RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 025280
(255 letters)
>2f1d_A IGPD 1, imidazoleglycerol-phosphate dehydratase 1; herbicide,
manganese, histidine biosynthesis, lyase; 3.00A
{Arabidopsis thaliana} SCOP: d.14.1.9 d.14.1.9
Length = 207
Score = 266 bits (682), Expect = 7e-91
Identities = 145/164 (88%), Positives = 158/164 (96%)
Query: 71 ASTSSAVDSGRIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDV 130
AS+SS++ GRIGEVKRVTKETNVSVKIN+DG+GVADSS+ IPFLDHMLDQLASHGLFDV
Sbjct: 1 ASSSSSMALGRIGEVKRVTKETNVSVKINLDGTGVADSSSGIPFLDHMLDQLASHGLFDV 60
Query: 131 HVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSLDLSG 190
HVRATGD+HIDDHHTNED+ LAIGTALL+ALG+RKGINRFGDFTAPLDEALIHVSLDLSG
Sbjct: 61 HVRATGDVHIDDHHTNEDIALAIGTALLKALGERKGINRFGDFTAPLDEALIHVSLDLSG 120
Query: 191 RPHLNYDLQIPTQRVGTYDTQLVEHFFQSLVNTSGMTLHIRQLK 234
RP+L Y+L+IPTQRVGTYDTQLVEHFFQSLVNTSGMTLHIRQL
Sbjct: 121 RPYLGYNLEIPTQRVGTYDTQLVEHFFQSLVNTSGMTLHIRQLA 164
>2ae8_A IGPD, imidazoleglycerol-phosphate dehydratase; beta-alpha-beta
sandwich, duplication of A half-domain; 2.01A
{Staphylococcus aureus subsp} SCOP: d.14.1.9 d.14.1.9
Length = 221
Score = 256 bits (655), Expect = 1e-86
Identities = 59/163 (36%), Positives = 100/163 (61%), Gaps = 1/163 (0%)
Query: 72 STSSAVDSGRIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVH 131
S + + I + +R T ET +++ I+ D + +T + FL+HML H ++
Sbjct: 21 SNIGSGSNAMIYQKQRNTAETQLNISIS-DDQSPSHINTGVGFLNHMLTLFTFHSGLSLN 79
Query: 132 VRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSLDLSGR 191
+ A GDI +DDHH ED+G+ IG LL+ + D+K R+G P+DE L V +D+SGR
Sbjct: 80 IEAQGDIDVDDHHVTEDIGIVIGQLLLEMIKDKKHFVRYGTMYIPMDETLARVVVDISGR 139
Query: 192 PHLNYDLQIPTQRVGTYDTQLVEHFFQSLVNTSGMTLHIRQLK 234
P+L+++ + ++VGT+DT+LVE FF+++V + +T HI ++
Sbjct: 140 PYLSFNASLSKEKVGTFDTELVEEFFRAVVINARLTTHIDLIR 182
>1rhy_A IGPD, imidazole glycerol phosphate dehydratase; dehydratases,
histidine biosynthesis, LEFT-handed B-A-B CROS motif,
gene duplication; 2.30A {Filobasidiella neoformans}
SCOP: d.14.1.9 d.14.1.9
Length = 202
Score = 252 bits (645), Expect = 2e-85
Identities = 69/159 (43%), Positives = 95/159 (59%), Gaps = 5/159 (3%)
Query: 81 RIGEVKRVTKETNVSVKINVD-----GSGVADSSTCIPFLDHMLDQLASHGLFDVHVRAT 135
RI V+R T ET++S I++D + ST I FLDHM LA HG + ++
Sbjct: 4 RIASVERTTSETHISCTIDLDHIPGVTEQKINVSTGIGFLDHMFTALAKHGGMSLQLQCK 63
Query: 136 GDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSLDLSGRPHLN 195
GD+HIDDHHT ED LA+G A +ALG+RKGI R+G APLDE+L +D+S RP+
Sbjct: 64 GDLHIDDHHTAEDCALALGEAFKKALGERKGIKRYGYAYAPLDESLSRAVIDISSRPYFM 123
Query: 196 YDLQIPTQRVGTYDTQLVEHFFQSLVNTSGMTLHIRQLK 234
L ++VG T++V H QS +G+TLHI ++
Sbjct: 124 CHLPFTREKVGDLSTEMVSHLLQSFAFAAGVTLHIDSIR 162
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 62.8 bits (152), Expect = 2e-11
Identities = 65/357 (18%), Positives = 108/357 (30%), Gaps = 134/357 (37%)
Query: 7 ARLVHLSISSTSSRRL----------LVKPKTNLSRKLL---PIS------TQ---YCSS 44
L L ++ + ++ L P + L PIS Q Y +
Sbjct: 193 ETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT 252
Query: 45 TRRMNSLTTP---RASLNPDGDSKHNNG--SASTSSAVDSGR---------------IG- 83
