RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4032
(84 letters)
>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6*
3m9s_6*
Length = 181
Score = 111 bits (278), Expect = 6e-33
Identities = 34/73 (46%), Positives = 49/73 (67%), Gaps = 2/73 (2%)
Query: 11 MLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 70
M P VISMG A + GG ++ +Y++V+ D ++PVD+YVPGCPP EAL+Y ++QLQK
Sbjct: 99 MPDPKWVISMGACA-SSGGMFN-NYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQK 156
Query: 71 KVKRMKILQSWYR 83
KV+ + R
Sbjct: 157 KVRGQAYNERGER 169
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1
Length = 283
Score = 44.3 bits (104), Expect = 6e-07
Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGG---GYYHYSYSV----VRGCDRIIPVDIYVPGCP 55
+ L+ + +++G + GG + + S ++I + + VPGCP
Sbjct: 106 MMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCP 165
Query: 56 PTAEALMYGILQL 68
P + ++ ++
Sbjct: 166 PHPDWMVGTLVAA 178
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 317
Score = 41.6 bits (97), Expect = 5e-06
Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 4 VSLLAQAMLGPVGVISMGGAAPNGGG---YYHYSYSV----VRGCDRIIPVDIYVPGCPP 56
V L + V+++G A GG + + G + I + +PGCPP
Sbjct: 136 VDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPP 195
Query: 57 TAEALMYGILQLQKKVKRMKILQSWYRR 84
+ ++ ++ +K+ +
Sbjct: 196 HPDWIVGTVVLALDAIKKNGLEGGLAEV 223
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A
{Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A
Length = 264
Score = 38.8 bits (90), Expect = 4e-05
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 5/71 (7%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYY-HYSYSVVRGCDRIIPV----DIYVPGCPPT 57
+ A+ VI++G A GG + + G + + I + GCPP
Sbjct: 92 MYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPN 151
Query: 58 AEALMYGILQL 68
+ ++ L
Sbjct: 152 PMNFVGTVVHL 162
>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD,
oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP:
e.19.1.1
Length = 317
Score = 38.5 bits (89), Expect = 6e-05
Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGG-YYHYSYSVVRGCDRIIP----VDIYVPGCPPT 57
+ + ++ + VI+ G A GG + + +G + + I + GCPP
Sbjct: 144 MLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPN 203
Query: 58 AEALMYGILQ 67
L+ I+
Sbjct: 204 PYNLVGTIVY 213
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution
[NIFE]hydrogenase, oxidoreductase, NI-A state, unready
state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}
SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S
1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S
1wuk_S 1wul_S 1e3d_A*
Length = 267
Score = 38.0 bits (88), Expect = 9e-05
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 17 VISMGGAAPNGGG-YYHYSYSVVRGCDRIIP----VDIYVPGCPPTAEALMYGILQ 67
VI+ G A GG + + +G + + I + GCPP L+ I+
Sbjct: 108 VIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVY 163
>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_S* 3use_S*
Length = 335
Score = 37.4 bits (86), Expect = 1e-04
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYY-HYSYSVVRGCDRIIP--VDIYVPGCPPTAE 59
+ L +A G +I+ G A G + + D++I I VPGCPP +
Sbjct: 95 FIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPD 154
Query: 60 ALMYGILQL 68
+ I +
Sbjct: 155 VMSAIITYM 163
>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase,
membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio
marinus} PDB: 3ayy_B 3ayz_B
Length = 283
Score = 37.3 bits (86), Expect = 2e-04
Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 6/72 (8%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYY-HYSYSVVRGCDRIIPVD-----IYVPGCPP 56
L + +IS G A G + + + + I VPGCPP
Sbjct: 101 FSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPP 160
Query: 57 TAEALMYGILQL 68
AE + I +
Sbjct: 161 IAEVMTGVITYM 172
>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase
unready state, oxidoreductase; 1.83A {Desulfovibrio
fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S
Length = 264
Score = 36.9 bits (85), Expect = 2e-04
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYY-HYSYSVVRGCDRIIPVDIY-VPGCPPTAEA 60
+ +A G+I +G + GG + S +G + V +PGCPP
Sbjct: 94 MIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPIN 153
Query: 61 LMYGILQL 68
+ ++ +
Sbjct: 154 FVGAVVHV 161
>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE]
