RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11676
(131 letters)
>2j5v_A Glutamate 5-kinase; proline biosynthesis, gamma glutamyl kinase,
amino-acid biosynthesis, transferase, feedback
regulation, PUA domain; HET: RGP; 2.5A {Escherichia
coli} PDB: 2j5t_A* 2w21_A
Length = 367
Score = 75.6 bits (187), Expect = 2e-17
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 25 LKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQK 84
+ ++ LVVKLG++V+T L + +V Q A+ H G ++VTSGA+A G++
Sbjct: 1 MSDSQTLVVKLGTSVLTGGS-RRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREH 59
Query: 85 L 85
L
Sbjct: 60 L 60
>2ako_A Glutamate 5-kinase; structural genomics, PSI, protein structure
initiative, NEW YORK SGX research center for structural
genomics, nysgxrc; HET: ADP; 2.20A {Campylobacter
jejuni} SCOP: c.73.1.3
Length = 251
Score = 68.7 bits (169), Expect = 3e-15
Identities = 24/57 (42%), Positives = 38/57 (66%), Gaps = 3/57 (5%)
Query: 29 RRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQKL 85
+R+VVK+GS VI+ +E+ L+ RL ++V +A+ E E I+VTS A++ G KL
Sbjct: 2 KRIVVKVGSHVIS--EENTLSFERLKNLVAFLAKLM-EKYEVILVTSAAISAGHTKL 55
>3ll9_A Isopentenyl phosphate kinase; mevalonate biosynthesis isoprenoid,
transferase; HET: ADP; 2.15A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 269
Score = 66.5 bits (163), Expect = 2e-14
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 28 ARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQKLAQ 87
+ +++KLG +VITR+D ++ +E +M+ GA +FG +
Sbjct: 2 SHMIILKLGGSVITRKDS-EEPAIDRDNLERIASEIGNASPSSLMIVHGAGSFGHPFAGE 60
Query: 88 ELLMSLSMRET 98
+ S E
Sbjct: 61 YRIGSEIENEE 71
>3d40_A FOMA protein; fosfomycin, antibiotic resistance, kinase,
phosphoryl transfer, transferase; 1.53A {Streptomyces
wedmorensis} PDB: 3d41_A* 3qun_A* 3quo_A* 3qur_A*
3qvf_A* 3qvh_A*
Length = 286
Score = 61.5 bits (149), Expect = 2e-12
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 1/79 (1%)
Query: 13 RRRVTSFSDRGQLKYARRLVVKLGSAVITREDEHG-LALGRLASIVEQVAECHLEGRECI 71
+ RG L +K+G ++ +R+DE G L + A R +
Sbjct: 8 HHHSSGLVPRGSHMTPDFLAIKVGGSLFSRKDEPGSLDDDAVTRFARNFARLAETYRGRM 67
Query: 72 MVTSGAVAFGKQKLAQELL 90
++ SG AFG +
Sbjct: 68 VLISGGGAFGHGAIRDHDS 86
>3ll5_A Gamma-glutamyl kinase related protein; alternate mevalonate
pathway, isopentenyl phsophate kinase, beta-alpha
sandwich fold; HET: MSE ADP IPE ATP IP8; 1.99A
{Thermoplasma acidophilum} PDB: 3lkk_A*
Length = 249
Score = 51.9 bits (125), Expect = 3e-09
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 28 ARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQKL 85
+++K+G +VIT + + + + + + + V G +FG K
Sbjct: 3 FTMMILKIGGSVITDKSAY---RTARTYAIRSIVKVLSGIEDLVCVVHGGGSFGHIKA 57
>2brx_A Uridylate kinase; UMP kinase, amino acid kinase, phosphoryl group
transfer, pyrimidine biosynthesis, transferase; 2.40A
{Pyrococcus furiosus} SCOP: c.73.1.3 PDB: 2ji5_A*
2bmu_A* 2bri_A*
Length = 244
Score = 47.7 bits (114), Expect = 1e-07
Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQ 83
+ + R+V +G +V+ E + + I Q+ + + ++V G +A
