RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6839
(264 letters)
>3ryc_A Tubulin alpha chain; alpha-tubulin, beta-tubulin, GTPase,
microtubule, tubulin, cell cycle; HET: GTP GDP; 2.10A
{Ovis aries} PDB: 3ryf_A* 3ryh_A* 3ryi_A* 3hke_A*
3hkc_A* 3hkd_A* 3hkb_A* 3n2g_A* 3n2k_A* 1sa0_A* 1sa1_A*
3edl_F* 1ffx_A* 1ia0_A* 2hxf_A* 2hxh_A* 2p4n_A* 1jff_A*
2wbe_A* 3dco_A* ...
Length = 451
Score = 158 bits (402), Expect = 6e-46
Identities = 94/99 (94%), Positives = 96/99 (96%), Gaps = 1/99 (1%)
Query: 167 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 226
VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG
Sbjct: 353 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 412
Query: 227 MEEGEFSEAREDLAALEKDYEEVGMDSVEGEGEG-AEEY 264
MEEGEFSEARED+AALEKDYEEVG+DSVEGEGE EEY
Sbjct: 413 MEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY 451
>3ryc_B Tubulin beta chain; alpha-tubulin, beta-tubulin, GTPase,
microtubule, tubulin, cell cycle; HET: GTP GDP; 2.10A
{Ovis aries} PDB: 3ryf_B* 3ryh_B* 3ryi_B* 3hke_B*
3du7_B* 3e22_B* 3hkc_B* 3hkd_B* 3hkb_B* 3n2g_B* 3n2k_B*
1z2b_B* 2xrp_A* 1tvk_B* 1tub_B* 1jff_B* 1ia0_B* 1ffx_B*
1sa0_B* 1sa1_B* ...
Length = 445
Score = 151 bits (383), Expect = 3e-43
Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 8/97 (8%)
Query: 167 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 226
+ PP ++ + + N+TAI E + R+ +F M+ ++AF+HWY GEG
Sbjct: 351 TAVCDIPPR--------GLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEG 402
Query: 227 MEEGEFSEAREDLAALEKDYEEVGMDSVEGEGEGAEE 263
M+E EF+EA ++ L +Y++ + + +GE EE
Sbjct: 403 MDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEE 439
>2bto_A Tubulin btuba; bacterial tubulin, polymerization, cytoskeleton,
protein COM cytoskeletal protein; HET: GTP; 2.5A
{Prosthecobacter dejongeii} SCOP: c.32.1.1 d.79.2.1 PDB:
2btq_A*
Length = 473
Score = 132 bits (335), Expect = 3e-36
Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 8/97 (8%)
Query: 167 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 226
+G QP ++++ +L+N T IA R+ H FD ++ ++AF +WY+ EG
Sbjct: 356 IGYVEQPGI--------SHRKSMVLLANNTEIARVLDRICHNFDKLWQRKAFANWYLNEG 407
Query: 227 MEEGEFSEAREDLAALEKDYEEVGMDSVEGEGEGAEE 263
M E + + R L + Y+ + + + +
Sbjct: 408 MSEEQINVLRASAQELVQSYQVAEESGAKAKVQDSAG 444
>3cb2_A Gamma-1-tubulin, tubulin gamma-1 chain; lattice, microtubule,
nucleation, GTPase, lateral interaction, structural
protein, hydrolase; HET: GDP; 2.30A {Homo sapiens} PDB:
1z5v_A* 1z5w_A*
Length = 475
Score = 132 bits (335), Expect = 4e-36
Identities = 19/100 (19%), Positives = 41/100 (41%), Gaps = 8/100 (8%)
Query: 167 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 226
V ++ + P + ++ M++N T+I+ + R ++D + + AF+ + E
Sbjct: 358 VALSRKSPYLPSAHRVS-----GLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKED 412
Query: 227 MEEGEFSE---AREDLAALEKDYEEVGMDSVEGEGEGAEE 263
M + F E +RE + L +Y G +
Sbjct: 413 MFKDNFDEMDTSREIVQQLIDEYHAATRPDYISWGTQEQV 452
>2btq_B Tubulin btubb; structural protein, cytoskeletal protein/complex,
bacterial tubulin, cytoskeleton, polymerization,
verrucomicrobia; HET: GDP; 3.2A {Prosthecobacter
dejongeii}
Length = 426
Score = 129 bits (327), Expect = 2e-35
Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 167 VGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG 226
+G P L L N T IA + RL +FD+M+ A+ HWY G
Sbjct: 351 LGYAETAPEGFASSGL--------ALVNHTGIAAVFERLIAQFDIMFDNHAYTHWYENAG 402
