RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16078
(111 letters)
>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 = 39.8 bits (92), Expect = 6e-05
Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 17/118 (14%)
Query: 1 MSFIPETPNEKNKEAFRRYLEQSGV--VDA-ITSALVMLYSIEEKPEDPLD----FIRRN 53
S P E +R+ ++ V A I + L+ L + D + + +
Sbjct: 361 SSLNVLEPAE-----YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS 415
Query: 54 LGDERPEVAEYEAVLQDLD-EAKAELDQLTATVANLKERLSKYEVVESDQ--PISDDN 108
L +++P+ E + + E K +L+ A ++ + + + +SD P D
Sbjct: 416 LVEKQPK--ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 29.5 bits (66), Expect = 0.23
Identities = 12/94 (12%), Positives = 29/94 (30%), Gaps = 5/94 (5%)
Query: 18 RYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEA----VLQDLDE 73
L+ +L + +R + AE +A V Q D
Sbjct: 2320 SQLQAQQSATPGNHSLFLFDGSHTFVLAYTQSVRAKMTPGCEAEAEAKAMYFFVQQFTDM 2379
Query: 74 AKAELDQLTATVANLKERLSKY-EVVESDQPISD 106
+ ++ + + L+ R++ +++ D
Sbjct: 2380 EQGKVLEALIPLQGLEARVAATVDLITQSHAGLD 2413
>2j5u_A MREC protein; bacterial cell shape determining protein MREC, cell
shape regulation; 2.5A {Listeria monocytogenes}
Length = 255
Score = 28.9 bits (65), Expect = 0.30
Identities = 5/41 (12%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 58 RPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVV 98
+ + E + ++ + K E L ++ + + Y+ +
Sbjct: 32 KERLEELAQLESEVADLKKENKDLKE-SLDITDSIRDYDPL 71
>3snx_A SUSD homolog, putative SUSD-like carbohydrate binding protein;
alpha-alpha superhelix, structural genomics; HET: MSE;
1.88A {Bacteroides thetaiotaomicron}
Length = 460
Score = 29.1 bits (65), Expect = 0.30
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 61 VAE-YEAVLQDLDEAKAELDQLTATVANLKERLSKY 95
VA+ Y+ + DL+ A+ L K + +
Sbjct: 156 VAQVYQQIFDDLNLAQDYLTNYVRKGDGQKFKPNTD 191
>3g36_A Protein DPY-30 homolog; X-type four-helix bundle, nucleus,
nuclear protein; 1.20A {Homo sapiens}
Length = 55
Score = 26.9 bits (60), Expect = 0.36
Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 10 EKNKEAFRRYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAE 63
+ R YL+Q+ VV + + +L +E+P +P++F+ L + + +
Sbjct: 3 DLQSLPTRAYLDQT-VVPILLQGMAVL--AKERPPNPIEFLASYLLKNKAQFED 53
>3lnn_A Membrane fusion protein (MFP) heavy metal cation ZNEB (CZCB-LIKE);
structural genomics, PSI-2, protein structure
initiative; 2.80A {Cupriavidus metallidurans}
Length = 359
Score = 28.1 bits (63), Expect = 0.47
Identities = 12/51 (23%), Positives = 23/51 (45%)
Query: 47 LDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEV 97
+ RRNL +R A +D ++A+++ DQ + RL++
Sbjct: 107 MTMARRNLDRQRELDKSEIAAKRDFEQAQSDYDQAASESQRADARLAQLGA 157
>1sl6_A C-type lectin DC-signr; sugar binding protein; HET: GAL NDG FUC;
2.25A {Homo sapiens} SCOP: d.169.1.1 PDB: 1xar_A
Length = 184
Score = 27.9 bits (62), Expect = 0.57
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 70 DLDEAKAELDQLTATVANLKERLSKYEVVES 100
L E EL QL A V L ++ + ++ +
Sbjct: 8 KLQEIYQELTQLKAAVGELPDQSKQQQIYQE 38
>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic
hypermutat protein-DNA complex, DNA mispair, cancer;
HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B*
2o8e_B* 2o8f_B*
Length = 1022
Score = 28.1 bits (63), Expect = 0.70
Identities = 9/56 (16%), Positives = 19/56 (33%)
Query: 44 EDPLDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVE 99
D + R E A ++ ++ DQ A + ++ L +Y +
Sbjct: 565 PDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQ 620
>3rkl_A STIV-A81; 4-helix bundle, hyperthermophilic viral protein, viral
prote; 1.70A {Sulfolobus turreted icosahedral virus}
