RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 018338
(357 letters)
>3hy3_A 5-formyltetrahydrofolate cyclo-ligase; antifolate, cancer,
ATP-binding, binding, magnesium, nucleotide-binding;
HET: 10F; 1.80A {Homo sapiens} PDB: 3hxt_A* 3hy4_A*
3hy6_A
Length = 203
Score = 56.1 bits (136), Expect = 1e-09
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 218 KVDLIVIGSVAVNPKTGARLGKGEGFAELEY-GMLRYMGAIDDSTPVVTSV-HDYQLVDD 275
+DLI + + + K G RLG+G+G+ Y L+ + P ++ Q+
Sbjct: 128 GLDLIFMPGLGFD-KHGNRLGRGKGY----YDAYLKRCLQHQEVKPYTLALAFKEQICLQ 182
Query: 276 IPVEKLLIHDVPVDIICTPTQVI 298
+PV + +D+ VD +
Sbjct: 183 VPVNE---NDMKVDEVLYEDSST 202
>1wkc_A HB8 TT1367 protein; structural genomics, riken structural
genomics/proteomi initiative, RSGI, unknown function;
1.70A {Thermus thermophilus} SCOP: c.124.1.6
Length = 184
Score = 54.5 bits (132), Expect = 4e-09
Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 12/96 (12%)
Query: 215 EIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVD 274
+ +DL+V+ +A + + G RLG G+GF Y R++ + +T V V L
Sbjct: 99 DPRVLDLVVVPGLAFD-REGYRLGHGQGF----YD--RFLKEVRAATVGV--VPQALLFP 149
Query: 275 DIPVEKLLIHDVPVDIICTPTQVIFTNTTIPKPQGI 310
+P + DVPVD + T V P P G+
Sbjct: 150 ALPRDP---WDVPVDHLATEAGVEAVKRPAPGPGGL 182
>2jcb_A 5-formyltetrahydrofolate cyclo-ligase family PROT; folate
metabolism; HET: ADP; 1.6A {Bacillus anthracis}
Length = 200
Score = 53.8 bits (130), Expect = 8e-09
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 215 EIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVD 274
++DL ++ VA + G R+G G G+ Y RY+ T ++ + +Q+V+
Sbjct: 123 NADEIDLQIVPGVAYT-ERGERIGYGGGY----YD--RYLVHYKGKT--LSLAYSFQMVE 173
Query: 275 DIPVEKLLIHDVPVDIICTPTQVIFTN 301
IPVE D V+ I T + N
Sbjct: 174 HIPVEP---FDKNVEKIITEKGTMVKN 197
>1ydm_A Hypothetical protein YQGN; northeast structural genomics, SR44,
X-RAY, PSI, protein structure initiative; 2.50A
{Bacillus subtilis}
Length = 187
Score = 51.0 bits (123), Expect = 7e-08
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 218 KVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVDDIP 277
++DL+++ V + G R+G G G+ Y RY+ + T + + + QL +P
Sbjct: 115 QIDLMIVPGVCFD-VNGFRVGFGGGY----YD--RYLSEYEGKTVSL--LLECQLFAHVP 165
Query: 278 VEKLLIHDVPVDIICTPTQVI 298
HD+PV + T ++I
Sbjct: 166 RLP---HDIPVHKLITEDRII 183
>1sou_A 5,10-methenyltetrahydrofolate synthetase; structural genomics, PSI,
protein structure initiative, northeast structural
genomics consortium; NMR {Aquifex aeolicus} SCOP:
c.124.1.6
Length = 194
Score = 50.7 bits (122), Expect = 9e-08
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 218 KVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVDDIP 277
VD I + VA + G RLG G+G+ Y R + + V + +Q+ + +P
Sbjct: 111 DVDFIAVPGVAFD-LEGYRLGFGKGY----YD--RLLKRV--KGLKVGVAYSFQVFERLP 161
Query: 278 VEKLLIHDVPVDIICTPTQVI 298
+ D+PVD++ T V
Sbjct: 162 RDA---WDIPVDVLVTEKNVR 179
>1sbq_A H91_ORF164, 5,10-methenyltetrahydrofolate synthetase homolog;
MTHFS, 5- formyltetrahydrofolate cyclo-ligase,
structural genomics; 2.20A {Mycoplasma pneumoniae} SCOP:
c.124.1.6 PDB: 1u3f_A* 1u3g_A*
Length = 189
Score = 46.5 bits (111), Expect = 2e-06
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 215 EIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLVD 274
E ++D +I V N K RLG G+G+ Y RY+ + P + + +Q D
Sbjct: 120 EPNQIDCFLIPLVGFN-KDNYRLGFGKGY----YD--RYLMQLTRQQPKIGIAYSFQKGD 172
Query: 275 DIPVEKLLIHDVPVDIICTP 294
+ DV +D+I
Sbjct: 173 -FLADP---WDVQLDLIIND 188
>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 = 45.8 bits (108), Expect = 2e-05
Identities = 37/191 (19%), Positives = 62/191 (32%), Gaps = 67/191 (35%)
Query: 16 PNNYLIT---KS--------RKSNRLSS-------FSQKKP-FTLSFKLGNNKARNGVAF 56
N +++ +S RK+ S FS++K F+ F L F
Sbjct: 374 AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF-L-----PVASPF 427
