RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18011
(163 letters)
>3rle_A Golgi reassembly-stacking protein 2; PDZ, tether, golgin, membrane
protein; 1.65A {Homo sapiens}
Length = 209
Score = 148 bits (375), Expect = 4e-46
Identities = 86/175 (49%), Positives = 118/175 (67%), Gaps = 26/175 (14%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
VQ+NSPG +AGLE FFDFIV+I+ RL++DNDTLK+LLK ++K +KM +YSSKT ++R
Sbjct: 23 VQENSPGHRAGLEPFFDFIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKTLELRE 82
Query: 61 VNITPSNSWGGQGLLGVSIRFCSFEGANENVWHILD------------------------ 96
++TPSN WGGQGLLGVSIRFCSF+GANENVWH+L+
Sbjct: 83 TSVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGADT 142
Query: 97 --QDNDTLKELLKNGIDKELKMAVYSSKTQDVRTVNITPSNSWGGQGLLGVSIRF 149
+++ L L++ K LK+ VY++ T + R V ITP+++WGG+G LG I +
Sbjct: 143 VMNESEDLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGY 197
Score = 70.5 bits (172), Expect = 8e-16
Identities = 48/69 (69%), Positives = 61/69 (88%)
Query: 95 LDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRTVNITPSNSWGGQGLLGVSIRFCSFEG 154
L++DNDTLK+LLK ++K +KM +YSSKT ++R ++TPSN WGGQGLLGVSIRFCSF+G
Sbjct: 49 LNKDNDTLKDLLKANVEKPVKMLIYSSKTLELRETSVTPSNLWGGQGLLGVSIRFCSFDG 108
Query: 155 ANENVWHIL 163
ANENVWH+L
Sbjct: 109 ANENVWHVL 117
>2zpm_A Regulator of sigma E protease; metalloproteinase, membrane
protein, PDZ domain, hydrolase, inner membrane,
membrane, metal-binding; HET: MLY MSE; 0.98A
{Escherichia coli} PDB: 3id2_A 3id3_A 3id4_A
Length = 91
Score = 39.4 bits (92), Expect = 4e-05
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 7/81 (8%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
VQ NS AGL+A D IV +D L Q L+++ L + + + +
Sbjct: 11 VQPNSAASXAGLQA-GDRIVXVDGQPLTQWVT-FVMLVRDNPGXSLALEI--ERQGSPLS 66
Query: 61 VNITPSNSWGGQ---GLLGVS 78
+ + P + G G +G+
Sbjct: 67 LTLIPESXPGNGXAIGFVGIE 87
>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 = 40.4 bits (94), Expect = 1e-04
Identities = 29/139 (20%), Positives = 51/139 (36%), Gaps = 42/139 (30%)
Query: 26 RLDQDNDTLKEL------LKNGIDKELKMAVYSSKTQDVRTVNITPSNSWGGQGL----- 74
+++ N L L NG V S Q + +N+T + GL
Sbjct: 352 YVNKTNSHLPAGKQVEISLVNGAK----NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI 407
Query: 75 ------LGVSIRF----CSFEGANENVWH--ILDQDNDTLKE-LLKNGID---KELKMAV 118
L S RF F H +L +D + + L+KN + K++++ V
Sbjct: 408 PFSERKLKFSNRFLPVASPF--------HSHLLVPASDLINKDLVKNNVSFNAKDIQIPV 459
Query: 119 YSSKT-QDVRTV--NITPS 134
Y + D+R + +I+
Sbjct: 460 YDTFDGSDLRVLSGSISER 478
Score = 39.3 bits (91), Expect = 3e-04
Identities = 42/191 (21%), Positives = 73/191 (38%), Gaps = 63/191 (32%)
Query: 1 VQDNSPGQ-----KAGLEAFFDFIVAIDNI-----RLDQDNDT----LKELLKN------ 40
V+ + GQ L F + + ++I +L Q+NDT KEL+KN
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI 131