Length = 87
Score = 27.0 bits (59), Expect = 0.74
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 53 NLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
N+ D E E VL +L E L ++ +A L E+LS+YE
Sbjct: 7 NIKDNTIEYGHKEFVLSNLQEDIKNLAEIVYQLAKLIEKLSQYE 50
>1lvw_A Glucose-1-phosphate thymidylyltransferase; protein nucleotide
complex, nucleotide binding fold; HET: TYD; 1.70A
{Methanothermobacter thermautotrophicusorganism_taxid}
SCOP: c.68.1.6
Length = 295
Score = 26.3 bits (59), Expect = 2.0
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 10/32 (31%)
Query: 17 RRYLEQSGVV--DAITSALVMLYSIEEKPEDP 46
R + GVV D+ + SIEEKP P
Sbjct: 144 RPF----GVVEFDSEGRVI----SIEEKPSRP 167
>1fxo_A Glucose-1-phosphate thymidylyltransferase; rhamnose,
nucleotidyltransferase, pyrophosphorylase, allostery;
HET: TMP; 1.66A {Pseudomonas aeruginosa} SCOP: c.68.1.6
PDB: 1fzw_A 1g0r_A* 1g1l_A* 1g23_A* 1g2v_A* 1g3l_A*
1h5r_A* 1h5s_C* 1h5t_A* 1h5s_D* 1h5s_A* 1h5r_B* 1h5s_B*
1h5t_B* 1iim_A* 1iin_A* 3pkp_A* 3pkq_A* 1mp5_A* 1mp3_A*
...
Length = 293
Score = 26.3 bits (59), Expect = 2.2
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 10/32 (31%)
Query: 17 RRYLEQSGVV--DAITSALVMLYSIEEKPEDP 46
RY GVV D A+ S+EEKP +P
Sbjct: 143 ERY----GVVEFDQGGKAI----SLEEKPLEP 166
>1mc3_A Glucose-1-phosphate thymidylyltransferase; glucose-1-phosphate
thymidylytransferase, RFFH; HET: TTP; 2.60A {Escherichia
coli} SCOP: c.68.1.6
Length = 296
Score = 26.3 bits (59), Expect = 2.4
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 10/32 (31%)
Query: 17 RRYLEQSGVV--DAITSALVMLYSIEEKPEDP 46
R+ GVV D A+ S+EEKP+ P
Sbjct: 144 ERF----GVVEFDDNFRAI----SLEEKPKQP 167
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_9
Length = 189
Score = 26.2 bits (57), Expect = 2.4
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
+V +LK ++S+ E D
Sbjct: 20 GTSVLDLKSQISQDMGFEIDM 40
>3ktd_A Prephenate dehydrogenase; structural genomics, joint center F
structural genomics, JCSG, protein structure initiative;
2.60A {Corynebacterium glutamicum atcc 13032}
Length = 341
Score = 26.2 bits (58), Expect = 2.8
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 65 EAVLQDLDEAKAELDQLTATVANLKERLSKY 95
+++ LDEA A L + + + + +
Sbjct: 250 GPLVKALDEALAILHEAREGLTAEQPNIEQL 280
>3gzs_A Uncharacterized SUSD superfamily protein; structural genomics,
joint center for structural genomics, J protein
structure initiative, PSI-2; 2.09A {Bacteroides
fragilis}
Length = 515
Score = 26.1 bits (56), Expect = 2.9
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 64 YEAVLQDLDEAKAELDQLTATVANL 88
Y + L++L+EA LD + +
Sbjct: 164 YRSFLKELEEAVQTLDDYSNKSKEV 188
>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin,
ubiquitin-like domain, structural genomics, signaling
protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1
Length = 100
Score = 25.4 bits (56), Expect = 3.1
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
T T+ LKE +S+ DQ
Sbjct: 41 TCTIQQLKEEISQRFKAHPDQ 61
>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP,
oligomerization, ubiquitin insertion, hydrolase binding;
2.17A {Bacillus amyloliquefaciens}
Length = 189
Score = 25.7 bits (56), Expect = 3.2
Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 13/73 (17%)
Query: 44 EDPLDFIRRNLGDER------------PEVAEYEAVLQDLDEAKAELD-QLTATVANLKE 90
E +++ +R + + ++ L L+ + + T+ N+K
Sbjct: 74 EADINYTSGFRNSDRILYSSDWLIYKTTDHYGGQIFVKTLTGKTITLEVEPSDTIENVKA 133
Query: 91 RLSKYEVVESDQP 103
++ E + DQ
Sbjct: 134 KIQDKEGIPPDQQ 146
>3p1u_A SUSD homolog; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-biology;
2.05A {Parabacteroides distasonis atcc 8503}
