RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5970
(169 letters)
>1l6j_A Matrix metalloproteinase-9; twisted beta sheet flanked by helices,
hydrolase; 2.50A {Homo sapiens} SCOP: a.20.1.2 d.92.1.11
g.14.1.2 g.14.1.2 g.14.1.2
Length = 425
Score = 85.3 bits (210), Expect = 4e-20
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 16/100 (16%)
Query: 4 ILQSYLANFGYLEASSNSEIANLRTKEQVTEA-----RFGNIPVTGIVDDATLALMKKPR 58
+ + YL +GY + + + A + ++P TG +D ATL M+ PR
Sbjct: 25 LAEEYLYRYGYTRVAEMR-----GESKSLGPALLLLQKQLSLPETGELDSATLKAMRTPR 79
Query: 59 CGLPDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSL 98
CG+PD + KW H ++T+ + + + L
Sbjct: 80 CGVPDLGR------FQTFEGDLKWHHHNITYWIQNYSEDL 113
>1slm_A Stromelysin-1; hydrolase, metalloprotease, fibroblast, collagen
degradation; 1.90A {Homo sapiens} SCOP: a.20.1.2
d.92.1.11
Length = 255
Score = 81.5 bits (200), Expect = 2e-19
Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 12/100 (12%)
Query: 4 ILQSYLANFGYLEASSNSEIANLRTKEQVTEA-----RFGNIPVTGIVDDATLALMKKPR 58
++Q YL N+ L+ + + V + +F + VTG +D TL +M+KPR
Sbjct: 16 LVQKYLENYYDLK-KDVKQFVRRKDSGPVVKKIREMQKFLGLEVTGKLDSDTLEVMRKPR 74
Query: 59 CGLPDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSL 98
CG+PD R KW T LT+R+++ L
Sbjct: 75 CGVPDVGH------FRTFPGIPKWRKTHLTYRIVNYTPDL 108
>1su3_A Interstitial collagenase; prodomain, hemopexin domain, exocite,
structural proteomics in europe, spine, structural
genomics, hydrolase; HET: EPE; 2.20A {Homo sapiens}
SCOP: a.20.1.2 b.66.1.1 d.92.1.11 PDB: 2clt_A 1fbl_A*
Length = 450
Score = 79.5 bits (195), Expect = 3e-18
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 12/100 (12%)
Query: 4 ILQSYLANFGYLEASSNSEIANLRTKEQVTEA-----RFGNIPVTGIVDDATLALMKKPR 58
++Q YL + L+ + ++ R V E F + VTG D TL +MK+PR
Sbjct: 14 LVQKYLEKYYNLK-NDGRQVEKRRNSGPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPR 72
Query: 59 CGLPDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSL 98
CG+PD T +W+ T LT+R+ + L
Sbjct: 73 CGVPDVAQ------FVLTEGNPRWEQTHLTYRIENYTPDL 106
>1eak_A 72 kDa type IV collagenase; hydrolase-hydrolase inhibitor complex,
hydrolyse, matrix metalloproteinase, gelatinase A,
hydrolase- hydrolase inhib complex; 2.66A {Homo sapiens}
SCOP: a.20.1.2 d.92.1.11 g.14.1.2 g.14.1.2 g.14.1.2 PDB:
1ks0_A 1cxw_A
Length = 421
Score = 75.3 bits (184), Expect = 1e-16
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 18/98 (18%)
Query: 6 QSYLANFGYLEASSNSEIANLRTKEQVTEA-----RFGNIPVTGIVDDATLALMKKPRCG 60
YL F S + + + +F +P TG +D T+ M+KPRCG
Sbjct: 20 VQYLNTFYGCPKESCN-------LFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCG 72
Query: 61 LPDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSL 98
PD F KWD +T+R++ L
Sbjct: 73 NPDVAN------YNFFPRKPKWDKNQITYRIIGYTPDL 104
>1ck7_A Protein (gelatinase A); hydrolase (metalloprotease), FULL-length,
metalloproteinase; 2.80A {Homo sapiens} SCOP: a.20.1.2
