RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1634
(132 letters)
>1omz_A Alpha-1,4-N-acetylhexosaminyltransferase EXTL2; rossmann fold, DXD
motif; HET: UD2; 2.10A {Mus musculus} SCOP: c.68.1.15
PDB: 1omx_A* 1on6_A* 1on8_A*
Length = 293
Score = 125 bits (315), Expect = 1e-36
Identities = 32/118 (27%), Positives = 51/118 (43%), Gaps = 8/118 (6%)
Query: 1 MLFLGAAFYHKYWNYMYTAHMPAPIRTYVDSHMNCEDIAMNFLVAHITAKAPI-KVTPRK 59
M+ +GA+F++ + ++ PA + +D NC+DIAMNFLV T K V P
Sbjct: 174 MVLIGASFFNSKYLELFQ-KQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPIN 232
Query: 60 KFKCPQCKN-SELLSSDTKHMIERSKCVSLFAEIYGEGGIKGSPLRSVEFRADPVLFR 116
+ N + +H ++RS C++ IY G PL+ F
Sbjct: 233 MVNLEKETNGYSGMWHRAEHFLQRSYCINKLVNIYD-----GMPLKYSNIMISQFGFP 285
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.5 bits (63), Expect = 0.57
Identities = 10/66 (15%), Positives = 19/66 (28%), Gaps = 26/66 (39%)
Query: 60 KFKCPQCKNSELLSSDTKHMIER--------SKCVSLFAEIYGEGGIKGSPLRSVEFRAD 111
CP+CK ++ER + C + + + E+R
Sbjct: 21 VLTCPECK------VYPPKIVERFSEGDVVCALC----GLVLSDKLVDTRS----EWRT- 65
Query: 112 PVLFRD 117
F +
Sbjct: 66 ---FSN 68
>2pqc_A 3-phosphoshikimate 1-carboxyvinyltransferase; inside-OUT alpha/beta
barrel; HET: RC1; 1.60A {Agrobacterium SP} PDB: 2pqb_A*
2gg6_A* 2gg4_A* 2gga_A* 2ggd_A* 2pqd_A*
Length = 445
Score = 27.5 bits (62), Expect = 1.2
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 29 VDSHMNCED--IAMNFLVAHITAKAPIKV 55
V +H+ D IAM+FLV + ++ P+ V
Sbjct: 393 VATHL---DHRIAMSFLVMGLVSENPVTV 418
>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4),
metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1
Length = 65
Score = 26.1 bits (57), Expect = 1.2
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 61 FKCPQCKNSELLSSDTKHMIER---SKCVSLFAEIYGEGGIK----GSPLRSVEFRADPV 113
CP+CK ++ + K M+ + C S ++ G G+PLR FR
Sbjct: 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR--VQ 61
Query: 114 LFRD 117
LF D
Sbjct: 62 LFED 65
>3slh_A 3-phosphoshikimate 1-carboxyvinyltransferase; structural genomics,
center for structural genomics of infec diseases, csgid;
HET: S3P GPJ SKM PGE 1PE PG4; 1.70A {Coxiella burnetii}
PDB: 3roi_A* 4egr_A* 3tr1_A
Length = 441
Score = 27.5 bits (62), Expect = 1.4
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 29 VDSHMNCED--IAMNFLVAHITAKAPIKV 55
V+S+ D IAM F VA AK P+++
Sbjct: 383 VNSYD---DHRIAMAFAVAGTLAKGPVRI 408
>3qcp_A QSOX from trypanosoma brucei (tbqsox); ERV fold, thioredoxin fold,
sulfhydryl oxidase, oxidoreducta; HET: FAD; 2.30A
{Trypanosoma brucei} PDB: 3qd9_A*
Length = 470
Score = 27.3 bits (59), Expect = 1.5
Identities = 4/26 (15%), Positives = 13/26 (50%)
Query: 25 IRTYVDSHMNCEDIAMNFLVAHITAK 50
I+ Y+ +C++ +F+ + +
Sbjct: 325 IQNYIRYFFSCKECRDHFIQFNFSPN 350
>3rmt_A 3-phosphoshikimate 1-carboxyvinyltransferase 1; structural
genomics, protein structure initiative; 2.80A {Bacillus
halodurans}
Length = 455
Score = 27.2 bits (61), Expect = 1.9
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 29 VDSHMNCED--IAMNFLVAHITAKAPIKV 55