Query: 41 ----GIDKELKMAVY-SSKTQDVRTVNITPSNSWGGQGLLGVSIRFCSFEGANE------ 89
DK+ A++ + + + V I +GGQG + FE E
Sbjct: 132 MAKRPFDKKSNSALFRAVGEGNAQLVAI-----FGGQG----NTDDY-FE---ELRDLYQ 178
Query: 90 ----NVWHILDQDNDTLKELLKNGIDKELKMAVYSSKTQDV----RTVNITPSNSWGGQG 141
V ++ +TL EL++ +D E V+ ++ ++ + TP +
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAE---KVF-TQGLNILEWLENPSNTPDKDY---- 230
Query: 142 LLGVSIRFCSF 152
LL + I S
Sbjct: 231 LLSIPI---SC 238
Score = 37.3 bits (86), Expect = 0.001
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 39/92 (42%)
Query: 21 AIDNIRLDQDNDTLKELLKNGID---KELKMAVYSSKT-QDVRTV--NITPSNSWGGQGL 74
A D I D L+KN + K++++ VY + D+R + +I+
Sbjct: 435 ASDLINKD--------LVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER-------- 478
Query: 75 LGVSIRFCSFEGANENV-W---------HILD 96
+ I V W HILD
Sbjct: 479 IVDCI-------IRLPVKWETTTQFKATHILD 503
Score = 31.9 bits (72), Expect = 0.079
Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 18/63 (28%)
Query: 1 VQDNSPGQK---AG-LEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQ 56
V N Q+ AG L A LD + L + ID +++ S +
Sbjct: 1844 VNYNVENQQYVAAGDLRA------------LDTVTNVLNFIKLQKIDI-IELQK-SLSLE 1889
Query: 57 DVR 59
+V
Sbjct: 1890 EVE 1892
>3id1_A Regulator of sigma E protease; hydrolase, cell inner membrane,
cell membrane, membrane, metal-binding,
metalloprotease, transmembrane; 1.67A {Escherichia coli
k-12} PDB: 2zpl_A
Length = 95
Score = 37.3 bits (86), Expect = 3e-04
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 1/67 (1%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
+ NS +A + + A+D I + +L+ D+ + V + R
Sbjct: 9 IAANSIAAEAQIAPG-TELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRD 67
Query: 61 VNITPSN 67
V + +
Sbjct: 68 VKLDLRH 74
>2pzd_A Serine protease HTRA2; PDZ domain, apoptosis, mitochondria, peptid
module, hydrolase; 2.75A {Homo sapiens} SCOP: b.36.1.4
Length = 113
Score = 35.0 bits (81), Expect = 0.002
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V SP +AGL D I+AI + D + E ++ +L + + + + T
Sbjct: 42 VILGSPAHRAGLRP-GDVILAIGEQMVQNAED-VYEAVRTQ--SQLAVQIRRGR--ETLT 95
Query: 61 VNITP 65
+ +TP
Sbjct: 96 LYVTP 100
>1lcy_A HTRA2 serine protease; apoptosis, PDZ domain, caspase activation,
binding, hydrolase; 2.00A {Homo sapiens} SCOP: b.36.1.4
b.47.1.1
Length = 325
Score = 34.1 bits (79), Expect = 0.013
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V SP +AGL D I+AI + D + E ++ +L + + + + T
Sbjct: 263 VILGSPAHRAGLRP-GDVILAIGEQMVQNAED-VYEAVRTQ--SQLAVQIRRGR--ETLT 316
Query: 61 VNITP 65
+ +TP
Sbjct: 317 LYVTP 321
>2l97_A HTRA, putative serine protease; HTRA-PDZ, protein binding; NMR
{Streptococcus pneumoniae}
Length = 134
Score = 32.2 bits (74), Expect = 0.028
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
VQ N P LE + D I +D+ + D L + I +K+ Y + + T