b.66.1.1 d.92.1.11 g.14.1.2 g.14.1.2 g.14.1.2 PDB:
1gxd_A
Length = 631
Score = 73.8 bits (180), Expect = 4e-16
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 18/98 (18%)
Query: 6 QSYLANFGYLEASSNSEIANLRTKEQVTEA-----RFGNIPVTGIVDDATLALMKKPRCG 60
YL F S + + + +F +P TG +D T+ M+KPRCG
Sbjct: 22 VQYLNTFYGCPKESCN-------LFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCG 74
Query: 61 LPDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSL 98
PD F KWD +T+R++ L
Sbjct: 75 NPDVAN------YNFFPRKPKWDKNQITYRIIGYTPDL 106
>1hv5_A Stromelysin 3; inhibition, phosphinic inhibitor, hydrolase; HET:
CPS RXP; 2.60A {Mus musculus} SCOP: d.92.1.11
Length = 165
Score = 36.0 bits (82), Expect = 0.002
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 75 FTLDGRKWDHTDLTWRVLS 93
F L G +W+ TDLT+R+L
Sbjct: 2 FVLSGGRWEKTDLTYRILR 20
>3ma2_D Matrix metalloproteinase-14; protein - protein complex, cleavage
on PAIR of basic residue disulfide bond, membrane,
metal-binding; 2.05A {Homo sapiens} PDB: 1bqq_M 1buv_M
Length = 181
Score = 35.2 bits (80), Expect = 0.004
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 75 FTLDGRKWDHTDLTWRVLSRVDSL 98
+ + G KW H ++T+ + + +
Sbjct: 1 YAIQGLKWQHNEITFCIQNYTPKV 24
>2xs4_A Karilysin protease; hydrolase, bacterial MMP, virulence factor,
metalloprotease, dependent, peptidase; 1.70A
{Tannerella forsythia} PDB: 2xs3_A
Length = 167
Score = 35.1 bits (80), Expect = 0.005
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 75 FTLDGRKWDHTDLTWRVLSRVDSL 98
+ L G KW+ T L + + + L
Sbjct: 1 YVLQGSKWNKTTLKYYIYNSSSHL 24
>1rm8_A MMP-16, matrix metalloproteinase-16, MT3-MMP; membrane type -
matrix metalloproteinase, batimastat, hydroxamate
inhibitor, protease, hydrolase; HET: BAT; 1.80A {Homo
sapiens} SCOP: d.92.1.11
Length = 169
Score = 33.7 bits (76), Expect = 0.015
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 79 GRKWDHTDLTWRVLSRVDSL 98
G+KW H +T+ + + +
Sbjct: 1 GQKWQHKHITYSIKNVTPKV 20
>1lbu_A Muramoyl-pentapeptide carboxypeptidase; hydrolase, nuclear
receptor; 1.80A {Streptomyces albus} SCOP: a.20.1.1
d.65.1.1
Length = 213
Score = 33.2 bits (75), Expect = 0.027
Identities = 20/115 (17%), Positives = 38/115 (33%), Gaps = 4/115 (3%)
Query: 5 LQSYLANFGYLEASSNSE-IANLRTKEQVTE--ARFGNIPVTGIVDDATLALMKKPRCGL 61
LQ +A + A + TK V + +G + GI AT + + +
Sbjct: 22 LQIRVAGYPGTGAQLAIDGQFGPATKAAVQRFQSAYG-LAADGIAGPATFNKIYQLQDDD 80
Query: 62 PDTPPLDRRRTKRFTLDGRKWDHTDLTWRVLSRVDSLIMKLLLRSVGNIVNSVNS 116
R D + T R + V ++ + ++G+ +VN
Sbjct: 81 CTPVNFTYAELNRCNSDWSGGKVSAATARANALVTMWKLQAMRHAMGDKPITVNG 135
>1hy7_A Stromelysin-1, MMP-3; mixed alpha beta structure, zinc protease,
inhibited, hydrol; HET: MBS; 1.50A {Homo sapiens} SCOP:
d.92.1.11 PDB: 1biw_A* 1bm6_A* 1bqo_A* 1b3d_A* 1cqr_A
1d5j_A* 1d7x_A* 1d8f_A* 1d8m_A* 1g05_A* 1g49_A* 1c3i_A*
1sln_A* 1uea_A 2srt_A* 1ums_A* 1umt_A* 2d1o_A* 3oho_A*
1ciz_A* ...
