RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3374
(72 letters)
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 121 bits (307), Expect = 2e-36
Identities = 35/64 (54%), Positives = 47/64 (73%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
RR + TG RVVNQLLTE+DG+E + V+++ AT+RPDIIDPA+LRPGRL ++ +
Sbjct: 118 RRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGL 177
Query: 66 PDLA 69
P A
Sbjct: 178 PPPA 181
>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48, ATP-binding, lipid-binding, nucle binding,
nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus
musculus}
Length = 301
Score = 110 bits (276), Expect = 1e-31
Identities = 34/67 (50%), Positives = 47/67 (70%), Gaps = 3/67 (4%)
Query: 6 RRGN---DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
RG D G DRV+NQ+LTE+DG+ + V+++GAT+RPDIIDPA+LRPGRL ++
Sbjct: 123 ARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 182
Query: 63 CTMPDLA 69
+PD
Sbjct: 183 IPLPDEK 189
>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
Length = 806
Score = 104 bits (262), Expect = 2e-28
Identities = 34/67 (50%), Positives = 47/67 (70%), Gaps = 3/67 (4%)
Query: 6 RRGN---DSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVH 62
RG D G DRV+NQ+LTE+DG+ + V+++GAT+RPDIIDPA+LRPGRL ++
Sbjct: 585 ARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 644
Query: 63 CTMPDLA 69
+PD
Sbjct: 645 IPLPDEK 651
Score = 71.0 bits (174), Expect = 1e-16
Identities = 27/64 (42%), Positives = 38/64 (59%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
+R V+ R+V+QLLT +DG++ V V+ AT+RP+ IDPAL R GR V +
Sbjct: 312 KREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGI 371
Query: 66 PDLA 69
PD
Sbjct: 372 PDAT 375
>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein;
HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A*
1e32_A* 1s3s_A* 2pjh_B
Length = 489
Score = 78.3 bits (193), Expect = 3e-19
Identities = 27/62 (43%), Positives = 38/62 (61%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTM 65
+R V+ R+V+QLLT +DG++ V V+ AT+RP+ IDPAL R GR V +
Sbjct: 312 KREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGI 371
Query: 66 PD 67
PD
Sbjct: 372 PD 373
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 76.5 bits (189), Expect = 6e-19
Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 4 GYRRGNDSTGVK---DRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSS 60
+R + TG R + QLL E+DG + V ++GAT+RPDI+DPA+LRPGR
Sbjct: 123 AAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRI 182
Query: 61 VHCTMPD 67
+ PD
Sbjct: 183 IEVPAPD 189
>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic;
photosynthesis, rubisco activase, AAA+ protein; 2.95A
{Nicotiana tabacum} PDB: 3zw6_A
Length = 293
Score = 73.3 bits (180), Expect = 1e-17
Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 12/78 (15%)
Query: 2 ITGYRRGNDSTGVKDRVVNQLLTEL------------DGVEGLEGVYVVGATSRPDIIDP 49
G G V +++VN L + + V ++ + +
Sbjct: 111 GAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYA 170
Query: 50 ALLRPGRLGSSVHCTMPD 67
L+R GR+ +
Sbjct: 171 PLIRDGRMEKFYWAPTRE 188
>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics,
structural G consortium, SGC, ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo
sapiens}
Length = 262
Score = 71.9 bits (177), Expect = 2e-17
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 8 GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
N +++ +NQLL E+DG+ + V V+ +T+R DI+D AL+RPGRL V +P
Sbjct: 122 SNTE---EEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPT 178
Query: 68 L 68
L
Sbjct: 179 L 179
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
3.20A {Thermus thermophilus} SCOP: c.37.1.20
Length = 278
Score = 71.6 bits (176), Expect = 4e-17
Identities = 29/61 (47%), Positives = 40/61 (65%), Gaps = 3/61 (4%)
Query: 8 GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
GND +++ +NQLL E+DG E + V+ AT+RPDI+DPALLRPGR + PD
Sbjct: 155 GNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD 211
Query: 68 L 68
+
Sbjct: 212 V 212
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A
{Escherichia coli} SCOP: c.37.1.20
Length = 257
Score = 71.2 bits (175), Expect = 4e-17
Identities = 30/61 (49%), Positives = 44/61 (72%), Gaps = 3/61 (4%)
Query: 8 GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
G+D +++ +NQ+L E+DG EG EG+ V+ AT+RPD++DPALLRPGR V +PD