Query: 227 MEEGEFSEAREDLAALEKDYEEV 249
+ ++AR +A L + Y +
Sbjct: 403 VSRDMMAKARNQIATLAQSYRDA 425
>2e4h_B Tubulin alpha-ubiquitous chain; cytoskeleton, CAP-Gly, complex
structure, solution structure, CLIP, structural protein;
NMR {Homo sapiens}
Length = 36
Score = 53.4 bits (128), Expect = 2e-10
Identities = 31/36 (86%), Positives = 33/36 (91%), Gaps = 1/36 (2%)
Query: 230 GEFSEAREDLAALEKDYEEVGMDSVEGEG-EGAEEY 264
GEFSEARED+AALEKDYEEVG+DSVEGEG E EEY
Sbjct: 1 GEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY 36
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 33.7 bits (76), Expect = 0.067
Identities = 39/220 (17%), Positives = 66/220 (30%), Gaps = 82/220 (37%)
Query: 62 SILAED--------EFYDAVESGSQNSEDLGSSRKSSIVSLIPA---------------- 97
SI+AE + + V N + L + +SS+ L PA
Sbjct: 331 SIIAESIRDGLATWDNWKHV-----NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 98 --PSSATANHRLWPEEENSNGTSILAEDEFYDAVESGSQNSEDLGSSRKSSI----VSLI 151
P+ + +W + S+ ++ + Y VE + S SI + L
Sbjct: 386 HIPTILLS--LIWFDVIKSDVMVVVNKLHKYSLVEKQPKES-------TISIPSIYLELK 436
Query: 152 PAPSSATANHRLWPEVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDL 211
+ A HR + +Y P DL LD
Sbjct: 437 VKLENEYALHRSIVD---HYNIPKTFDSDDLIPPY------------------LD----- 470
Query: 212 MYAKRAFVHWYVG---EGMEEGE-FSEARE---DLAALEK 244
Y + ++G + +E E + R D LE+
Sbjct: 471 QY-----FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ 505
Score = 32.9 bits (74), Expect = 0.10
Identities = 30/283 (10%), Positives = 79/283 (27%), Gaps = 80/283 (28%)
Query: 27 REFFGTTLFQSHTIY---HINNLNQDTLAQIEENSN---------GTSILA--------- 65
R + +F + + L + L ++ N G + +A
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKL-RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176
Query: 66 EDEFYDAV---ESGSQNSEDLGSSRKSSIVSLIPAPSSATANH----------------R 106
+ + + + NS + ++ I ++ ++H R
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR 236
Query: 107 LWPEEENSNGTSILAEDEFYDA-------------VESGSQNSEDLGSSRKSSIVSLIPA 153
L + N +L +A + + + D S+ ++ +SL
Sbjct: 237 LLKSKPYENCLLVL--LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294
Query: 154 PSSATANHRL-----WPEVGINYQ--PPTVVPGGDLAKVQRAVCM----LSNTTAIAEAW 202
+ T + + + Q P V+ + + + + A + W
Sbjct: 295 SMTLTPDEVKSLLLKY--LDCRPQDLPREVLTTNPRR-----LSIIAESIRDGLATWDNW 347
Query: 203 ARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKD 245
++ L + + +E E+ + + L+
Sbjct: 348 KHVNCD-KLTTIIESSL-----NVLEPAEYRKMFDRLSVFPPS 384
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.1 bits (69), Expect = 0.19
Identities = 9/37 (24%), Positives = 13/37 (35%), Gaps = 13/37 (35%)
Query: 134 QNSEDLGSSRKSSIVSLIPAPSSATANHRLWPEVGIN 170
Q + L +S K + A SA P + I
Sbjct: 20 QALKKLQASLK------LYADDSA-------PALAIK 43
Score = 26.8 bits (58), Expect = 4.8
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 6/26 (23%)
Query: 78 QNSEDLGSSRKSSIVSLIPAPSSATA 103
Q + L +S K + A SA A
Sbjct: 20 QALKKLQASLK------LYADDSAPA 39
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 30.0 bits (67), Expect = 0.85
Identities = 31/233 (13%), Positives = 55/233 (23%), Gaps = 76/233 (32%)
Query: 25 FLREFFGTTLFQSHTIYHINNLNQDTLA---------QIEENSNGTSILAEDEFYDAVES 75
++ +G F +I I N L +I EN + ++ +
Sbjct: 1652 HFKDTYG---F---SILDIVINNPVNLTIHFGGEKGKRIRENYSAMI-------FETIVD 1698
Query: 76 GSQNSEDLGSSRKSSIVSLI-PAPS---SATAN------------HRLWPEEENSNGTSI 119
G +E + S + SAT + +