Length = 173
Score = 32.9 bits (74), Expect = 0.028
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 74 RFTLDGRKWDHTDLTWRVLSRVDSL 98
R KW T LT+R+++ L
Sbjct: 2 RTFPGIPKWRKTHLTYRIVNYTPDL 26
>1i76_A MMP-8;, neutrophil collagenase; hydrolase, complex
(metalloprotease/inhibitor); HET: BSI; 1.20A {Homo
sapiens} SCOP: d.92.1.11 PDB: 1i73_A* 1jao_A* 1jap_A
1jaq_A* 1jj9_A* 1mmb_A* 1zp5_A* 1zs0_A* 1zvx_A* 3dng_A*
3dpe_A* 3dpf_A* 1kbc_A* 1jan_A* 1bzs_A* 1mnc_A* 2oy2_A
1a86_A* 1jh1_A* 1a85_A ...
Length = 163
Score = 32.5 bits (73), Expect = 0.033
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 75 FTLDGRKWDHTDLTWRVLSRVDSL 98
T KW+ T+LT+R+ + L
Sbjct: 2 LTPGNPKWERTNLTYRIRNYTPQL 25
>1y93_A Macrophage metalloelastase; matrix metalloproteinase, MMP12,
complex (elastase inhibitor), acetohydroxamic acid,
hydrola; 1.03A {Homo sapiens} SCOP: d.92.1.11 PDB:
1rmz_A 1ycm_A* 1z3j_A* 2hu6_A* 2oxu_A 2oxw_A 2oxz_A
3lik_A* 3lil_A* 3lir_A* 3ljg_A* 1os9_A 1os2_A 3f17_A*
3ehy_A* 3ehx_A* 3f15_A* 3f16_A* 3f18_A* 3f19_A* ...
Length = 159
Score = 30.9 bits (69), Expect = 0.10
Identities = 4/15 (26%), Positives = 8/15 (53%)
Query: 79 GRKWDHTDLTWRVLS 93
G W +T+R+ +
Sbjct: 2 GPVWRKHYITYRINN 16
>3ba0_A Macrophage metalloelastase; FULL-length MMP-12, hemopexin domain,
catalytic domain, domain interaction., calcium,
extracellular matrix; 3.00A {Homo sapiens} PDB: 2jxy_A
Length = 365
Score = 31.5 bits (70), Expect = 0.11
Identities = 4/15 (26%), Positives = 8/15 (53%)
Query: 79 GRKWDHTDLTWRVLS 93
G W +T+R+ +
Sbjct: 1 GPVWRKHYITYRINN 15
>2y6d_A Matrilysin; hydrolase; HET: TQJ; 1.60A {Homo sapiens} PDB:
2ddy_A* 1mmq_A* 1mmp_A* 1mmr_A* 2y6c_A*
Length = 174
Score = 30.9 bits (69), Expect = 0.13
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 75 FTLDGRKWDHTDLTWRVLSRVDSL 98
+ KW +T+R++S L
Sbjct: 4 LFPNSPKWTSKVVTYRIVSYTRDL 27
>3ayu_A 72 kDa type IV collagenase; protease, hydrolase-hydrolase
inhibitor complex; 2.00A {Homo sapiens} PDB: 1qib_A
1hov_A*
Length = 167
Score = 30.5 bits (68), Expect = 0.15
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 74 RFTLDGRKWDHTDLTWRVLS 93
F KWD +T+R++
Sbjct: 2 NFFPRKPKWDKNQITYRIIG 21
>830c_A MMP-13, MMP-13; matrix metalloprotease; HET: RS1; 1.60A {Homo
sapiens} SCOP: d.92.1.11 PDB: 456c_A* 1you_A* 4a7b_A*
3tvc_A* 1eub_A* 1xuc_A* 1xud_A* 1xur_A* 2yig_A* 3elm_A*
3i7g_A* 3i7i_A* 3zxh_A* 2ow9_A* 2ozr_A* 3kek_A* 3kej_A*
3kec_A* 2d1n_A* 1fls_A* ...