Sbjct: 64 VQSNMPA-NGHLEKY-DVITKVDDKEIASSTDLQSALYNHSIGDTIKITYYRNGKE--ET 119
Query: 61 VNIT 64
+I
Sbjct: 120 TSIK 123
>3num_A Serine protease HTRA1; DEGP, hydrolase; 2.75A {Homo sapiens} PDB:
3nzi_A 3nwu_A 2ytw_A 2joa_A
Length = 332
Score = 32.6 bits (75), Expect = 0.038
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V ++P + GL+ D I++I+ + ND + +++K L M V +
Sbjct: 261 VIPDTPAEAGGLKE-NDVIISINGQSVVSAND-VSDVIKRE--STLNMVVRRGN--EDIM 314
Query: 61 VNITP 65
+ + P
Sbjct: 315 ITVIP 319
>2p3w_A Probable serine protease HTRA3; PDZ domain, phage derived high
affinity ligand, protein BIND; 1.70A {Homo sapiens}
Length = 112
Score = 31.5 bits (72), Expect = 0.043
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V NSP Q+ G++ D IV ++ L ++ L+E + L + V D
Sbjct: 42 VAPNSPSQRGGIQD-GDIIVKVNGRPLVDSSE-LQEAVLTE--SPLLLEVRRGN--DDLL 95
Query: 61 VNITP 65
+I P
Sbjct: 96 FSIAP 100
>3k50_A Putative S41 protease; structural genomics, joint center for
structural genomics, JCSG, protein structure initiative;
2.00A {Bacteroides fragilis nctc 9343}
Length = 403
Score = 32.1 bits (73), Expect = 0.072
Identities = 7/33 (21%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDT 33
V SP ++AGL+ +I+ ++ + + ++
Sbjct: 97 VVPGSPAEEAGLQR-GHWIMMMNGDYITKKVES 128
>3qo6_A Protease DO-like 1, chloroplastic; protease, HTRA, PH-sensor,
hydrolase, photosynthesis; 2.50A {Arabidopsis thaliana}
Length = 348
Score = 30.7 bits (70), Expect = 0.19
Identities = 12/74 (16%), Positives = 30/74 (40%), Gaps = 12/74 (16%)
Query: 1 VQDNSPGQKAGLEAFF----------DFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAV 50
+ P KAGL++ D I +++ ++ +D + L + + E+ + V
Sbjct: 258 APPSGPAGKAGLQSTKRDGYGRLVLGDIITSVNGTKVSNGSDLYRILDQCKVGDEVTVEV 317
Query: 51 YSSKTQDVRTVNIT 64
+ +++T
Sbjct: 318 LRGDHK--EKISVT 329
>2kl1_A YLBL protein; structure genomics, structural genomics, PSI-2,
protein STRU initiative, northeast structural genomics
consortium; NMR {Geobacillus thermodenitrificans}
Length = 94
Score = 29.2 bits (66), Expect = 0.20
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 2/79 (2%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V N P LEA D I AID ++ + + + +++ + Q
Sbjct: 12 VLPNMPA-AGRLEAG-DRIAAIDGQPINTSEQIVSYVREKQAGDRVRVTFIRDRKQHEAE 69
Query: 61 VNITPSNSWGGQGLLGVSI 79
+ + P Q LGV++
Sbjct: 70 LVLKPFPHHPNQIGLGVTL 88
>1k32_A Tricorn protease; protein degradation, substrate gating, serine
protease, beta propeller, proteasome, hydrolase; 2.00A
{Thermoplasma acidophilum} SCOP: b.36.1.3 b.68.7.1
b.69.9.1 c.14.1.2 PDB: 1n6e_A 1n6d_A 1n6f_A*
Length = 1045
Score = 30.9 bits (69), Expect = 0.21
Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 2/65 (3%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
+ SP + G++ I ID + ++ + +L ++ + K D R
Sbjct: 763 EGEKSPIFEYGIDPTGYLIEDIDGETVGAGSN-IYRVLSEKAGTSARIRLS-GKGGDKRD 820