Sbjct: 127 GHDE---REQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPD 183
Query: 68 L 68
+
Sbjct: 184 V 184
>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB:
1iy0_A* 1iy1_A*
Length = 254
Score = 71.2 bits (175), Expect = 4e-17
Identities = 29/61 (47%), Positives = 40/61 (65%), Gaps = 3/61 (4%)
Query: 8 GNDSTGVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
GND +++ +NQLL E+DG E + V+ AT+RPDI+DPALLRPGR + PD
Sbjct: 131 GNDE---REQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD 187
Query: 68 L 68
+
Sbjct: 188 V 188
>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A
{Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB:
2cea_A* 3kds_E*
Length = 476
Score = 72.2 bits (178), Expect = 4e-17
Identities = 27/49 (55%), Positives = 35/49 (71%)
Query: 20 NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
NQLL E+DG + EG+ V+ AT+RPDI+DPALLRPGR + PD+
Sbjct: 140 NQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDM 188
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 71.9 bits (177), Expect = 5e-17
Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 20 NQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
NQLL E+DG E + V+ AT+RPDI+DPALLRPGR + PD+
Sbjct: 155 NQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDV 203
>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding,
cell CELL division, hydrolase, membrane, metal-binding;
3.30A {Helicobacter pylori} PDB: 2r65_A*
Length = 268
Score = 66.5 bits (163), Expect = 3e-15
Identities = 25/50 (50%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 20 NQLLTELDG-VEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
NQLL E+DG V V+ AT+RP+I+DPAL+RPGR V PD
Sbjct: 136 NQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDF 185
>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA
ATPase, ATP-binding, coiled coil, membrane,
nucleotide-binding, phosphorylation; HET: ATP; 3.00A
{Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A
2jq9_A 2k3w_A 1yxr_A
Length = 444
Score = 65.4 bits (159), Expect = 1e-14
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVEG-LEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
R + + R+ + L ++ GV +G+ V+GAT+ P ++D A+ R R ++
Sbjct: 242 SRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIP 299
Query: 65 MPDLA 69
+P+
Sbjct: 300 LPEAH 304
>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta
domain, C-terminal helix, ATP-binding, E
nucleotide-binding; 2.90A {Saccharomyces cerevisiae}
PDB: 2qpa_A*
Length = 355
Score = 65.2 bits (159), Expect = 1e-14
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
RG + R+ +LL +++GV +GV V+GAT+ P +D A+ R R ++
Sbjct: 158 TRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIP 215
Query: 65 MPDLA 69
+PDLA
Sbjct: 216 LPDLA 220
>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase,
ATP-binding cassette, ATP-binding, endosome, MEM
nucleotide-binding; 2.70A {Saccharomyces cerevisiae}
PDB: 3eih_A* 2rko_A 3mhv_C
Length = 322
Score = 65.1 bits (159), Expect = 1e-14
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGV-EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
RG + R+ +LL +++GV +GV V+GAT+ P +D A+ R R ++
Sbjct: 125 TRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIP 182
Query: 65 MPDLA 69
+PDLA
Sbjct: 183 LPDLA 187
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 63.9 bits (156), Expect = 3e-14
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVE-GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCT 64
R + + R+ + L ++ GV +G+ V+GAT+ P ++D A+ R R ++
Sbjct: 120 SRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIP 177
Query: 65 MPDLA 69
+P+
Sbjct: 178 LPEPH 182
>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural
genomics consortium, ATP- hydrolase, magnesium,
metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo
sapiens}
Length = 357
Score = 60.5 bits (147), Expect = 7e-13
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGV--EGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
+RG+ R+ + L +LDG + + VVGAT+RP ID A R RL ++
Sbjct: 191 QRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYI 248
Query: 64 TMPD 67
+P+
Sbjct: 249 PLPE 252
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding,
hydrolase; 2.70A {Drosophila melanogaster}
Length = 297
Score = 58.5 bits (142), Expect = 3e-12
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 2 ITGYRRGNDSTGVKDRVVNQLLTELDGV---EGLEGVYVVGATSRPDIIDPALLRPGRLG 58
