodulin Isoform 4
Complexed With The Vacuolar Calcium Atpase Bca1 Peptide
Length = 149
Score = 28.5 bits (62), Expect = 8.8, Method: Composition-based stats.
Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 19/103 (18%)
Query: 129 DAISSMEFDYVASGHYAKVVHSSADQEYKPSVLELSKDKVKDQTYFLSHLSQAQLKRLIF 188
D ++EFD S KV + A++E K + KD+ ++S ++L+ ++
Sbjct: 58 DGNGTIEFDEFLSLMAKKVKDTDAEEELKEAFKVFDKDQN-------GYISASELRHVMI 110
Query: 189 PLG-CISKEEVRKFATQFDLPNKDRKDSQGICFLGKIKFSEFV 230
LG ++ EEV + + DL G++ + EFV
Sbjct: 111 NLGEKLTDEEVEQMIKEADLDGD-----------GQVNYEEFV 142
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 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,988,019
Number of Sequences: 62578
Number of extensions: 651701
Number of successful extensions: 1651
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1627
Number of HSP's gapped (non-prelim): 24
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
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: 53 (25.0 bits)