RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5271
(113 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 = 137 bits (348), Expect = 5e-43
Identities = 36/72 (50%), Positives = 54/72 (75%), Gaps = 1/72 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M +P+WVISMG+CA+ GG ++ +Y++V+ D ++PVD+YVPGCPP EAL+Y ++QLQKK
Sbjct: 99 MPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKK 157
Query: 101 VKRMKILQSWYR 112
V+ + R
Sbjct: 158 VRGQAYNERGER 169
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1
Length = 283
Score = 52.4 bits (125), Expect = 2e-09
Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSV--------VRGCDRIIPVDIYVPGCPPTAEALMY 92
+ +++G+C+ GG +V ++I + + VPGCPP + ++
Sbjct: 114 APKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVG 173
Query: 93 GILQLQKKVK 102
++ V
Sbjct: 174 TLVAAWSHVL 183
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 317
Score = 48.9 bits (116), Expect = 3e-08
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 41 MLEPRWVISMGSCANGGG----YYHYSYSV----VRGCDRIIPVDIYVPGCPPTAEALMY 92
V+++G+CA GG + + G + I + +PGCPP + ++
Sbjct: 143 GPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVG 202
Query: 93 GILQLQKKVKRMKILQSWYRR 113
++ +K+ +
Sbjct: 203 TVVLALDAIKKNGLEGGLAEV 223
>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 = 46.6 bits (110), Expect = 2e-07
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 24 EPGSTTCKASAVTTTSWMLE----PRWVISMGSCANGGG--YYHYSYSVVRGCDRIIP-- 75
K + T + VI+ G+CA GG + + +G + +
Sbjct: 131 AANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHL 190
Query: 76 --VDIYVPGCPPTAEALMYGILQ 96
I + GCPP L+ I+
Sbjct: 191 GVKAINIAGCPPNPYNLVGTIVY 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 = 45.8 bits (108), Expect = 4e-07
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 24 EPGSTTCKASAVTTTSWMLE----PRWVISMGSCANGGG--YYHYSYSVVRGCDRIIP-- 75
K + T + VI+ G+CA GG + + +G + +
Sbjct: 81 AANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHL 140
Query: 76 --VDIYVPGCPPTAEALMYGILQ 96
I + GCPP L+ I+
Sbjct: 141 GVKAINIAGCPPNPYNLVGTIVY 163
>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 = 44.2 bits (104), Expect = 1e-06
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 44 PRWVISMGSCANGGG--YYHYSYSVVRGCDRIIPV----DIYVPGCPPTAEALMYGILQL 97
+ VI++G+CA GG + + G + + I + GCPP + ++ L
Sbjct: 103 AKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHL 162
>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 = 43.9 bits (103), Expect = 2e-06
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 11/85 (12%)
Query: 24 EPGSTTCKASAVTTTSWMLE----PRWVISMGSCANGGGYY--HYSYSVVRGCDRIIPVD 77
+C + + + +IS GSCA+ G + + + +
Sbjct: 88 NQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGG 147
Query: 78 -----IYVPGCPPTAEALMYGILQL 97
I VPGCPP AE + I +
Sbjct: 148 YDKPIIKVPGCPPIAEVMTGVITYM 172
>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_S* 3use_S*
Length = 335
Score = 42.7 bits (100), Expect = 4e-06
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 43 EPRWVISMGSCANGGG--YYHYSYSVVRGCDRIIP--VDIYVPGCPPTAEALMYGILQL 97
+I+ G+CA+ G + + D++I I VPGCPP + + I +
Sbjct: 105 GASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYM 163
>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 = 42.7 bits (100), Expect = 5e-06
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 22 RIEPGSTTCKASAVTTTSWMLE----PRWVISMGSCANGGG--YYHYSYSVVRGCDRIIP 75
G + + + +I +G+C+ GG + S +G +
Sbjct: 79 PTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALG 138
Query: 76 VDIY-VPGCPPTAEALMYGILQL 97
V +PGCPP + ++ +
Sbjct: 139 VKTINIPGCPPNPINFVGAVVHV 161
>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE]
hydrogenase, high-resolution knallgasbacteria,
proteobacteria; 1.50A {Ralstonia eutropha}
Length = 339
Score = 42.0 bits (98), Expect = 8e-06
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 43 EPRWVISMGSCANGGGYY--HYSYSVVRGCDRIIPVD--IYVPGCPPTAEALMYGILQL 97
+ + +IS GSCA+ G + + ++I I VPGCPP AE + I +
Sbjct: 105 DAKAIISWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYM 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 = 40.4 bits (94), Expect = 3e-05
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 8/85 (9%)
Query: 21 PRIEPGSTTCKASAVTTTSWMLE----PRWVISMGSCANGGGYY--HYSYSVVRGCDRII 74
P + + + S ++E VI++G+CA GG + + ++
Sbjct: 77 PGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLV 136
Query: 75 PVD--IYVPGCPPTAEALMYGILQL 97
I VPGCPP + I
Sbjct: 137 RDKPVINVPGCPPIPMVITGVIAHY 161
>3rst_A Signal peptide peptidase SPPA; alpha/beta protein fold, signal
peptide digestion, bacterial membrane, hydrolase; 2.37A
