RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16768
(154 letters)
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 102 bits (254), Expect = 4e-26
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 2 ETNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61
E + +L+TDGIN+ + D + Y N + GIEA +++E++NV
Sbjct: 1305 ERADEWVLETDGINLTEAMTVEGV-DATRTYSNSFVEILQILGIEATRSALLKELRNVIE 1363
Query: 62 VYGIEVDPRHLSLVADYMTHS 82
G V+ RHL+L+ D MT
Sbjct: 1364 FDGSYVNYRHLALLCDVMTSR 1384
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 99.4 bits (247), Expect = 4e-25
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 2 ETNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61
+ +L+TDG+N++ + + D ++Y N + GIEA + +EV NV A
Sbjct: 1299 VKEPEWVLETDGVNLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIA 1357
Query: 62 VYGIEVDPRHLSLVADYMTHS 82
G V+ RH++L+ D MT
Sbjct: 1358 SDGSYVNYRHMALLVDVMTTQ 1378
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 83.3 bits (205), Expect = 8e-20
Identities = 30/82 (36%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 1 METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 60
+ ++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+ V
Sbjct: 243 QKKGDEYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISKVL 301
Query: 61 AVYGIEVDPRHLSLVADYMTHS 82
A G++VD RH+ LVAD MT +
Sbjct: 302 AEQGLDVDMRHILLVADVMTRT 323
>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 = 31.9 bits (72), Expect = 0.065
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 16/69 (23%)
Query: 19 ISQYRHLLDL-------NKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVY-------G 64
+ Q+ +L+L L NDIH +A+ + N + + K + Y
Sbjct: 77 VGQFDQVLNLCLTEFENCYLEGNDIHALAAK--LLQENDTTLVKTKELIKNYITARIMAK 134
Query: 65 IEVDPRHLS 73
D + S
Sbjct: 135 RPFDKKSNS 143
>3aek_A Light-independent protochlorophyllide reductase S; iron/sulfur
cluster, oxidoreductase, bacteriochlorophyll
biosynthesis; HET: PMR; 2.30A {Rhodobacter capsulatus}
PDB: 3aeq_A* 3aes_A* 3aer_A* 3aet_A 3aeu_A
Length = 437
Score = 29.1 bits (64), Expect = 0.58
Identities = 11/68 (16%), Positives = 21/68 (30%)
Query: 1 METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 60
+E LL G+ + R + N +A + E + R K +
Sbjct: 196 VEDQCLSLLTQLGVGPVRMLPARRSDIEPAVGPNTRFILAQPFLGETTGALERRGAKRIA 255
Query: 61 AVYGIEVD 68
A + +
Sbjct: 256 APFPFGEE 263
>2oqo_A Penicillin-binding protein 1A (PBP-1A) (PBP1A); transferase; HET:
EPE CPS; 2.10A {Aquifex aeolicus} SCOP: d.2.1.10 PDB:
3d3h_A* 3nb7_A 3nb6_A
Length = 200
Score = 27.9 bits (63), Expect = 1.2
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 31 LYVNDIHYMASTYGIEAANRV 51
LY+N I+ + YG+EAA +V
Sbjct: 116 LYLNQIYLGSGAYGVEAAAQV 136
>1ua2_A CAK, cell division protein kinase 7; cell cycle, phosphorylation,
protein-protein interaction, PR kinase, cell cycle,
transferase; HET: TPO ATP; 3.02A {Homo sapiens} SCOP:
d.144.1.7
Length = 346
Score = 27.9 bits (63), Expect = 1.4
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 14/60 (23%)
Query: 53 IREVK--------NVFAVYGIEVDPRHLSLVADYMTHSEFDL-IIMVSKSWMLDE--VKS 101
+RE+K N+ + ++SLV D+M DL +I+ S +L +K+
Sbjct: 60 LREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMET---DLEVIIKDNSLVLTPSHIKA 116
>3hzs_A Monofunctional glycosyltransferase; transglycosylase,
peptidoglycan, moenomycin, membrane, cell shape; HET:
M0E; 2.10A {Staphylococcus aureus subsp}
Length = 209
Score = 26.8 bits (60), Expect = 2.3
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 31 LYVNDIHYMASTYGIEAANRV 51
Y+N+I++ + Y +E A
Sbjct: 116 FYLNNIYFGDNQYTLEGAANH 136
>3vmt_A Monofunctional glycosyltransferase; transmembrane, bacterial cell
WALL SYNT membrane; HET: LHI; 2.30A {Staphylococcus
aureus} PDB: 3vmr_A* 3vms_A 3vmq_A*
Length = 263
Score = 27.0 bits (60), Expect = 2.5
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 31 LYVNDIHYMASTYGIEAANRV 51
Y+N+I++ + Y +E A
Sbjct: 169 FYLNNIYFGDNQYTLEGAANH 189