Length = 168
Score = 30.5 bits (68), Expect = 0.18
Identities = 5/25 (20%), Positives = 11/25 (44%)
Query: 74 RFTLDGRKWDHTDLTWRVLSRVDSL 98
KW +LT+R+++ +
Sbjct: 2 NVFPRTLKWSKMNLTYRIVNYTPDM 26
>2ovx_A Matrix metalloproteinase-9 (EC 3.4.24.35) (MMP-9) type IV
collagenase) (92 kDa gelatinase)...; S1-prime pocket,
hydrolase-hydrola inhibitor complex; HET: 4MR; 2.00A
{Homo sapiens} SCOP: d.92.1.11 PDB: 2ovz_A* 2ow0_A*
2ow1_A* 2ow2_A* 1gkd_A* 1gkc_A*
Length = 159
Score = 29.4 bits (65), Expect = 0.40
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 81 KWDHTDLTWRVLSRVDSL 98
KW H ++T+ + + + L
Sbjct: 6 KWHHHNITYWIQNYSEDL 23
>2jsd_A Matrix metalloproteinase-20; MMP-NNGH, structural genomics,
structural proteomics in europe, spine, spine-2,
spine2-complexes, hydrolase; HET: NGH; NMR {Homo
sapiens}
Length = 160
Score = 29.4 bits (65), Expect = 0.42
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 81 KWDHTDLTWRVLSRVDSL 98
KW LT+R+ S+
Sbjct: 4 KWKKNTLTYRISKYTPSM 21
>1vi6_A 30S ribosomal protein S2P; structural genomics, ribosome; 1.95A
{Archaeoglobus fulgidus} SCOP: c.23.15.1 PDB: 1vi5_A
Length = 208
Score = 29.2 bits (66), Expect = 0.53
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 32 VTEARFGNIPVTGIVD 47
V+EA IPV + D
Sbjct: 131 VSEATAVGIPVVALCD 146
>1cge_A Fibroblast collagenase; hydrolase (metalloprotease); 1.90A {Homo
sapiens} SCOP: d.92.1.11 PDB: 2j0t_A 1ayk_A 1hfc_A*
2ayk_A 2tcl_A* 3ayk_A* 4ayk_A* 1cgl_A* 1cgf_A 966c_A*
3shi_A
Length = 168
Score = 28.9 bits (64), Expect = 0.55
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 81 KWDHTDLTWRVLSRVDSL 98
+W+ T L +R+ + L
Sbjct: 7 RWEQTHLRYRIENYTPDL 24
>2vqe_B 30S ribosomal protein S2; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: c.23.15.1 PDB: 1gix_E*
1hnw_B* 1hnx_B* 1hnz_B* 1hr0_B 1ibk_B* 1ibl_B* 1ibm_B
1j5e_B 1jgo_E* 1jgp_E* 1jgq_E* 1ml5_E* 1n32_B* 1n33_B*
1n34_B 1n36_B 1xmo_B* 1xmq_B* 1xnq_B* ...
Length = 256
Score = 27.9 bits (63), Expect = 1.5
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 29 KEQ--VTEARFGNIPVTGIVD 47
KE V EAR IPV + D
Sbjct: 169 KEAIAVREARKLFIPVIALAD 189
>2xzm_B RPS0E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_B
Length = 241
Score = 27.5 bits (61), Expect = 1.8
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 32 VTEARFGNIPVTGIVD 47
+ EA + NIPV + D
Sbjct: 130 IKEASYVNIPVIALCD 145
>3r8n_B 30S ribosomal protein S2; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_B 3fih_B* 2wwl_B 3oar_B 3oaq_B 3ofb_B
3ofa_B 3ofp_B 3ofx_B 3ofy_B 3ofo_B 3r8o_B 4a2i_B 3i1m_B
1vs7_B* 3e1a_B 3e1c_B 1vs5_B 3i1o_B 3i1q_B ...