+ + TP R+ L G + H+ G +A + DS IG
Sbjct: 253 AKLLG--FTPGELRSYLK--GATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
Query: 84 EVKRVTKETNVSVKINVD----GSGVADSSTCIPFLDHML-------DQLASH-GLFDVH 131
T++ I D GV ML +Q+ + + H
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPS---------PMLSISNLTQEQVQDYVNKTNSH 359
Query: 132 VRATGDIHI-----DDHHTNEDV---------GLAI-------GTALLQA---LGDRK-- 165
+ A + I + V GL + + L Q+ +RK
Sbjct: 360 LPAGKQVEISLVNGAKNL----VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLK 415
Query: 166 GINRFGDFTAP-----LDEALIHVSLDLSGRPHLNY---DLQIPTQRVGTYDT------- 210
NRF +P L A ++ DL + ++++ D+QIP V YDT
Sbjct: 416 FSNRFLPVASPFHSHLLVPASDLINKDLV-KNNVSFNAKDIQIP---V--YDTFDGSDLR 469
Query: 211 --------QLVEHFFQSLVN----TSGMTLHIRQLKRGSTT---ILILHGIHGLGMG 252
++V+ + V T HI G + +L G G+
Sbjct: 470 VLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVR 526
Score = 33.9 bits (77), Expect = 0.054
Identities = 26/151 (17%), Positives = 45/151 (29%), Gaps = 59/151 (39%)
Query: 6 PARLVHLSISSTSSRRLLVKPKTNLS------RKL------LPIS----TQYCSSTRRM- 48
P L L+ + R+ + S RKL LP++ + +
Sbjct: 383 PQSLYGLN---LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 49 ------NSLTTPRASLN-P-----DG-DSKHNNGS---------------------ASTS 74
N+++ + P DG D + +GS +
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499
Query: 75 SAVDSGRIGEVKRVTKETNVSVKINVDGSGV 105
+D G G + T+ N DG+GV
Sbjct: 500 HILDFGP-GGASGLGVLTHR----NKDGTGV 525
Score = 31.9 bits (72), Expect = 0.23
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 7/39 (17%)
Query: 188 LSGRP----H--LNYDLQIPTQRVGTYDTQLVEHFFQSL 220
S RP H L + L +PT +QL E F + L
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFFIA-SQLQEQFNKIL 41
>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 = 51.0 bits (121), Expect = 1e-07
Identities = 46/275 (16%), Positives = 83/275 (30%), Gaps = 63/275 (22%)
Query: 10 VH-LSISSTSSRRLLVKPKTNLSRKLLPISTQYCSST----RRMNSLTTPRASLNPDGDS 64
+ L++ + +S +++ L ++ P T + R++S+ L
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK--SK 241
Query: 65 KHNNGSASTSSAV-DSGRIGEV--KRVTKETNVSVKINV---DGSGVADS----STCIPF 114
+ N V V + N+S KI + V D +T
Sbjct: 242 PYEN-----CLLVLL-----NVQNAKAWNAFNLSCKILLTTRF-KQVTDFLSAATTTHIS 290
Query: 115 LDHMLDQLA---SHGLFD--VHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINR 169
LDH L L + R D+ + TN + +++ R G+
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRP-QDLPREVLTTNP---RRL--SIIAES-IRDGLAT 343
Query: 170 FGDFTAPLDEAL---IHVSLD-LSG---RPH------LNYDLQIPTQRVGTY----DTQL 212
+ ++ + L I SL+ L R IPT +
Sbjct: 344 WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 213 VEHFFQSLVNTSGMTLHIRQLKRGSTTILILHGIH 247
V L S L +Q K + +I I+
Sbjct: 404 VMVVVNKLHKYS---LVEKQPKESTISI---PSIY 432
Score = 28.7 bits (63), Expect = 2.3
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 11/64 (17%)
Query: 192 PHLNYDLQIPTQRVGTY-DTQLVEHFFQSLVNTSGMTLHIR----QLKRGSTTILILHGI 246
P + + I QR Y D Q+ + V+ L +R +L+ +++ G+
Sbjct: 105 PSMMTRMYI-EQRDRLYNDNQVFAKYN---VSRLQPYLKLRQALLELRPAK--NVLIDGV 158
Query: 247 HGLG 250
G G
Sbjct: 159 LGSG 162