Sbjct: 16 RGSH-MRIVFDIGGSVLVPE---NPDIDFIKEIAYQLTKVSEDHEVAVVVGGGKLARKYI 71
Query: 84 KLAQELLMS 92
++A++ S
Sbjct: 72 EVAEKFNSS 80
>2va1_A Uridylate kinase; UMPK, transferase, pyrimidine biosynthesis,
amino acid kinase family; 2.50A {Ureaplasma parvum}
Length = 256
Score = 38.8 bits (90), Expect = 2e-04
Identities = 10/64 (15%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 20 SDRGQLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVA 79
++ +R+V+K+ A + + D + ++ + EQ+ + + I++ G +
Sbjct: 17 RGSHMMRK-QRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIW 75
Query: 80 FGKQ 83
G
Sbjct: 76 RGSI 79
>3k4o_A Isopentenyl phosphate kinase; small molecule kinase, ATP-binding,
transferase, methanocald jannaschii, isopentenyl
monophosphate; 2.05A {Methanocaldococcus jannaschii}
PDB: 3k4y_A* 3k52_A* 3k56_A*
Length = 266
Score = 38.7 bits (90), Expect = 2e-04
Identities = 10/70 (14%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 29 RRLVVKLGSAVITRED-EHGLALGRLASIVEQVAECHLEGREC-----IMVTSGAVAFGK 82
++KLG ++++ ++ + + L I ++ + +++ G AFG
Sbjct: 7 MLTILKLGGSILSDKNVPYSIKWDNLERIAMEIKNALDYYKNQNKEIKLILVHGGGAFGH 66
Query: 83 QKLAQELLMS 92
+ L +
Sbjct: 67 PVAKKYLKIE 76
>1z9d_A Uridylate kinase, UK, UMP kinase; structural genomics, protein
structure initiative, NYSGXRC, PYRH, putative uridylate
kinase, PSI; 2.80A {Streptococcus pyogenes} SCOP:
c.73.1.3
Length = 252
Score = 34.5 bits (79), Expect = 0.005
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSG 76
+ KY +R+++KL + E G+ + + +I +++AE H+ G + +V G
Sbjct: 4 EPKY-QRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGG 55
>2jjx_A Uridylate kinase, UMP kinase; structural genomics, pyrimidine
biosynthesis, ATP-binding, nucleotide-binding, OPPF,
PYRH, cytoplasm; HET: ATP; 2.82A {Bacillus anthracis}
Length = 255
Score = 34.1 bits (78), Expect = 0.006
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 1/60 (1%)
Query: 17 TSFSDRGQLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSG 76
Y +R+++KL + + + RL I ++ G E +V G
Sbjct: 2 AHHHHHHMRPY-KRVLIKLSGGALADQTGNSFNSKRLEHIANEILSIVDLGIEVSIVIGG 60
>4a7w_A Uridylate kinase; transferase; HET: GTP; 1.80A {Helicobacter
pylori} PDB: 4a7x_A*
Length = 240
Score = 34.1 bits (78), Expect = 0.006
Identities = 10/57 (17%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSGAVAF 80
++K +R++VK + +++ G+ + L I +++ E +V G
Sbjct: 4 KIKN-KRVLVKFSGEALAGDNQFGIDIHVLDHIAKEIKSLVENDIEVGIVIGGGNII 59
>1ybd_A Uridylate kinase; alpha/beta/alpha fold, hexamer, structural
genomics, structure initiative, PSI; 2.60A {Neisseria
meningitidis} SCOP: c.73.1.3
Length = 239
Score = 33.7 bits (77), Expect = 0.008
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSG 76
Q+KY +R+++KL + D G+ + V ++AE G + +V G
Sbjct: 4 QIKY-KRVLLKLSGESLMGSDPFGINHDTIVQTVGEIAEVVKMGVQVGIVVGG 55
>3ek6_A Uridylate kinase; UMPK unique GTP B site, allosteric regulation,
ATP-binding, nucleotid binding, pyrimidine
biosynthesis, transferase; 2.34A {Xanthomonas
campestris PV} PDB: 3ek5_A
Length = 243