Query: 61 VNITP 65
+ I
Sbjct: 821 LMIDI 825
>1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli}
SCOP: d.67.3.1 PDB: 1ek8_A* 1zn0_A 1zn1_A 2rdo_8
Length = 185
Score = 29.8 bits (68), Expect = 0.25
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VA+ N+ D ND +K LLK+
Sbjct: 126 VAVRNVGRDA-NDKVKALLKDK 146
>3lf9_A 4E10_D0_1IS1A_001_C (T161); epitope-scaffold, immune system;
2.00A {Artificial gene}
Length = 121
Score = 29.5 bits (67), Expect = 0.25
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VA+ NI D + L L K+
Sbjct: 54 VAVRNIARDA-ANDLAALGKDK 74
>3lhp_S 4E10_D0_1ISEA_004_N (T93); epitope-scaffold, immune system; 2.70A
{Artificial gene} PDB: 1y69_8
Length = 123
Score = 29.5 bits (67), Expect = 0.28
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VA+ N+ D ND L K+
Sbjct: 64 VAVRNVGRDA-NDKAAALGKDK 84
>4gfq_A Ribosome-recycling factor; structural genomics, niaid, national
institute of allergy AN infectious diseases; 2.65A
{Bacillus anthracis}
Length = 209
Score = 29.9 bits (68), Expect = 0.28
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VA+ N+R D ND LK+L K G
Sbjct: 150 VAVRNVRRDG-NDDLKKLEKAG 170
>1y8t_A Hypothetical protein RV0983; serine protease, structural genomics,
PSI, protein structure initiative; 2.00A {Mycobacterium
tuberculosis} SCOP: b.36.1.4 b.47.1.1 PDB: 2z9i_A
Length = 324
Score = 30.0 bits (68), Expect = 0.29
Identities = 8/64 (12%), Positives = 20/64 (31%), Gaps = 2/64 (3%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V AG+ + +D+ ++ + + + + + RT
Sbjct: 249 VVAGGAAANAGVPK-GVVVTKVDDRPINSADALVAAVRSKAPGATVALTFQDPSGGS-RT 306
Query: 61 VNIT 64
V +T
Sbjct: 307 VQVT 310
>1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle,
protein synthesis, translation; 2.15A {Mycobacterium
tuberculosis} SCOP: d.67.3.1 PDB: 1wqf_A 1wqh_A
Length = 185
Score = 29.8 bits (68), Expect = 0.29
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
V++ NIR + L + K G
Sbjct: 126 VSVRNIRRKA-MEELHRIRKEG 146
>1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio
parahaemolyticus} SCOP: d.67.3.1 PDB: 3r8n_Y
Length = 185
Score = 29.8 bits (68), Expect = 0.29
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VA+ NIR D N+ LK LLK+
Sbjct: 126 VAVRNIRRDA-NNDLKALLKDK 146
>1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A
{Thermus thermophilus} SCOP: d.67.3.1 PDB: 2qbe_6 2qbg_6
2qbi_6* 2qbk_6* 2v46_Y* 2v48_Y* 2z4l_6* 2z4n_6* 3j0d_J
3j0e_G
Length = 185
Score = 29.8 bits (68), Expect = 0.30
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
VAI NIR + D LK+L K
Sbjct: 127 VAIRNIRREA-LDKLKKLAKEL 147
>1te0_A Protease DEGS; two domains, serine protease, PDZ, alpha-beta
protein, hydro; 2.20A {Escherichia coli} SCOP: b.36.1.4
b.47.1.1 PDB: 3gdv_A* 3gcn_A* 3gds_A* 3gdu_A* 3gco_A*