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 30.1 bits (68), Expect = 0.83
Identities = 7/44 (15%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 149 VGLAIGTALLQALGDRKGINRFGDFTAPLDEAL-IHVSLDLSGR 191
+ ++ A++Q + G++ + +++ + VS ++ GR
Sbjct: 48 IEVSEEYAVIQVFEETTGLDLATTSVSLVEDVARLGVSKEMLGR 91
>1a6m_A Myoglobin; heme protein, model compounds, oxygen storage, ligand
binding geometry, conformational substates, oxygen
transpor; HET: HEM; 1.00A {Physeter catodon} SCOP:
a.1.1.2 PDB: 1a6k_A* 1a6n_A* 2jho_A* 1ufp_A* 2eb9_A*
2eb8_A* 2w6w_A* 2ekt_A* 105m_A* 104m_A* 1ajh_A* 1ajg_A*
1bvc_A* 1bvd_A* 1bz6_A* 1bzr_A* 1cq2_A* 1duk_A* 1ebc_A*
1hjt_A* ...
Length = 151
Score = 29.0 bits (64), Expect = 0.91
Identities = 15/71 (21%), Positives = 23/71 (32%), Gaps = 7/71 (9%)
Query: 110 TCIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINR 169
T + L +L + H + ++ H H I A++ L R
Sbjct: 67 TVLTALGAILKKKGHH---EAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP--- 120
Query: 170 FGDFTAPLDEA 180
GDF A A
Sbjct: 121 -GDFGADAQGA 130
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 28.9 bits (65), Expect = 2.0
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 149 VGLAIGTALLQALGDRKGINRFGDFTAPLDEAL-IHVSLDLSGR 191
+ + ++Q G+++ E L + S+DL GR
Sbjct: 54 LDSSADIVVVQVFEGTGGLDK-DCGVIFTGETLKLPASVDLLGR 96
>3ovx_A Cathepsin S; hydrolase, covalent inhibitor, aldehyde warhead is
covalently bound to Cys25, lysosomeal protein; HET: O64;
1.49A {Homo sapiens} PDB: 2h7j_A* 2f1g_A* 2hh5_B*
2hhn_A* 2hxz_A* 2op3_A* 2frq_A* 2fra_A* 2fq9_A* 2ft2_A*
2fud_A* 2g7y_A* 1ms6_A* 2r9m_A* 2r9n_A* 2r9o_A* 3n3g_A*
3n4c_A* 3mpe_A* 1nqc_A* ...
Length = 218
Score = 27.1 bits (61), Expect = 4.5
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 7/31 (22%)
Query: 94 VSVKINVDG-------SGVADSSTCIPFLDH 117
VSV ++ SGV +C ++H
Sbjct: 135 VSVGVDARHPSFFLYRSGVYYEPSCTQNVNH 165
>1o97_C Electron transferring flavoprotein beta-subunit; FAD binding; HET:
AMP FAD; 1.6A {Methylophilus methylotrophus} SCOP:
c.26.2.3 PDB: 1o95_C* 1o96_A* 1o94_C* 3clr_C* 3cls_C*
3clt_C* 3clu_C*
Length = 264
Score = 27.2 bits (61), Expect = 4.8
Identities = 6/21 (28%), Positives = 8/21 (38%), Gaps = 1/21 (4%)
Query: 85 VKRVTKETNVSVKINVDGSGV 105
VK+ +I DG V
Sbjct: 7 VKQTA-ALEEDFEIREDGMDV 26
>1c7c_A Protein (deoxyhemoglobin (alpha chain)); heme, oxygen delivery
vehicle, blood substitute, oxygen storage/transport
complex; HET: HEM; 1.80A {Homo sapiens} SCOP: a.1.1.2
a.1.1.2 PDB: 1aby_A* 1abw_A* 1o1p_A* 1c7d_A* 1o1j_A*
1o1l_A* 1o1n_A* 1o1m_A*
Length = 283
Score = 26.8 bits (58), Expect = 6.7
Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 4/67 (5%)
Query: 114 FLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDF 173
D + + +A + A D+H + + LL L +F
Sbjct: 204 VADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLP----AEF 259
Query: 174 TAPLDEA 180
T + +
Sbjct: 260 TPAVHAS 266
>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent
O-methyltransferase; HET: SAH; 1.80A {Lolium perenne}
PDB: 3p9i_A* 3p9k_A*
Length = 364
Score = 26.7 bits (59), Expect = 7.5
