RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3809
(112 letters)
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 133 bits (336), Expect = 1e-39
Identities = 78/109 (71%), Positives = 90/109 (82%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ VDDLLTPCSP PGA+EM
Sbjct: 214 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMT 273
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+MDVP DKLLEP VSM +L+SL +KPTVN+ D++KL+KF EDFGQEG
Sbjct: 274 WMDVPGDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLKKFTEDFGQEG 322
>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 = 132 bits (333), Expect = 2e-38
Identities = 77/109 (70%), Positives = 91/109 (83%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ V+DLLTPCSP PGA+EM
Sbjct: 336 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMT 395
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+MDVP DKLLEP VSM +L+SL ++KPTVN+ D++KL+KF EDFGQEG
Sbjct: 396 WMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKKFTEDFGQEG 444
>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 = 121 bits (305), Expect = 4e-35
Identities = 52/109 (47%), Positives = 77/109 (70%), Gaps = 6/109 (5%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSG+DI++VV+DALMQP+R +QSATHF S LTPCSP GA+EM+
Sbjct: 219 YSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRK------LTPCSPGDDGAIEMS 272
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 273 WTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 321
>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 = 118 bits (297), Expect = 1e-33
Identities = 51/109 (46%), Positives = 76/109 (69%), Gaps = 6/109 (5%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSG+DI++VV+DALMQP+R +QSATHF S LTP SP GA+EM+
Sbjct: 252 YSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRK------LTPSSPGDDGAIEMS 305
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 306 WTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 354
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 64.1 bits (156), Expect = 2e-13
Identities = 15/109 (13%), Positives = 39/109 (35%), Gaps = 37/109 (33%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSG+D++ + +DA + P+R ++
Sbjct: 317 YSGSDLTALAKDAALGPIRELK-----------------------------------PEQ 341
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
++ + ++ + + +SL+ K +V+ + ++ +DFG
Sbjct: 342 VKNMSASEM--RNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFGDTT 388
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding,
hydrolase; 2.70A {Drosophila melanogaster}
Length = 297
Score = 63.1 bits (154), Expect = 2e-13
Identities = 15/107 (14%), Positives = 35/107 (32%), Gaps = 37/107 (34%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSG+D++ + +DA ++P+R + + + S
Sbjct: 224 YSGSDLTALAKDAALEPIR--------------------ELNVEQVKCLDISAM------ 257
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQ 110
++ SL+ + +V + K+ +D+G
Sbjct: 258 -----------RAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQDYGD 293
>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 = 61.7 bits (150), Expect = 9e-13
Identities = 18/106 (16%), Positives = 39/106 (36%), Gaps = 37/106 (34%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
+SGAD++ + R+A + P+R +Q+A
Sbjct: 286 FSGADMTQLCREASLGPIRSLQTADIA--------------------------------- 312
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFG 109
+ D++ P++ + T +P+V+ D+ + + FG
Sbjct: 313 --TITPDQV--RPIAYIDFENAFRTVRPSVSPKDLELYENWNKTFG 354
>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 = 43.4 bits (103), Expect = 3e-06
Identities = 14/105 (13%), Positives = 35/105 (33%), Gaps = 24/105 (22%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
+SGAD++ + + A +R + + + +D P
Sbjct: 220 FSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPE----------- 268
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDF 108
+ H +++ ++ +V+D+D+ K F +
Sbjct: 269 -------------IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL 300
>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 = 42.5 bits (100), Expect = 6e-06
Identities = 15/107 (14%), Positives = 36/107 (33%), Gaps = 24/107 (22%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
+SGAD++ + + A +R + + + +D P
Sbjct: 682 FSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPE----------- 730
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQ 110
+ H +++ ++ +V+D+D+ K F + Q
Sbjct: 731 -------------IRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQ 764
Score = 27.5 bits (61), Expect = 0.98
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPV--DPSKTVDDLLTPCSPSTPGAVE 61
+ GAD++ + +A +Q +R + + V + T+DD S S P A+
Sbjct: 406 HVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALR 465
Query: 62 MNFMDVPS 69
++VP
Sbjct: 466 ETVVEVPQ 473
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 32.9 bits (76), Expect = 0.010
Identities = 14/96 (14%), Positives = 31/96 (32%), Gaps = 38/96 (39%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
Y+GAD+S +VR+A + +R +
Sbjct: 217 YTGADLSALVREASICALR--------------------------------------QEM 238
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMV 99
++ E VS H ++ + + +++ D +
Sbjct: 239 ARQKSGNEKGELKVSHKHFEEAFKKVRSSISKKDQI 274
>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin,
S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber
suppression; HET: PBF; 2.05A {Mus musculus} PDB:
2dwz_B* 2dvw_B*
Length = 83
Score = 25.7 bits (57), Expect = 2.0
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 4 YSGADISIVVRDALMQPVR 22
SGADI+ + +++ M VR
Sbjct: 35 ISGADINSICQESGMLAVR 53
>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 = 26.6 bits (58), Expect = 2.5
Identities = 16/133 (12%), Positives = 34/133 (25%), Gaps = 66/133 (49%)
Query: 2 YS----YSGADISIVVRDALMQPVRLVQSATHFVR-----------TSGPSP-----VDP 41
Y+ + +SI V +V F R G S ++P
Sbjct: 1767 YAALASLADV-MSI--ESL----VEVV-----FYRGMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 42 SK--------TVDDLLTPCSPST-----------PG----------AVE-----MNFMDV 67
+ + ++ T A++ +NF+ +
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKL 1874
Query: 68 PSDKLLEPPVSMH 80
++E S+
Sbjct: 1875 QKIDIIELQKSLS 1887
Score = 25.4 bits (55), Expect = 6.5
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 13/61 (21%)
Query: 32 RTSGPSPVDPSKTVDDLLTPCSPSTPGAVE--------MNFMDVPSDK-----LLEPPVS 78
+T D K + L+ +T A + + +++ PS+ LL P+S
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 79 M 79
Sbjct: 238 C 238
>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats,
A-helical domain, structural genomics, NPPSFA; 2.20A
{Saccharomyces cerevisiae} PDB: 2dzo_B
Length = 82
Score = 25.4 bits (56), Expect = 2.6
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 4 YSGADISIVVRDALMQPVR 22
SGA I+ ++++A ++ VR
Sbjct: 32 LSGAVIAAIMQEAGLRAVR 50
>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 = 26.3 bits (58), Expect = 2.9
Identities = 6/19 (31%), Positives = 13/19 (68%)
Query: 4 YSGADISIVVRDALMQPVR 22
+ GAD++ + +A +Q +R
Sbjct: 406 HVGADLAALCSEAALQAIR 424
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 24.9 bits (55), Expect = 5.8
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 4 YSGADISIVVRDALMQPVR 22
GA++ + +A M +R
Sbjct: 222 CVGAELKAICTEAGMNAIR 240
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 0.132 0.381
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: 1,687,735
Number of extensions: 88022
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 222
Number of HSP's successfully gapped: 40
Length of query: 112
Length of database: 6,701,793
Length adjustment: 76
Effective length of query: 36
Effective length of database: 4,579,797
Effective search space: 164872692
Effective search space used: 164872692
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: 51 (23.6 bits)