>2olv_A Penicillin-binding protein 2; transpeptidase fold,
glycosyltransferase family 51, lysozyme transferase;
HET: M0E; 2.80A {Staphylococcus aureus} SCOP: d.2.1.10
e.3.1.1 PDB: 2olu_A* 3dwk_A*
Length = 669
Score = 26.9 bits (60), Expect = 2.7
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 31 LYVNDIHYMASTYGIEAA 48
+Y+N I+Y GI+AA
Sbjct: 132 VYLNKIYYSDGVTGIKAA 149
>3udf_A Penicillin-binding protein 1A; transglycosylase, transpeptidase;
HET: MES; 1.70A {Acinetobacter baumannii} PDB: 3udi_A*
3udx_A* 3ue0_A* 3ue1_A*
Length = 731
Score = 26.5 bits (59), Expect = 4.0
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 31 LYVNDIHYMASTYGIEAANRV 51
LYVN I + YGI AA ++
Sbjct: 135 LYVNKIFLGKNAYGIAAAAKI 155
>1f2q_A High affinity immunoglobulin epsilon receptor ALP subunit;
immunoglobulin fold, glycoprotein, IGE-binding Pro
immune system; HET: NAG MAN; 2.40A {Homo sapiens} SCOP:
b.1.1.4 b.1.1.4 PDB: 1j86_A* 1rpq_A* 2y7q_A* 1f6a_A*
1j88_A* 1j89_A* 1j87_A*
Length = 176
Score = 26.0 bits (57), Expect = 4.4
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 88 IMVSKSWMLDEVKSTTAR---SVTPACEPNSHHDVKKIEFKKQNKILPLVLQNS 138
+ V W+L + + + C + DV K+ + K + L +N
Sbjct: 81 LEVFSDWLLLQASAEVVMEGQPLFLRCHGWRNWDVYKVIYYKDGEALKYWYENH 134
>2pqp_A HD7A, histone deacetylase 7A; HDAC, structural genomics, structural
genomics consortium, SGC; HET: TSN; 1.80A {Homo sapiens}
PDB: 2pqo_A* 2nvr_A 3c0y_A 3c0z_A 3c10_A* 2vqm_A*
2vqj_A* 2vqw_G 2vqq_A* 2vqo_A* 2vqv_A*
Length = 421
Score = 25.9 bits (57), Expect = 7.1
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 44 GIEAANRVIIREVKNVFAV 62
+ A +V RE+KN FAV
Sbjct: 163 VTDLAFKVASRELKNGFAV 181
>3g17_A Similar to 2-dehydropantoate 2-reductase; structural genomics,
putative 2-dehydropantoate 2-reductase, protein
structure initiative; 2.30A {Staphylococcus aureus
subsp}
Length = 294
Score = 25.7 bits (57), Expect = 7.9
Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 4/65 (6%)
Query: 51 VIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPA 110
+I R K + + + + + FD+II+ K+ LD V +T
Sbjct: 30 LIGRHAKTITYYTVPHAPAQDIVVKGYEDVTNTFDVIIIAVKTHQLDAV----IPHLTYL 85
Query: 111 CEPNS 115
++
Sbjct: 86 AHEDT 90
>1a62_A RHO; transcription termination, termination, RNA binding domain,
transcription regulation, OB fold, F1-ATPase; 1.55A
{Escherichia coli BL21} SCOP: a.140.3.1 b.40.4.5 PDB:
1a63_A 2a8v_A 1a8v_A
Length = 130
Score = 24.9 bits (55), Expect = 9.4
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 24 HLLDLNKLYVNDIHYMASTYGIEAANR 50
+L +L V+++ + G+E R
Sbjct: 2 NLTELKNTPVSELITLGENMGLENLAR 28
>2jch_A Penicillin-binding protein 1B; peptidoglycan synthesis
multifunctional enzyme, cell WALL, peptidoglycan, gamma
lactam antibiotics; HET: PL7; 2.4A {Streptococcus
pneumoniae} PDB: 2jci_A* 2je5_A*
Length = 720
Score = 25.5 bits (56), Expect = 9.6
Identities = 4/21 (19%), Positives = 6/21 (28%)
Query: 28 LNKLYVNDIHYMASTYGIEAA 48
LN + + G A
Sbjct: 152 LNVAPFGRNNKGQNIAGARQA 172
>4agu_A Cyclin-dependent kinase-like 1; transferase, phospho-mimetic; HET:
D15; 2.40A {Homo sapiens}
Length = 311
Score = 25.2 bits (56), Expect = 9.8
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 53 IREVK--------NVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKS 101
+RE++ N+ + + R L LV +Y H+ + + VKS
Sbjct: 50 LREIRMLKQLKHPNLVNLLEVFRRKRRLHLVFEYCDHTVLHELDRYQRGVPEHLVKS 106
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
0.318 0.134 0.388
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,389,832
Number of extensions: 133059
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 273
Number of HSP's successfully gapped: 33
Length of query: 154
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 69
Effective length of database: 4,328,508
Effective search space: 298667052
Effective search space used: 298667052
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.7 bits)