+ R ++ R+ + L E DG+ + + V+ AT+RP +D A LR R
Sbjct: 125 LLSERSSSEH-EASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFT 181
Query: 59 SSVHCTMPDLA 69
V+ ++PD
Sbjct: 182 KRVYVSLPDEQ 192
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 57.9 bits (140), Expect = 5e-12
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 6 RRGNDSTGVKDRVVNQLLTELDGVE--GLEGVYVVGATSRPDIIDPALLRPGRLGSSVHC 63
R R+ + L E DGV+ G + V V+GAT+RP +D A+LR R V+
Sbjct: 222 ERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYV 279
Query: 64 TMPD 67
++P+
Sbjct: 280 SLPN 283
>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain,
ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus}
SCOP: c.37.1.20 PDB: 1nsf_A*
Length = 272
Score = 49.0 bits (117), Expect = 6e-09
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 17 RVVNQLLTELDGVEGL-EGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPDL 68
V+ LL L + ++G TSR D++ + +++H +P++
Sbjct: 149 LVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH--VPNI 198
>2wfg_A Cytosolic leucyl-tRNA synthetase; ligase, editing domain,
hydrolysis of MIS-charged trnas, benzoxaborole,
anti-fungal; HET: ZZB; 2.20A {Candida albicans} PDB:
2wfe_A*
Length = 261
Score = 25.3 bits (55), Expect = 1.8
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 12 TGVKDRVVN------QLLTELDGVEGLEGVYVVGATSRP 44
G+K R+ + +L + VY+V AT RP
Sbjct: 4 VGIKIRLTDVAPQAQELFKKESLDVKENKVYLVAATLRP 42
>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate,
CHEY homologue, homodimer, (beta/alpha)5, signaling
protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP:
c.23.1.1
Length = 140
Score = 24.1 bits (52), Expect = 4.2
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 15 KDRVVNQLLTELDGVEGLEGVYVVGA---TSRPDIIDPALLRPGRLGSSV 61
V ++++T DG+E + + G SRPD+I L P + G V
Sbjct: 24 NSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREV 73
>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC,
PSI-II, respose regulator, structure initiative,
structural genomics; 2.40A {Rhodospirillum rubrum}
Length = 152
Score = 23.4 bits (51), Expect = 6.4
Identities = 6/38 (15%), Positives = 13/38 (34%), Gaps = 5/38 (13%)
Query: 15 KDRVVNQLLTELDGVEGLE-----GVYVVGATSRPDII 47
+ V N+++ DG L + R ++
Sbjct: 26 RAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLV 63
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 23.9 bits (52), Expect = 6.5
Identities = 7/41 (17%), Positives = 15/41 (36%), Gaps = 4/41 (9%)
Query: 13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLR 53
G+ R ++ + E + L + + DP + R
Sbjct: 195 GITQRELSYFIQEFERTGALSRSVLFLNKAD----DPTIER 231
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 23.5 bits (51), Expect = 8.3
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLR 53
G+ + +++ + LE V + DPA+ R
Sbjct: 193 GITNEEAQYFMSDFEKTGALERAVVFLNLAD----DPAVER 229
>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural
genomics, protein structure initiative; 1.50A
{Legionella pneumophila subsp}
Length = 143
Score = 22.9 bits (50), Expect = 9.4
Identities = 6/35 (17%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 15 KDRVVNQLLTELDGVEGLEGVYVVGATS--RPDII 47
K + ++ G + L+ +Y + P +I
Sbjct: 29 KISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLI 63
>2vm8_A Dihydropyrimidinase-related protein 2; neurogenesis,
phosphoprotein, differentiation, CRMP, cytoplasm, TIM
barrel, polymorphism, axonal pathfinding; 1.9A {Homo
sapiens} PDB: 2gse_A 1kcx_A
Length = 501
Score = 23.4 bits (51), Expect = 9.5
Identities = 10/55 (18%), Positives = 18/55 (32%), Gaps = 10/55 (18%)
Query: 13 GVKDRVVNQLLTELDGVEGLEGVYVVGATSRPDIIDPALLRPGRLGSSVHCTMPD 67
++D ++ Q+ L G++ + P ID MPD
Sbjct: 47 YMEDGLIKQIGENLIVPGGVKTIEAHSRMVIPGGIDV----------HTRFQMPD 91
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 0.140 0.408
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,156,010
Number of extensions: 57117
Number of successful extensions: 114
Number of sequences better than 10.0: 1
Number of HSP's gapped: 104
Number of HSP's successfully gapped: 35
Length of query: 72
Length of database: 6,701,793
Length adjustment: 42
Effective length of query: 30
Effective length of database: 5,529,111
Effective search space: 165873330
Effective search space used: 165873330
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: 51 (23.6 bits)