RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12189
(131 letters)
>3rvy_A ION transport protein; tetrameric ION channel, voltage-gated
sodium-selective ION C membrane, metal transport; HET:
PX4; 2.70A {Arcobacter butzleri} PDB: 3rvz_A* 3rw0_A*
Length = 285
Score = 41.3 bits (97), Expect = 3e-05
Identities = 9/57 (15%), Positives = 24/57 (42%)
Query: 1 MLTLFEVLSFKGWLDVRDILKTQLGDAHVIYIHVYIFLGCMIGLTLFVGVVIANYSE 57
TLF+V++ + W ++ ++ +IF+ + + L V + + +
Sbjct: 185 FYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAICVDAMAI 241
Score = 29.7 bits (67), Expect = 0.19
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 82 QPLHLPPRPDAFKYRARIYDVTQNLWFKRLIAAVVLINSMLL 123
L PR RI ++ ++ +F + I ++++N + +
Sbjct: 8 DKGSLVPRGSHM--YLRITNIVESSFFTKFIIYLIVLNGITM 47
>4dxw_A Navrh, ION transport protein; tetrameric, voltage-gated sodium
channel, sodium selective, gated ION channel; HET: BNG
PX4; 3.05A {Alpha proteobacterium HIMB114}
Length = 229
Score = 39.2 bits (92), Expect = 1e-04
Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 1 MLTLFEVLSFKGWLDV-RDILKTQLGDAHVIYIHVYIFLGCMIGLTLFVGVVIANYSENK 59
++TLF+VL+ W V + + +Y +I + + L L + +++ + K
Sbjct: 170 LITLFQVLTLSSWETVMLPMQEI--YWWSWVYFFSFIIICSITILNLVIAILVDVVIQKK 227
Score = 25.4 bits (56), Expect = 6.5
Identities = 4/28 (14%), Positives = 15/28 (53%)
Query: 96 RARIYDVTQNLWFKRLIAAVVLINSMLL 123
+ N F+ + +++++N++L+
Sbjct: 2 TPFFSSLKDNRIFQFTVVSIIILNAVLI 29
>1byy_A Protein (sodium channel alpha-subunit); membrane protein; NMR
{Rattus norvegicus} SCOP: j.12.1.1
Length = 53
Score = 35.2 bits (81), Expect = 4e-04
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 62 ALLTVDQRRWCDLKKRLKIAQPLHLPPRPDAFKYRARIYD 101
+T +Q+++ + K+L +P PRP A K++ ++D
Sbjct: 15 IFMTEEQKKYYNAMKKLGSKKPQKPIPRP-ANKFQGMVFD 53
>4djc_B Sodium channel protein type 5 subunit alpha; EF-hand,
calcium-binding protein; 1.35A {Homo sapiens}
Length = 35
Score = 28.3 bits (63), Expect = 0.10
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 65 TVDQRRWCDLKKRLKIAQPLHLPPRPDAFKYRARIY 100
+ Q+++ + K+L +P PRP KY+ I+
Sbjct: 1 SNAQKKYYNAMKKLGSKKPQKPIPRP-LNKYQGFIF 35
>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 = 29.8 bits (66), Expect = 0.24
Identities = 23/144 (15%), Positives = 50/144 (34%), Gaps = 42/144 (29%)
Query: 9 SFKGWLDVRDI---LKTQLGDAHVIYI--------HVYIFLGCMI-----GLTLFVGVVI 52
+F D +D+ K+ L + +I ++ + FV V+
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL 87
Query: 53 A-NYS--------ENKGTALLTVDQRRWCDLKKRL----KIAQPLHLPPRPDAF-KYRAR 98
NY E + +++T R + + + RL ++ ++ R + K R
Sbjct: 88 RINYKFLMSPIKTEQRQPSMMT---RMYIEQRDRLYNDNQVFAKYNV-SRLQPYLKLRQA 143
Query: 99 IYDVTQNLWFKRLIAAVVLINSML 122
+ ++ VLI+ +L
Sbjct: 144 LLELRPAKN--------VLIDGVL 159
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 0.33
Identities = 8/29 (27%), Positives = 11/29 (37%), Gaps = 7/29 (24%)
Query: 74 LKK---RLKIAQPLHLPPRPDAFKYRARI 99
LKK LK+ P A +A +
Sbjct: 22 LKKLQASLKLYADDSAP----ALAIKATM 46
>2xp1_A SPT6; transcription, IWS1, histone chaperone, mRNA export; 2.20A
{Antonospora locustae}
Length = 178
Score = 27.5 bits (61), Expect = 1.0
Identities = 5/24 (20%), Positives = 8/24 (33%), Gaps = 2/24 (8%)
Query: 90 PDAFKYRARIYDVTQNL--WFKRL 111
D Y + + + KRL
Sbjct: 154 SDMLTYNNSTFKDIDSFVAYRKRL 177
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 27.1 bits (60), Expect = 2.0
Identities = 5/26 (19%), Positives = 7/26 (26%), Gaps = 2/26 (7%)
Query: 90 PDAFKYRARIYDVTQNL--WFKRLIA 113
+ Y L FK L+
Sbjct: 1182 NTGYFLVNYNYPSVIQLCNGFKTLLK 1207
>3or8_A Transcription elongation factor SPT6; SH2, CTD binding; HET: MES;
1.60A {Candida glabrata} PDB: 3pjp_A* 3psj_A* 3psk_A
2l3t_A 3gxw_A 3gxx_A
Length = 197
Score = 26.8 bits (59), Expect = 2.2
Identities = 6/25 (24%), Positives = 7/25 (28%), Gaps = 2/25 (8%)
Query: 90 PDAFKYRARIYDVTQNL--WFKRLI 112
F Y L FK L+
Sbjct: 166 HTGFFLVNYNYPTVIQLCNGFKTLL 190
>2iu8_A LPXD, UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase;
UDP-3- O-acyl-glucosamine N-acyltransferase, lipid A
biosynthesis; HET: PLM UD1; 2.2A {Chlamydia trachomatis}
PDB: 2iu9_A* 2iua_A*
Length = 374
Score = 26.1 bits (58), Expect = 4.2
Identities = 8/32 (25%), Positives = 11/32 (34%), Gaps = 2/32 (6%)
Query: 23 QLGDAHVIYIHVYIFLGCMIG--LTLFVGVVI 52
+G A I I +G + VVI
Sbjct: 156 HVGSACHIGSGSVIGAYSTVGEHSYIHPRVVI 187
>3pmo_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltr; lipid A
biosynthesis pathway, transferase; 1.30A {Pseudomonas
aeruginosa}
Length = 372
Score = 25.7 bits (57), Expect = 5.2
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 22 TQLGDAHVIYIHVYIFLGCMIG--LTLFVGVVI 52
++G I H I +IG L V +
Sbjct: 150 ARIGAGVSIGAHCVIGARSVIGEGGWLAPRVTL 182
>3eh0_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N- acyltransferase; LPXD,
LEFT-handed parallel beta helix, acyl carrier protein,
antibiotic resistance; 2.60A {Escherichia coli}
Length = 341
Score = 25.6 bits (57), Expect = 5.5
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 22 TQLGDAHVIYIHVYIFLGCMIG--LTLFVGVVI 52
+LGD +I ++ IG L+ V I
Sbjct: 128 VELGDNVIIGAGCFVGKNSKIGAGSRLWANVTI 160
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
0.331 0.144 0.449
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,063,678
Number of extensions: 113347
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 17
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 52 (23.8 bits)