1sot_A 1soz_A 1vcw_A 2r3y_A
Length = 318
Score = 29.8 bits (68), Expect = 0.31
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAV 50
V + P AG++ D I+++DN +T+ ++ + + + V
Sbjct: 251 VSPDGPAANAGIQV-NDLIISVDNKPAISALETMDQVAEIRPGSVIPVVV 299
>1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta
sandwich; 2.55A {Thermotoga maritima} SCOP: d.67.3.1
PDB: 1t1m_C
Length = 185
Score = 29.4 bits (67), Expect = 0.39
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 20 VAIDNIRLDQDNDTLKELLKNG 41
+AI NIR + +KE K G
Sbjct: 126 IAIRNIRREI-LKKIKEDQKEG 146
>2kjp_A Uncharacterized protein YLBL; mixed alpha-beta protein, cell
membrane, hydrolase, membrane, protease, serine
protease, transmembrane; NMR {Bacillus subtilis}
Length = 91
Score = 28.4 bits (64), Expect = 0.40
Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 2/79 (2%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V +N P K +E D I++ D + + ++ + + + + T
Sbjct: 8 VVENMPA-KGKIEVG-DKIISADGKNYQSAEKLIDYISSKKAGDKVTLKIEREEKEKRVT 65
Query: 61 VNITPSNSWGGQGLLGVSI 79
+ + + +GVS+
Sbjct: 66 LTLKQFPDEPDRAGIGVSL 84
>1fc6_A Photosystem II D1 protease; D1 C-terminal processing protease,
serine protease, serine- lysine catalytic DYAD, PDZ
domain, photosynthesis; 1.80A {Scenedesmus obliquus}
SCOP: b.36.1.3 c.14.1.2 PDB: 1fc9_A 1fc7_A 1fcf_A
Length = 388
Score = 29.5 bits (67), Expect = 0.43
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 3 DNSPGQKAGLEAFFDFIVAIDN 24
P +KAG A D IV +D
Sbjct: 108 PGGPAEKAGARA-GDVIVTVDG 128
>3pv2_A DEGQ; trypsin fold, PDZ domain, chaperone protease, hydrolase;
2.15A {Legionella fallonii} PDB: 3pv3_A 3pv5_A 3pv4_A
Length = 451
Score = 29.2 bits (66), Expect = 0.56
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V NSP + AGL+A D I I++ ++ Q + + +K+ V T
Sbjct: 289 VNPNSPAELAGLKA-GDIITQINDTKITQATQVKTTISLLRVGSTVKIIVERDNKP--LT 345
Query: 61 VNIT 64
++
Sbjct: 346 LSAV 349
>3stj_A Protease DEGQ; serine protease, PDZ domain, protease, chaperone,
DEGP, DEGQ hydrolase; 2.60A {Escherichia coli}
Length = 345
Score = 29.1 bits (66), Expect = 0.65
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V S KAG++A D I +++ L+ + + ++K+ + +
Sbjct: 270 VLPGSGSAKAGVKA-GDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKP--LE 326
Query: 61 VNIT 64
V +T
Sbjct: 327 VEVT 330
>4a8c_A Periplasmic PH-dependent serine endoprotease DEGQ; chaperone,
hydrolase; 7.50A {Escherichia coli} PDB: 4a8a_A 4a8b_A
4a9g_A
Length = 436
Score = 29.2 bits (66), Expect = 0.67
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V S KAG++A D I +++ L+ + + ++K+ + +
Sbjct: 270 VLPGSGSAKAGVKA-GDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKP--LE 326
Query: 61 VNIT 64
V +T
Sbjct: 327 VEVT 330
>1ky9_A Protease DO, DEGP, HTRA; protein quality control, serine protease,