Identities = 9/47 (19%), Positives = 16/47 (34%)
Query: 104 GVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVG 150
A + +D +L LAS+ + V D + + V
Sbjct: 67 PSAANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVC 113
>2dc3_A Cytoglobin; myoglobin, heme, oxygen transport, oxygen storage,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; HET: HEM; 1.68A {Homo sapiens} PDB:
1v5h_A* 3ag0_A* 1urv_A* 1umo_A* 1ury_A* 1ut0_A* 1ux9_A*
Length = 193
Score = 26.6 bits (58), Expect = 7.6
Identities = 9/73 (12%), Positives = 21/73 (28%), Gaps = 4/73 (5%)
Query: 108 SSTCIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGI 167
+ + L+ +++ L + G H H + +L+ + +
Sbjct: 85 ACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFA- 143
Query: 168 NRFGDFTAPLDEA 180
DF A
Sbjct: 144 ---SDFPPETQRA 153
>1it2_A Hemoglobin; hagfish, deoxy form, oxygen storage/transport complex;
HET: HEM; 1.60A {Eptatretus burgeri} SCOP: a.1.1.2 PDB:
1it3_A*
Length = 146
Score = 26.2 bits (57), Expect = 8.3
Identities = 3/85 (3%), Positives = 21/85 (24%)
Query: 86 KRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHHT 145
K + + D + ++ +++ + + ++ H
Sbjct: 50 ASFPKFSTKKSNLEQDPEVKHQAVVIFNKVNEIINSMDNQEEIIKSLKDLSQKHKTVFKV 109
Query: 146 NEDVGLAIGTALLQALGDRKGINRF 170
+ + + + + +
Sbjct: 110 DSIWFKELSSIFVSTIDGGAEFEKL 134
>3ip3_A Oxidoreductase, putative; structural genomics, PSI-2, protein
structure initiative, NEW YORK SGX research center for
structural genomics; 2.14A {Thermotoga maritima}
Length = 337
Score = 26.5 bits (59), Expect = 8.8
Identities = 17/88 (19%), Positives = 26/88 (29%), Gaps = 16/88 (18%)
Query: 76 AVDSGRIGEVKRVTKETNVSVKINVDGSGVADSSTCI-PFLD---HMLDQLASHGLF--- 128
V G +GE++ V T S K+ T H +D + +
Sbjct: 141 LVSEGAVGEIRLVN--TQKSYKLGQRPDFYKKRETYGGTIPWVGIHAIDWI----HWITG 194
Query: 129 --DVHVRATGDIHIDDHHTN-EDVGLAI 153
+ V AT + H E L
Sbjct: 195 KKFLSVYATHSRLHNSGHGELETTALCH 222
>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 = 26.4 bits (59), Expect = 9.4
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 85 VKRVTKETNVSVKINVDGSGV 105
VKR+ + NV ++ DGSGV
Sbjct: 7 VKRLI-DYNVKARVKSDGSGV 26
>2c0y_A Procathepsin S; proenzyme, proteinase, hydrolase, thiol protease,
prosegment binding loop, glycoprotein, lysosome,
protease, zymogen; 2.1A {Homo sapiens}
Length = 315
Score = 26.4 bits (59), Expect = 9.7
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 7/31 (22%)
Query: 94 VSVKINVDG-------SGVADSSTCIPFLDH 117
VSV ++ SGV +C ++H
Sbjct: 232 VSVGVDARHPSFFLYRSGVYYEPSCTQNVNH 262
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
0.318 0.134 0.383
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,762,754
Number of extensions: 218176
Number of successful extensions: 556
Number of sequences better than 10.0: 1
Number of HSP's gapped: 554
Number of HSP's successfully gapped: 28
Length of query: 255
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 164
Effective length of database: 4,160,982
Effective search space: 682401048
Effective search space used: 682401048
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.5 bits)