Length = 529
Score = 26.0 bits (56), Expect = 3.4
Identities = 4/35 (11%), Positives = 12/35 (34%), Gaps = 2/35 (5%)
Query: 56 DERPEVAEYEAVLQDLDEAKAELDQLTATVANLKE 90
++ Y+ ++LD A + + +
Sbjct: 138 KSLKDI--YDEYFRELDAAINGFNDSAQPIFSDAG 170
>3sp1_A Cysteinyl-tRNA synthetase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid, LYME
disease; HET: AMP; 2.55A {Borrelia burgdorferi}
Length = 501
Score = 25.7 bits (57), Expect = 4.3
Identities = 5/41 (12%), Positives = 17/41 (41%)
Query: 71 LDEAKAELDQLTATVANLKERLSKYEVVESDQPISDDNSAI 111
L +K + L ++ E L ++ ++ + + ++
Sbjct: 343 LQASKIARENLINKLSYFYESLDPVDLNTLNKDLKNFGFSV 383
>3okq_A BUD site selection protein 6; coiled-coil, protein binding; 2.04A
{Saccharomyces cerevisiae} PDB: 3onx_A
Length = 141
Score = 25.3 bits (55), Expect = 4.5
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 58 RPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSK 94
+P + E V +DL+ A+A++ +L + K K
Sbjct: 50 QPAKKKLETVSKDLENAQADVLKLQEFIDTEKPHWKK 86
>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.15.1.1
Length = 96
Score = 24.7 bits (54), Expect = 4.7
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
+ V K+++SKY +D+
Sbjct: 36 NSNVRRFKKQISKYLHCNADR 56
>2tmg_A Protein (glutamate dehydrogenase); metabolic role, mutant,
oxidoreductase; 2.90A {Thermotoga maritima} SCOP:
c.2.1.7 c.58.1.1 PDB: 1b26_A 1b3b_A
Length = 415
Score = 25.5 bits (57), Expect = 4.8
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 59 PEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVESDQPISDDN 108
PE + YE ++ + A + +D + L+ V + P+ D+
Sbjct: 1 PEKSLYEMAVEQFNRAASLMDLESDLAEVLRRPKRVLIV---EFPVRMDD 47
>3ibx_A TENA, HP1287, putative thiaminase II; vitamin B1, hydrol; 2.40A
{Helicobacter pylori} PDB: 2rd3_A
Length = 221
Score = 25.4 bits (55), Expect = 4.9
Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 1/92 (1%)
Query: 13 KEAFRRYLEQSGV-VDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDL 71
++ FR Y+ Q + + + +F E++ + +++L
Sbjct: 38 RDKFRFYIIQDYLYLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIREL 97
Query: 72 DEAKAELDQLTATVANLKERLSKYEVVESDQP 103
+ EL T+AN
Sbjct: 98 QITQKELQNACPTLANKSYTSYMLAEGFKGSI 129
>3odg_A Xanthosine phosphorylase; structural genomics, PSI-2, protein
structure initiative, NE SGX research center for
structural genomics; HET: XAN; 1.64A {Yersinia
pseudotuberculosis} PDB: 1yqq_A* 1yqu_A* 1yr3_A*
Length = 287
Score = 25.2 bits (56), Expect = 4.9
Identities = 6/34 (17%), Positives = 16/34 (47%)
Query: 29 ITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVA 62
+ S + + E P + +I++ +P++A
Sbjct: 4 VNSNINVDADFNELPFQAVKYIQKIKPGFKPQIA 37
>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A*
2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*
Length = 934
Score = 25.4 bits (56), Expect = 5.2
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 58 RPEVAEYEAVLQDLDEAKAELDQLT--ATVANLKER 91
+ Y +Q L++ A+LD + A V+N
Sbjct: 582 VNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPV 617
>4dk0_A Putative MACA; alpha-hairpin, lipoyl, beta-barrel, periplasmic
protein, MEM protein; 3.50A {Aggregatibacter
actinomycetemcomitans} PDB: 4dk1_A
Length = 369
Score = 25.1 bits (55), Expect = 5.3
Identities = 5/37 (13%), Positives = 12/37 (32%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVV 98
A ++D + + Q V + L ++
Sbjct: 122 ATLNNAKAEMDVVQENIKQAEIEVNTAETNLGYTKIT 158
Score = 24.7 bits (54), Expect = 9.0
Identities = 7/36 (19%), Positives = 14/36 (38%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEV 97
L+ AKAE+D + + + ++ E