trypsin, chaperone, PDZ, ATP-independent,
temperature-regulated, periplasm; 2.80A {Escherichia
coli} SCOP: b.36.1.4 b.47.1.1 PDB: 3ou0_A 4a8d_A 3otp_A
3mh7_A 3mh4_A 3mh5_A* 3mh6_A* 3cs0_A 2zle_A
Length = 448
Score = 29.2 bits (66), Expect = 0.67
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V NS KAG++A D I +++ + ++ + +L + + Q
Sbjct: 293 VLPNSSAAKAGIKA-GDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQ--VN 349
Query: 61 VNIT 64
VN+
Sbjct: 350 VNLE 353
>3tqg_A 2-methylcitrate synthase; energy metabolism, transferase; 2.30A
{Coxiella burnetii}
Length = 375
Score = 28.2 bits (64), Expect = 1.1
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 15/52 (28%)
Query: 86 GANENVWHIL------DQDNDTLKELLKNGIDKELKM----AVYSSKTQDVR 127
GANE ++ + +K L N KEL M AVY + +D R
Sbjct: 223 GANEAAMDLIMLYKTPSEAIAGIKRKLAN---KELIMGFGHAVY--RERDPR 269
>1w9e_A Syntenin 1; cell adhesion, adhesion/complex, PDZ domain,
scaffolding protein signaling protein; 1.56A {Homo
sapiens} SCOP: b.36.1.1 b.36.1.1 PDB: 1n99_A 1v1t_A
1obz_A 1w9o_A 1w9q_A 1ybo_A
Length = 166
Score = 27.9 bits (62), Expect = 1.2
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 2/91 (2%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRL-DQDNDTLKELLKNGIDKELKMAVYSSKTQDVR 59
VQ NSP GL D ++ I+ +D ++LK +++ M + +
Sbjct: 34 VQANSPASLVGLRF-GDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTI 92
Query: 60 TVNITPSNSWGGQGLLGVSIRFCSFEGANEN 90
T++ + G G A N
Sbjct: 93 TMHKDSTGHVGFIFKNGKITSIVKDSSAARN 123
>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 = 27.9 bits (61), Expect = 1.7
Identities = 17/123 (13%), Positives = 36/123 (29%), Gaps = 41/123 (33%)
Query: 17 DFI-VAIDNIRLDQD----NDTLKELLKNGIDKELKMAVYSSKTQDVRTVNITPSNSWGG 71
D + V D + D D K +L +E+ + SK T+ +
Sbjct: 20 DILSVFEDAFVDNFDCKDVQDMPKSILSK---EEID-HIIMSKDAVSGTLRL-------- 67
Query: 72 QGLLGVSIRFCSFEGANENVWHILDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRTVNI 131
W +L + + +++ ++ + Y ++T
Sbjct: 68 -------------------FWTLLSKQEEMVQKFVEEVLRIN-----YKFLMSPIKTEQR 103
Query: 132 TPS 134
PS
Sbjct: 104 QPS 106
>3o8j_A 2-methylcitrate synthase; short chain fatty acids, propionate
metabolism, 2-methylcitr cycle, PRPC or 2-MCS, GLTA or
CS, 2-methy synthase; 2.41A {Salmonella enterica}
Length = 404
Score = 27.9 bits (63), Expect = 1.8
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 15/52 (28%)
Query: 86 GANENVWHIL------DQDNDTLKELLKNGIDKELKM----AVYSSKTQDVR 127
GANE I D+ +++ ++N KE+ + VY D R
Sbjct: 252 GANEVSLEIQQRYETPDEAEADIRKRVEN---KEVVIGFGHPVY--TIADPR 298
>3hwk_A Methylcitrate synthase; niaid, ssgcid, structural genomics, seattle
structural genomics center for infectious disease,
tubercluosis; 2.30A {Mycobacterium tuberculosis}
Length = 414
Score = 26.8 bits (60), Expect = 4.2
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 15/52 (28%)