Length = 218
Score = 27.5 bits (62), Expect = 1.9
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 29 KEQ--VTEARFGNIPVTGIVD 47
E + EA IPV IVD
Sbjct: 160 HEHIAIKEANNLGIPVFAIVD 180
>3a11_A Translation initiation factor EIF-2B, delta subun; isomerase,
hexamer, rossmann fold; 2.50A {Thermococcus
kodakaraensis} PDB: 3a9c_A* 3vm6_A*
Length = 338
Score = 27.3 bits (61), Expect = 2.6
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 39 NIPVTGIVDDATLALMKK 56
IPV +VD A MK
Sbjct: 192 GIPVIYVVDSAARHYMKM 209
>3u5c_A 40S ribosomal protein S0-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_A 3o30_A 3o2z_A 3u5g_A 3jyv_B* 1s1h_B
Length = 252
Score = 26.8 bits (59), Expect = 3.7
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 32 VTEARFGNIPVTGIVD 47
+ EA + NIPV + D
Sbjct: 133 IKEASYVNIPVIALTD 148
>3bbn_B Ribosomal protein S2; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 231
Score = 26.7 bits (60), Expect = 3.9
Identities = 5/21 (23%), Positives = 9/21 (42%), Gaps = 2/21 (9%)
Query: 29 KEQ--VTEARFGNIPVTGIVD 47
+E + E IP ++D
Sbjct: 168 EEYTALRECITLGIPTICLID 188
>1vb5_A Translation initiation factor EIF-2B; 2.20A {Pyrococcus horikoshii}
SCOP: c.124.1.5
Length = 276
Score = 26.8 bits (60), Expect = 4.0
Identities = 3/18 (16%), Positives = 5/18 (27%)
Query: 39 NIPVTGIVDDATLALMKK 56
I I D ++
Sbjct: 160 GIEFEVITDAQMGLFCRE 177
>1oih_A Putative alkylsulfatase ATSK; non-heme Fe(II) alphaketoglutarate
dependent dioxygenase, jelly roll, oxidoreductase; 1.89A
{Pseudomonas putida} SCOP: b.82.2.5 PDB: 1oii_A* 1oij_B*
1vz4_A 1vz5_A 1oik_A* 1oij_A* 1oij_C*
Length = 301
Score = 26.4 bits (59), Expect = 5.5
Identities = 13/59 (22%), Positives = 18/59 (30%), Gaps = 20/59 (33%)
Query: 35 ARFGNI---PVTGIVDDATLALMKKPRCGLPDTPPLDRRRTKRFTLDGRKWDHTDLTWR 90
G P +VD G LD + +R W HTD+T+
Sbjct: 73 KLLGEPVAHPTVPVVD------------GTRYLLQLDGAQGQR----ANSW-HTDVTFV 114
>1otj_A Alpha-ketoglutarate-dependent taurine dioxygenase; jelly roll
motif, alpha ketoglutarate-dependent dioxygenase,
oxidoreductase; 1.90A {Escherichia coli} SCOP: b.82.2.5
PDB: 1gqw_A* 1os7_A* 1gy9_A
Length = 283
Score = 26.0 bits (58), Expect = 5.9
Identities = 8/34 (23%), Positives = 10/34 (29%), Gaps = 6/34 (17%)
Query: 60 GLPDTP---PLDRRRTKRFTLDGRKWDHTDLTWR 90
LD D W HTD+T+
Sbjct: 75 HAEGVDEIIVLDTHNDNP--PDNDNW-HTDVTFI 105
>3ecs_A Translation initiation factor EIF-2B subunit alpha; eukaryotic
translation initiation factor 2balpha (EIF2balpha);
2.65A {Homo sapiens}
Length = 315
Score = 26.2 bits (58), Expect = 6.8
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 39 NIPVTGIVDDATLALMKK 56
N+PVT ++D A +M+K
Sbjct: 172 NVPVTVVLDAAVGYIMEK 189
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
0.320 0.134 0.394
Gapped
Lambda K H
0.267 0.0494 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,376,726
Number of extensions: 126460
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 238
Number of HSP's successfully gapped: 35
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.1 bits)