hydrogenase, high-resolution knallgasbacteria,
proteobacteria; 1.50A {Ralstonia eutropha}
Length = 339
Score = 35.4 bits (81), Expect = 6e-04
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 17 VISMGGAAPNGGGYY-HYSYSVVRGCDRIIPVD--IYVPGCPPTAEALMYGILQL 68
+IS G A G + + ++I I VPGCPP AE + I +
Sbjct: 109 IISWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYM 163
>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 269
Score = 33.4 bits (76), Expect = 0.003
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 3/69 (4%)
Query: 3 GVSLLAQAMLGPVGVISMGGAAPNGGGY-YHYSYSVVRGCDRIIPVD--IYVPGCPPTAE 59
S+L + + VI++G A GG + + ++ I VPGCPP
Sbjct: 93 NYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPIPM 152
Query: 60 ALMYGILQL 68
+ I
Sbjct: 153 VITGVIAHY 161
>2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2;
phosphorylation, nucleotide biosynthesis, transferase;
2.55A {Homo sapiens} PDB: 2c4k_A*
Length = 379
Score = 26.6 bits (59), Expect = 0.85
Identities = 5/27 (18%), Positives = 9/27 (33%), Gaps = 8/27 (29%)
Query: 38 VRGCDRIIPVDIYV--PGCPPTAEALM 62
VRG D +++ +M
Sbjct: 77 VRGKD------VFIIQTVSKDVNTTIM 97
>3qfu_A 78 kDa glucose-regulated protein homolog; HSP70, KAR2, BIP,
chaperone; HET: ADP; 1.80A {Saccharomyces cerevisiae}
PDB: 3qfp_A 3qml_A 3ldo_A* 3ldl_A 3ldn_A* 3ldp_A*
Length = 394
Score = 26.3 bits (59), Expect = 1.1
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 56 PTAEALMYGILQLQKKVKRMKIL 78
PTA A+ YG L K K +I+
Sbjct: 190 PTAAAIAYG---LDKSDKEHQII 209
>3s5j_B Ribose-phosphate pyrophosphokinase 1; nucleotide synthesis,
transferase; 2.02A {Homo sapiens} PDB: 2hcr_A* 3efh_A
2h06_A 2h07_A 2h08_A
Length = 326
Score = 26.4 bits (59), Expect = 1.2
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 8/27 (29%)
Query: 38 VRGCDRIIPVDIYV--PGCPPTAEALM 62
VRG D +Y+ GC + LM
Sbjct: 48 VRGED------VYIVQSGCGEINDNLM 68
>3dah_A Ribose-phosphate pyrophosphokinase; pyrophosphoki seattle
structural genomics center for infectious disease,
magnesium, metal binding; HET: AMP; 2.30A {Burkholderia
pseudomallei}
Length = 319
Score = 26.0 bits (58), Expect = 1.4
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 8/27 (29%)
Query: 38 VRGCDRIIPVDIYV--PGCPPTAEALM 62
VRG D ++V C PT + LM
Sbjct: 52 VRGKD------VFVLQSTCAPTNDNLM 72
>2kho_A Heat shock protein 70; molecular chaperone, HSP70, peptide binding,
protein folding, acetylation, ATP-binding, cell inner
membrane; NMR {Escherichia coli}
Length = 605
Score = 26.1 bits (58), Expect = 1.5
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 56 PTAEALMYGILQLQKKVKRMKIL 78
PTA AL YG L K I
Sbjct: 172 PTAAALAYG---LDKGTGNRTIA 191
>1dkg_D Molecular chaperone DNAK; HSP70, GRPE, nucleotide exchange factor,
coiled-coil, complex (HSP24/HSP70); 2.80A {Escherichia
coli} SCOP: c.55.1.1 c.55.1.1
Length = 383
Score = 26.0 bits (58), Expect = 1.6
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 56 PTAEALMYGILQLQKKVKRMKIL 78
PTA AL YG L K I
Sbjct: 172 PTAAALAYG---LDKGTGNRTIA 191
>3h04_A Uncharacterized protein; protein with unknown function,
structural genomics, MCSG, PS protein structure
initiative; 1.90A {Staphylococcus aureus subsp}
Length = 275
Score = 24.8 bits (54), Expect = 4.1
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 35 YSVVRGCDRIIPVDIYVPGCPPTAEALMY 63
Y V+ +P I PT ++Y
Sbjct: 6 YKVITKDAFALPYTIIKAKNQPTKGVIVY 34
>3rst_A Signal peptide peptidase SPPA; alpha/beta protein fold, signal
peptide digestion, bacterial membrane, hydrolase; 2.37A
{Bacillus subtilis}
Length = 240
Score = 24.5 bits (54), Expect = 5.1
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 4 VSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRII 45
+ + + P+ +SMG A + GGYY + D+I
Sbjct: 71 LEEIKKETKKPI-YVSMGSMAAS-GGYY-----ISTAADKIF 105
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 0.142 0.447
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,418,390
Number of extensions: 76043
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 25
Length of query: 84
Length of database: 6,701,793
Length adjustment: 52
Effective length of query: 32
Effective length of database: 5,249,901
Effective search space: 167996832
Effective search space used: 167996832
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 (21.5 bits)
S2: 51 (23.5 bits)