V SH D I M +A + A+ P+ V
Sbjct: 385 VSSHG---DHRIGMAMAIAALLAEKPVTV 410
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon,
hyperthermophilic, extremophIle; NMR {Thermococcus
celer} SCOP: g.41.3.1
Length = 57
Score = 24.8 bits (54), Expect = 3.0
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 53 IKVTPRKKFKCPQCKNSE 70
+K P K CP+C N
Sbjct: 8 LKTLPTTKITCPKCGNDT 25
>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger;
NMR {Homo sapiens} SCOP: g.41.3.1
Length = 62
Score = 24.8 bits (54), Expect = 3.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 56 TPRKKFKCPQCKNS 69
T R FKCP C ++
Sbjct: 10 TNRASFKCPVCSST 23
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan
synthesis, cell WALL biogenesis/degradation, secreted,
cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis}
PDB: 2vfw_A* 2vg1_A*
Length = 227
Score = 25.9 bits (58), Expect = 4.1
Identities = 7/17 (41%), Positives = 9/17 (52%), Gaps = 3/17 (17%)
Query: 14 NYMYTAHMPAP---IRT 27
+YT+ P P IRT
Sbjct: 167 ENLYTSGQPDPDLVIRT 183
>3qas_B Undecaprenyl pyrophosphate synthase; alpha-helix, isoprenoid
biosynthesis, transferase; 1.70A {Escherichia coli} PDB:
1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A*
2e9c_A* 2e9d_A* 1ueh_A 1x09_A* 1x08_A*
Length = 253
Score = 25.9 bits (58), Expect = 4.5
Identities = 3/17 (17%), Positives = 6/17 (35%), Gaps = 3/17 (17%)
Query: 14 NYMYTAHMPAP---IRT 27
++ + IRT
Sbjct: 179 QHVCMHELAPVDLVIRT 195
>2dmi_A Teashirt homolog 3; zinc finger protein 537, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 115
Score = 25.5 bits (55), Expect = 4.6
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 59 KKFKCPQCKNS-ELLSSDTKHMIE 81
KF+C C + + L T HM E
Sbjct: 18 SKFRCKDCSAAYDTLVELTVHMNE 41
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 25.2 bits (56), Expect = 7.6
Identities = 3/17 (17%), Positives = 7/17 (41%), Gaps = 3/17 (17%)
Query: 14 NYMYTAHMPAP---IRT 27
++ +P +RT
Sbjct: 217 RHLQRPDIPDVDLFLRT 233
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW
fold for isoprenoid synthase, peptidoglycan synthesis,
transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1
Length = 249
Score = 25.2 bits (56), Expect = 8.4
Identities = 9/17 (52%), Positives = 12/17 (70%), Gaps = 3/17 (17%)
Query: 14 NYMYTAHMPAP---IRT 27
Y++TA+MP P IRT
Sbjct: 182 EYLFTANMPDPELLIRT 198
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 24.8 bits (55), Expect = 9.2
Identities = 5/17 (29%), Positives = 9/17 (52%), Gaps = 3/17 (17%)
Query: 14 NYMYTAHMPAP---IRT 27
N + T ++P +RT
Sbjct: 176 NRLDTRNLPEVDLLLRT 192
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
0.324 0.138 0.433
Gapped
Lambda K H
0.267 0.0805 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,012,024
Number of extensions: 101910
Number of successful extensions: 376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 373
Number of HSP's successfully gapped: 22
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (23.7 bits)