{Bacillus subtilis}
Length = 240
Score = 28.4 bits (64), Expect = 0.39
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 47 VISMGSCANGGGYYHYSYSVVRGCDRII 74
+SMGS A GGYY + D+I
Sbjct: 83 YVSMGSMAASGGYY-----ISTAADKIF 105
>2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2;
phosphorylation, nucleotide biosynthesis, transferase;
2.55A {Homo sapiens} PDB: 2c4k_A*
Length = 379
Score = 27.7 bits (62), Expect = 0.87
Identities = 5/27 (18%), Positives = 9/27 (33%), Gaps = 8/27 (29%)
Query: 67 VRGCDRIIPVDIYV--PGCPPTAEALM 91
VRG D +++ +M
Sbjct: 77 VRGKD------VFIIQTVSKDVNTTIM 97
>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 = 27.1 bits (61), Expect = 1.2
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 8/27 (29%)
Query: 67 VRGCDRIIPVDIYV--PGCPPTAEALM 91
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 = 27.1 bits (61), Expect = 1.3
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 8/27 (29%)
Query: 67 VRGCDRIIPVDIYV--PGCPPTAEALM 91
VRG D ++V C PT + LM
Sbjct: 52 VRGKD------VFVLQSTCAPTNDNLM 72
>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 = 26.7 bits (60), Expect = 1.9
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 85 PTAEALMYGILQLQKKVKRMKIL 107
PTA A+ YG L K K +I+
Sbjct: 190 PTAAAIAYG---LDKSDKEHQII 209
>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 = 26.4 bits (59), Expect = 2.0
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 85 PTAEALMYGILQLQKKVKRMKIL 107
PTA AL YG L K I
Sbjct: 172 PTAAALAYG---LDKGTGNRTIA 191
>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 = 26.4 bits (59), Expect = 2.0
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 85 PTAEALMYGILQLQKKVKRMKIL 107
PTA AL YG L K I
Sbjct: 172 PTAAALAYG---LDKGTGNRTIA 191
>3bf0_A Protease 4; bacterial, hydrolase, inner membrane, membrane,
transmembrane; 2.55A {Escherichia coli} PDB: 3bez_A
Length = 593
Score = 26.1 bits (57), Expect = 2.8
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 45 RWVISMGSCANGGGYYHYSYSVVRGCDRII 74
+ V ++G + G YY S+ ++I
Sbjct: 121 KPVYAVGENYSQGQYYLASF-----ANKIW 145
Score = 25.7 bits (56), Expect = 3.8
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 47 VISMGSCANGGGYYHYSYSVVRGCDRII 74
V+SMG A GGY+ + + I+
Sbjct: 375 VVSMGGMAASGGYW-----ISTPANYIV 397
>3bjr_A Putative carboxylesterase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; 2.09A {Lactobacillus plantarum WCFS1}
Length = 283
Score = 26.0 bits (57), Expect = 3.3
Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 2/56 (3%)
Query: 40 WMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGIL 95
W ++P+ + G GG+ Y+ +++ P L Y ++
Sbjct: 119 WHIDPQQITPAGFSV--GGHIVALYNDYWATRVATELNVTPAMLKPNNVVLGYPVI 172
>3h04_A Uncharacterized protein; protein with unknown function,
structural genomics, MCSG, PS protein structure
initiative; 1.90A {Staphylococcus aureus subsp}
Length = 275
Score = 26.0 bits (57), Expect = 3.4
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 64 YSVVRGCDRIIPVDIYVPGCPPTAEALMY 92
Y V+ +P I PT ++Y
Sbjct: 6 YKVITKDAFALPYTIIKAKNQPTKGVIVY 34
>1pix_A Glutaconyl-COA decarboxylase A subunit; biotin-dependent ION pump,
carboxyltransferase, lyase; 2.20A {Acidaminococcus
fermentans} SCOP: c.14.1.4 c.14.1.4
Length = 587
Score = 25.0 bits (55), Expect = 7.1
Identities = 5/10 (50%), Positives = 6/10 (60%)
Query: 50 MGSCANGGGY 59
G+ GGGY
Sbjct: 189 YGTNPAGGGY 198
>3gf3_A Glutaconyl-COA decarboxylase subunit A; sodium ION transport,
biotin, glutamate fermentation, lyase; HET: COO; 1.75A
{Clostridium symbiosum} PDB: 3gf7_A 3glm_A* 3gma_A*
Length = 588
Score = 25.0 bits (55), Expect = 7.5
Identities = 5/10 (50%), Positives = 6/10 (60%)
Query: 50 MGSCANGGGY 59
G+ GGGY
Sbjct: 190 YGTNPAGGGY 199
>3e7j_A Heparinase II protein; alpha and beta lyase, alpha6/alpha6
incomplete toroid, sugar protein, lyase; HET: NAG GCU
GCD; 2.10A {Pedobacter heparinus} PDB: 3e80_A* 2fut_A*
2fuq_A*
Length = 749
Score = 24.7 bits (52), Expect = 10.0
Identities = 2/24 (8%), Positives = 6/24 (25%)
Query: 39 SWMLEPRWVISMGSCANGGGYYHY 62
++ W + G +
Sbjct: 214 EHLVARNWFYPSHNYHQGMSALNV 237
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 0.452
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,844,943
Number of extensions: 96422
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 33
Length of query: 113
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 36
Effective length of database: 4,551,876
Effective search space: 163867536
Effective search space used: 163867536
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: 51 (23.4 bits)