Query: 86 GANENVWHIL------DQDNDTLKELLKNGIDKELKM----AVYSSKTQDVR 127
GANE V H + + L+ L KE M VY + D R
Sbjct: 265 GANEAVMHDMIEIGDPANAREWLRAKLAR---KEKIMGFGHRVY--RHGDSR 311
>3i18_A LMO2051 protein; alpha-beta protein, structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; 1.70A {Listeria monocytogenes}
PDB: 2kjk_A 3i1e_A
Length = 100
Score = 25.7 bits (57), Expect = 4.4
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 9/82 (10%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVY---SSKTQD 57
V+D+ P L A D I ID + + + + +K+ ++ D
Sbjct: 14 VKDDVPAADV-LHAG-DLITEIDGNAFKSSQEFIDYIHSKKVGDTVKINYKHGDKNEQAD 71
Query: 58 VRTVNITPSNSWGGQGLLGVSI 79
++ I + G +G+++
Sbjct: 72 IKLTAIDKKGTPG----IGITL 89
>3ftb_A Histidinol-phosphate aminotransferase; structural genomics, PSI,
MCSG, protein structure initiative; 2.00A {Clostridium
acetobutylicum}
Length = 361
Score = 26.3 bits (59), Expect = 5.2
Identities = 19/128 (14%), Positives = 42/128 (32%), Gaps = 38/128 (29%)
Query: 4 NSPGQKAGLEAFFD--FIVA-IDNIRLDQDNDTLKELLKNGIDK-ELKMAVYSS------ 53
N + A + D +I + I+ ++ ++K V+S
Sbjct: 248 NCFAEMAAINCLKDTNYIEESLLWIK------KERKRFIEELNKIGFIKRVFSPHANFVL 301
Query: 54 -KTQDVRTVNITPSNSWGGQGLL--GVSIRFCS-FEGANENVWHI-----LDQDND---- 100
+ +++ + LL + IR C F G +++ + ++ N
Sbjct: 302 CRLENISGEKLY-------DSLLKEDIVIRRCCNFIGLDDS--FVRFAIKDEKKNTKFLR 352
Query: 101 TLKELLKN 108
LK + N
Sbjct: 353 ALKGVENN 360
>3kzx_A HAD-superfamily hydrolase, subfamily IA, variant; ssgcid, NIH,
niaid, SBRI, UW, emerald biostructures, ehrlich
chaffeensis; 1.90A {Ehrlichia chaffeensis}
Length = 231
Score = 26.1 bits (58), Expect = 5.6
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 13 EAFFDFIVAIDNIRL-DQDNDTLKELLKNGIDKELKMAVYSSKTQD 57
E + DN L D + L L +N I MA+ S+K +
Sbjct: 90 ENSLEKSQKSDNFMLNDGAIELLDTLKENNI----TMAIVSNKNGE 131
>1iom_A Citrate synthase; open form, riken structural genomics/proteomics
in RSGI, structural genomics, lyase; 1.50A {Thermus
thermophilus} SCOP: a.103.1.1 PDB: 1ixe_A*
Length = 377
Score = 25.9 bits (58), Expect = 6.7
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 86 GANENVWHILDQ--DNDTLKELLKNGIDKELKM-----AVYSSKTQDVR 127
GANE V ++ + + +E ++ + K+ ++ VY K D R
Sbjct: 221 GANEAVMRMIQEIGTPERAREWVREKLAKKERIMGMGHRVY--KAFDPR 267
>2vsp_A PDZ domain-containing protein 1; membrane, cytoplasm,
phosphoprotein, transport protein, CAsp; 2.60A {Homo
sapiens} PDB: 2eej_A
Length = 91
Score = 24.9 bits (55), Expect = 6.7
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDN-DTLKELLKNGIDKELKMAVYSSKTQD 57
VQ P AGLE D I+ ++ + + + + + + +++ K + + V K QD
Sbjct: 34 VQKGGPADLAGLED-EDVIIEVNGVNVLDEPYEKVVDRIQSS-GKNVTLLVCGKKAQD 89
>2c6x_A Citrate synthase 1; tricarboxylic acid cycle, transferase,
allosteric enzyme, enzyme thermostability; HET: COZ CIT;
3.4A {Bacillus subtilis}