Score = 33.3 bits (76), Expect = 0.012
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSG 76
+L Y RR+++KL + + ++G+ + + +V E G + +V G
Sbjct: 6 ELSY-RRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGG 57
>2a1f_A Uridylate kinase; PYRH, structural genomics, PSI, protein ST
initiative, NEW YORK SGX research center for structural
GEN nysgxrc; 2.10A {Haemophilus influenzae} SCOP:
c.73.1.3 PDB: 2bne_A* 2bnf_A* 2v4y_A* 2bnd_A*
Length = 247
Score = 33.4 bits (76), Expect = 0.012
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 24 QLKYARRLVVKLGSAVITREDEHGLALGRLASIVEQVAECHLEGRECIMVTSG 76
Q Y +R+++KL + ED G+ L + ++ E G E +V G
Sbjct: 5 QPIY-KRILLKLSGEALQGEDGLGIDPAILDRMAVEIKELVEMGVEVSVVLGG 56
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 31.4 bits (72), Expect = 0.047
Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 15/87 (17%)
Query: 10 TAERRRVTSFSDRGQLKYAR---RLVVKLGSAVITREDEHGLALG-RLASIVEQVAECHL 65
T +R + SFS Y +VV A T D G +G + ++ +
Sbjct: 76 TPKREQQVSFSQ----PYYEGLSAVVVTRKGAYHTFADLKGKKVGLENGTTHQRYLQDKQ 131
Query: 66 EGRECIMVTSGAVAFGKQKLAQELLMS 92
+ VA+ A L +
Sbjct: 132 QAIT-------PVAYDSYLNAFTDLKN 151
>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 = 31.1 bits (69), Expect = 0.053
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 30/57 (52%)
Query: 3 QAIRSLQTAERRRVTSFSDRGQLK-YARRLVVKLGSAVITREDEHGLALGRLASIVE 58
QA++ LQ + LK YA SA LA+ A++ E
Sbjct: 20 QALKKLQAS-------------LKLYAD------DSA-------PALAIK--ATM-E 47
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 29.1 bits (66), Expect = 0.37
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 10 TAERRRVTSFSDRGQLKYAR---RLVVKLGSAVI-TREDEHGLALG-RLASIVEQVAECH 64
T +R++ +FSD K RL+ GS + T E G +G S E A +
Sbjct: 74 TDKRQQEIAFSD----KLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDN 129
Query: 65 LE 66
Sbjct: 130 WR 131
>1efp_B ETF, protein (electron transfer flavoprotein); electron transport,
glutaric acidemia type II; HET: FAD AMP; 2.60A
{Paracoccus denitrificans} SCOP: c.26.2.3
Length = 252
Score = 29.1 bits (66), Expect = 0.37
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 1 GNQAI--RSLQTAERRRVTSFSDRGQLKYARRLVVKLGSAVITREDEHGL 48
G QAI T + + + Q +A ++ ++ A +TRE + GL
Sbjct: 120 GKQAIDNDMNATGQM--LAAILGWAQATFASKVEIEGAKAKVTREVDGGL 167
>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 = 29.4 bits (65), Expect = 0.38
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 39/95 (41%)
Query: 62 ECHLEGRECIM--------VTSGAVAFGKQKLAQELLMS-------------LSMRETLS 100
+ +L+ R+ ++ + G + GK +A ++ +S L+++ S
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 101 PKD----------------HSRSNHFDSENPKTNI 119
P+ SRS+H S N K I
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDH--SSNIKLRI 227
>1vd6_A Glycerophosphoryl diester phosphodiesterase; glycerophosphod
phosphodiesterase, HB8; 1.30A {Thermus thermophilus}
SCOP: c.1.18.3 PDB: 1v8e_A
Length = 224
Score = 28.3 bits (64), Expect = 0.56
Identities = 16/74 (21%), Positives = 20/74 (27%), Gaps = 10/74 (13%)