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADAT 1758
Query: 120 LA-------------------EDE----FY------DAVESGSQNSEDLG--SSRKSSIV 148
A E FY AV + G + +
Sbjct: 1759 FAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA 1818
Query: 149 SLIPAPSSATANHRLWPEVG-----INYQPP--TVVPGGDLAKVQRAVCMLSN 194
+ + R+ G +NY V GDL + +L+
Sbjct: 1819 ASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNF 1871
Score = 30.0 bits (67), Expect = 0.97
Identities = 19/109 (17%), Positives = 32/109 (29%), Gaps = 29/109 (26%)
Query: 140 GSSRKSSIVSLIPAPSSATANHRLWPEVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIA 199
GS + L+P S A+ +L + PT D T A
Sbjct: 14 GSLE-HVL--LVPTASFFIAS-QLQEQFNKILPEPTEGFAAD-----------DEPTTPA 58
Query: 200 EAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEE 248
E + F+ YV +E + + + L ++E
Sbjct: 59 ELVGK-------------FLG-YVSSLVEPSKVGQFDQVLNLCLTEFEN 93
>3hfw_A Protein ADP-ribosylarginine hydrolase; all alpha-helical,
magnesium; HET: ADP; 1.92A {Homo sapiens}
Length = 357
Score = 28.9 bits (64), Expect = 1.8
Identities = 6/50 (12%), Positives = 10/50 (20%)
Query: 195 TTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEK 244
A AEA L Y + + + +
Sbjct: 60 HLATAEALVEAGKAPKLTQLYYLLAKHYQDCMEDMDGRAPGGASVHNAMQ 109
>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A
{Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A
Length = 86
Score = 26.4 bits (59), Expect = 3.6
Identities = 10/57 (17%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 196 TAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGMD 252
+ + L + D A E E +E R + +Y+E+ +D
Sbjct: 17 AKLRDLEDSLARERDTSRRLLAEK---------EREMAEMRARMQQQLDEYQEL-LD 63
>2xv5_A Lamin-A/C; structural protein, intermediate filaments, nuclear
membrane LEFT-handed coiled coil, right-handed coiled
coil; HET: MSE; 2.40A {Homo sapiens}
Length = 74
Score = 25.4 bits (56), Expect = 5.3
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 229 EGEFSEAREDLAALEKDYEEVGMD 252
E E +E R + +Y+E+ +D
Sbjct: 18 EREMAEMRARMQQQLDEYQEL-LD 40
>1f0x_A DLDH, D-lactate dehydrogenase; oxidoreductase; HET: FAD; 1.90A
{Escherichia coli} SCOP: d.58.32.2 d.145.1.1
Length = 571
Score = 27.3 bits (60), Expect = 5.7
Identities = 27/179 (15%), Positives = 45/179 (25%), Gaps = 27/179 (15%)
Query: 96 PAPSSATANHRLWPEEENSNGT--------SILAEDEFYDAVESGSQNSEDLGSSRKSSI 147
P+ A+ E G ++ G+ E L R+ +
Sbjct: 238 DTPARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHIL 297
Query: 148 VSLIPAPSSATANHRLWPEVGINYQPPTVVPGGDL--AKVQRAVCMLSNTTAIAEAWARL 205
+ P + HR ++ Y T + L K+ + T A+ E
Sbjct: 298 ANFENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFF 357
Query: 206 DHKF-----------------DLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYE 247
F M R ++ M EA+ L K E
Sbjct: 358 RPHFTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAE 416
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.313 0.130 0.375
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,990,628
Number of extensions: 232281
Number of successful extensions: 341
Number of sequences better than 10.0: 1
Number of HSP's gapped: 334
Number of HSP's successfully gapped: 19
Length of query: 264
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 172
Effective length of database: 4,133,061
Effective search space: 710886492
Effective search space used: 710886492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.5 bits)