Length = 363
Score = 26.0 bits (58), Expect = 6.9
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 86 GANENVWHILDQ--DNDTLKELLKNGIDKELKM-----AVYSSKTQDVR 127
GA V +L+ + + + LK ++K ++ VY KT+D R
Sbjct: 214 GAPSAVTKMLEDIGEKEHAEAYLKEKLEKGERLMGFGHRVY--KTKDPR 260
>3fkd_A L-threonine-O-3-phosphate decarboxylase; structural genomic, ,
structural genomics, PSI-2, protein structure
initiative; 2.50A {Porphyromonas gingivalis}
Length = 350
Score = 26.0 bits (58), Expect = 7.1
Identities = 19/121 (15%), Positives = 37/121 (30%), Gaps = 22/121 (18%)
Query: 4 NSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKT--QDVRTV 61
N+ +A IR +++ + V+ S T +R
Sbjct: 229 NALAIEAAKFILIHPAQFTLPIRK---WQRNTVDFITALNRLDGVEVHPSGTTFFLLRLK 285
Query: 62 NITPSNSWGGQGLL---GVSIRFCS-FEGANENVWHI-----LDQDND----TLKELLKN 108
T + + +L + IR S F G +E+ ++ N L+ L+
Sbjct: 286 KGTAAELK--KYMLEEYNMLIRDASNFRGLDES--YVRITTQRPAQNQLFIKALETFLEK 341
Query: 109 G 109
Sbjct: 342 Y 342
>1lc5_A COBD, L-threonine-O-3-phosphate decarboxylase; PLP-dependent
decarboxylase cobalamin, lyase; 1.46A {Salmonella
enterica} SCOP: c.67.1.1 PDB: 1lc7_A* 1lc8_A* 1lkc_A*
Length = 364
Score = 25.6 bits (57), Expect = 8.6
Identities = 16/126 (12%), Positives = 34/126 (26%), Gaps = 38/126 (30%)
Query: 4 NSPGQKAGLEAFFD--FIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKT------ 55
N+ AG A D + + + + VY +
Sbjct: 249 NALAALAGEVALQDSAW---QQATW--HWLREEGARFYQALCQLPLLTVYPGRANYLLLR 303
Query: 56 --QDVRTVNITPSNSWGGQGLL--GVSIRFC-SFEGANENVWHI-----LDQDND----T 101
++ + + LL + IR C ++ G + + N+
Sbjct: 304 CEREDIDLQ---------RRLLTQRILIRSCANYPGLDSR--YYRVAIRSAAQNERLLAA 352
Query: 102 LKELLK 107
L+ +L
Sbjct: 353 LRNVLT 358
>2go7_A Hydrolase, haloacid dehalogenase-like family; structural genomics,
joint center for structural genomics, J protein
structure initiative; 2.10A {Streptococcus pneumoniae}
SCOP: c.108.1.6
Length = 207
Score = 25.2 bits (56), Expect = 9.6
Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 32 DTLKELLKNGIDKELKMAVYSSKTQDVRTV 61
+ L ++GI + +Y+ K + T+
Sbjct: 92 EVLAWADESGI----QQFIYTHKGNNAFTI 117
Score = 25.2 bits (56), Expect = 9.6
Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 100 DTLKELLKNGIDKELKMAVYSSKTQDVRTV 129
+ L ++GI + +Y+ K + T+
Sbjct: 92 EVLAWADESGI----QQFIYTHKGNNAFTI 117
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
0.315 0.134 0.397
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,443,218
Number of extensions: 134400
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 63
Length of query: 163
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 77
Effective length of database: 4,300,587
Effective search space: 331145199
Effective search space used: 331145199
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 (21.6 bits)
S2: 53 (24.1 bits)