Sbjct: 115 DTLNTAKATLNNAKAEMDVVQENIKQAEIEVNTAET 150
>2f1m_A Acriflavine resistance protein A; helical hairpin, lipoyl domain,
beta barrel, transport prote; 2.71A {Escherichia coli}
Length = 277
Score = 25.3 bits (56), Expect = 5.6
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVESDQPIS 105
A Y+A D AK +L + A + +++Y+ + Q IS
Sbjct: 56 ATYQA---TYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYIS 96
>4f7a_A Putative uncharacterized protein; TPR-like protein, mucin O-glycan
binding, structural genomic center for structural
genomics, JCSG; HET: PGE; 1.85A {Bacteroides vulgatus}
Length = 511
Score = 25.2 bits (54), Expect = 6.0
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 64 YEAVLQDLDEAKAELDQLTATVANLK 89
Y+A DLD+A LD
Sbjct: 155 YKAFFDDLDKAVDALDTYLKEGGKED 180
>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 106
Score = 24.6 bits (54), Expect = 6.2
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
T T+ LKE +S+ DQ
Sbjct: 36 TCTIQQLKEEISQRFKAHPDQ 56
>4ecm_A Glucose-1-phosphate thymidylyltransferase; HET: DAU; 2.30A
{Bacillus anthracis} PDB: 3hl3_A*
Length = 269
Score = 24.8 bits (55), Expect = 6.3
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 38 SIEEKPEDP 46
IEEKP++P
Sbjct: 178 EIEEKPKEP 186
>3hm7_A Allantoinase; metallo-dependent hydrolase, protein structure
initiative, PSI-2, NEW YORK structural genomix research
CON nysgxrc; 2.60A {Bacillus halodurans}
Length = 448
Score = 24.8 bits (55), Expect = 6.7
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 12/69 (17%)
Query: 14 EAFRRYLEQSGVV------DAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAV 67
+ ++ ++ + + +AL + IEE+ D+ + RP V+E EAV
Sbjct: 173 KGMKKIAALGSILAVHAESNEMVNALTTIA-IEEQRLTVKDY-----SEARPIVSELEAV 226
Query: 68 LQDLDEAKA 76
+ L A+
Sbjct: 227 ERILRFAQL 235
>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure,
northeast structural genomics consortium, protein
structure initiative, NESG; NMR {Homo sapiens}
Length = 88
Score = 24.3 bits (53), Expect = 6.9
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
T TVA+LK+++S E V+ D
Sbjct: 24 TQTVAHLKQQVSGLEGVQDDL 44
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 24.6 bits (54), Expect = 7.0
Identities = 4/16 (25%), Positives = 8/16 (50%)
Query: 61 VAEYEAVLQDLDEAKA 76
VAEY ++ ++
Sbjct: 50 VAEYSGLICLMETMLR 65
>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein
structur initiative, northeast structural genomics
consortium, NESG; NMR {Homo sapiens}
Length = 101
Score = 23.9 bits (52), Expect = 8.5
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 82 TATVANLKERLSKYEVVESDQ 102
++V KE +SK +DQ
Sbjct: 44 NSSVQQFKEEISKRFKSHTDQ 64
>1vf7_A Multidrug resistance protein MEXA; alpha hairpin, beta barrel,
membrane protein; 2.40A {Pseudomonas aeruginosa} SCOP:
f.46.1.1 PDB: 2v4d_A 1t5e_A
Length = 369
Score = 24.5 bits (54), Expect = 8.6
Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 69 QDLDEAKAELDQLTATVANLKERLSKYEVVESDQPIS 105
Q +A A Q A V + L Y V S PIS
Sbjct: 112 QQYADANAAYLQSKAAVEQARINLR-YTKVLS--PIS 145
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
0.309 0.129 0.340
Gapped
Lambda K H
0.267 0.0517 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,655,614
Number of extensions: 96165
Number of successful extensions: 450
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 102
Length of query: 111
Length of database: 6,701,793
Length adjustment: 75
Effective length of query: 36
Effective length of database: 4,607,718
Effective search space: 165877848
Effective search space used: 165877848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.9 bits)