Query: 5 IRSLQTAERRRVTSFSDRGQLKYARRLVVKLGSAVITREDEHGLALGRLASIV------- 57
L+ E V+SF L R+ L + ED L V
Sbjct: 116 AALLRGREGVWVSSFDPL-ALLALRKAAPGLPLGFLMAEDHSALLPCLGVEAVHPHHALV 174
Query: 58 --EQVAECHLEGRE 69
E VA G
Sbjct: 175 TEEAVAGWRKRGLF 188
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 27.6 bits (62), Expect = 1.2
Identities = 7/58 (12%), Positives = 21/58 (36%), Gaps = 9/58 (15%)
Query: 10 TAERRRVTSFSDRGQLKYAR---RLVVKLGSAVI-TREDEHGLALG-RLASIVEQVAE 62
T R++ F+D Y + + + +++ G +G + + + +
Sbjct: 72 TTARQKEVDFTD----PYYTNSVSFIADKNTPLTLSKQGLKGKIIGVQGGTTFDSYLQ 125
>1zcc_A Glycerophosphodiester phosphodiesterase; NYSGXRC, agrobacterium
tumefaciens STR. C58, structural genomics; 2.50A
{Agrobacterium tumefaciens str} SCOP: c.1.18.3
Length = 248
Score = 26.8 bits (60), Expect = 2.2
Identities = 10/79 (12%), Positives = 21/79 (26%), Gaps = 13/79 (16%)
Query: 3 QAIRSLQTAERRRVTSFSDRGQLKYARRLV--VKLGSAVITREDEHGLALGRLASIV--- 57
+R L SFS+ + + + + + + + ASI+
Sbjct: 119 ALVRHLGMVRDTFYFSFSEE-MRQGLQSIAPEFRRMMTLDIAKSPSLVGAVHHASIIEIT 177
Query: 58 -------EQVAECHLEGRE 69
+ G E
Sbjct: 178 PAQMRRPGIIEASRKAGLE 196
>1mio_A Nitrogenase molybdenum iron protein (alpha chain); HET: HCA CFM
CLP; 3.00A {Clostridium pasteurianum} SCOP: c.92.2.3
Length = 533
Score = 25.7 bits (56), Expect = 5.8
Identities = 8/65 (12%), Positives = 24/65 (36%), Gaps = 3/65 (4%)
Query: 29 RRLVVKLGSAVITREDEHGLA--LGRLASIVEQVAECHLEGRECIMVTSGAVAFGKQKLA 86
R + +T+ E +A + + ++ E L+G+ + G+ + +
Sbjct: 296 RDMAKCFDDPELTKRTEEVIAEEIAAIQDDLDYFKE-KLQGKTACLYVGGSRSHTYMNML 354
Query: 87 QELLM 91
+ +
Sbjct: 355 KSFGV 359
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 24.9 bits (55), Expect = 6.4
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 44 DEHGLALGRLASIV 57
+ GL LGRLAS V
Sbjct: 5 NADGLILGRLASRV 18
>1vq8_J 50S ribosomal protein L13P; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: c.21.1.1 PDB:
1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K*
1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K*
1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Length = 145
Score = 24.9 bits (55), Expect = 6.9
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 44 DEHGLALGRLASIV 57
D +GR+AS V
Sbjct: 13 DARDCIMGRVASQV 26
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 25.0 bits (54), Expect = 9.4
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 44 DEHGLALGRLASIV 57
D G LGRLA+IV
Sbjct: 10 DGRGHLLGRLAAIV 23
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_K
Length = 206
Score = 24.9 bits (54), Expect = 9.5
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 44 DEHGLALGRLASIV 57
D LGRLASIV
Sbjct: 15 DARHHMLGRLASIV 28
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
0.319 0.131 0.359
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,856,457
Number of extensions: 100473
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 207
Number of HSP's successfully gapped: 36
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: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.1 bits)