Query: 57 DESAY--EA-ERLSMDAKARDLMAETSK-----RETESG-------AEDDPKSWKWIIRK 101
S A + ++ D ++ +T G + IIR
Sbjct: 428 -HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRL 486
Query: 102 RI-WDLMEVQNIAQNPRPVHHRIPNF-------VGASVAAKNL--TGLEEFRV--AGCVK 149
+ W+ + H I +F +G + +N TG+ RV AG +
Sbjct: 487 PVKWET------TTQFKATH--ILDFGPGGASGLG-VLTHRNKDGTGV---RVIVAGTLD 534
Query: 150 VNPDSPQ--KQ 158
+NPD KQ
Sbjct: 535 INPDDDYGFKQ 545
Score = 33.5 bits (76), Expect = 0.14
Identities = 47/301 (15%), Positives = 90/301 (29%), Gaps = 109/301 (36%)
Query: 101 KRIWDLMEVQNIAQNPRPVHHRIPNFVGASVAAKNLTGLEEFRVAGCVKVNPDSPQKQVR 160
+ +W+ + +H + G F + V NP V
Sbjct: 1643 QDVWNRAD-----------NHFKDTY-----------G---FSILDIVINNP------VN 1671
Query: 161 LLTLSGGKKLLTPQPRLRTGFFSVLDSSMLSPST--------INEACTS----------- 201
L GG+K R+R + +++ +++ INE TS
Sbjct: 1672 LTIHFGGEKGK----RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Query: 202 -----------VGVAKYG--KQIGLDEIIKVDLIVIG-S-------VAV----NPKTGAR 236
+ A + K GL I D G S ++ + ++
Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSKGL---IPADATFAGHSLGEYAALASLADVMSIESLVE 1784
Query: 237 L----GKGEGFA--ELEYGMLRY-MGAIDDSTPVVTSVHD--YQLVDDIPVEKLLIHDVP 287
+ G A E G Y M AI+ + + +V+ + +
Sbjct: 1785 VVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL---- 1840
Query: 288 VDII---CTPTQVIFTNTTIPKPQGIYWDKLSPE----KLGQIRILRELKGRIEQETGKE 340
V+I+ Q + + + D ++ KL +I I+ EL+ + E +
Sbjct: 1841 VEIVNYNVENQQYVAAGDL----RAL--DTVTNVLNFIKLQKIDII-ELQKSLSLEEVEG 1893
Query: 341 Q 341
Sbjct: 1894 H 1894
>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 = 34.8 bits (79), Expect = 0.047
Identities = 57/348 (16%), Positives = 108/348 (31%), Gaps = 97/348 (27%)
Query: 68 MDAKARDLMA---ETSKRETE-SGAEDDPKSWKWIIRKRIWDLMEVQNIAQNPRPVH--H 121
+ +D+++ + + +D PKS I+ K E+ +I + V
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKS---ILSKE-----EIDHIIMSKDAVSGTL 65
Query: 122 RIPNFVGASVAAKNLTGLEEFRVAGCVKVN-----------PDSPQKQVRLLT-----LS 165
R+ F ++ +K +++F V +++N P R+ L
Sbjct: 66 RL--FW--TLLSKQEEMVQKF-VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY 120
Query: 166 GGKKLLTPQPRLRTGFFSVLDSSM--LSPSTINEACTSVGVAKYGKQIGLDEIIKVDLIV 223
++ R + L ++ L P + GV GK V
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRP---AKNVLIDGVLGSGKTW-----------V 166
Query: 224 IGSVAVNPKTGARLGKGEGF---------AELEYGML---------RYMGAIDDSTPVVT 265
V ++ K ++ + F E ML + D S+ +
Sbjct: 167 ALDVCLSYKVQCKMD-FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 266 SVHDYQ-----LVDDIPVEK-LLI-HDV-------PVDIICTPTQVIFTNTTIPKPQGIY 311
+H Q L+ P E LL+ +V ++ C +++ T T + + +
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC---KILLT--T--RFKQVT 278
Query: 312 WDKLSPEKLGQIRILRELKGRIEQET----GKEQTCGPSEKLPPMAKR 355
D LS I + E K C P + LP
Sbjct: 279 -DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD-LPREVLT 324
Score = 33.3 bits (75), Expect = 0.13
Identities = 47/338 (13%), Positives = 98/338 (28%), Gaps = 86/338 (25%)
Query: 48 NKARNGVA-FDESA----YE--AERLSMDAKARDLMAETSKRETESGAEDDPKSWKWIIR 100
+K V F E Y+ + + + +M + + D+ K+ +
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV- 131
Query: 101 KRIWDLMEVQNIAQNPRPVHHRIPNFV-------GASVAAKNLTGLEEFRVAGC------ 147
R+ ++++ RP N + G + A ++ ++V
Sbjct: 132 SRLQPYLKLRQALLELRPA----KNVLIDGVLGSGKTWVALDV--CLSYKVQCKMDFKIF 185
Query: 148 -VKV-NPDSPQKQVRLLTLSGGKKLLTPQPRLRTGFFSVLDSSMLSPSTINEACTSVGVA 205
+ + N +SP+ + +L +KLL ++ + S D S I+ +
Sbjct: 186 WLNLKNCNSPETVLEML-----QKLLY---QIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 206 KYGKQ-----IGLD-----EIIKV------------DLIVIGSVAVNPKTGARLGK-GEG 242
K + L + V ++ T L
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 243 FAELE-YGML-RYMGAIDDSTPVVTSVHDYQLVDDIPVEKLLIHDVPVDIICTPTQVIFT 300
E +L +Y+ D+P E L + + II +
Sbjct: 298 LTPDEVKSLLLKYLDCR---------------PQDLPREVLTTNPRRLSIIAESIR-DGL 341
Query: 301 NTTIPKPQGIYWDKLSPEKLGQIR--ILRELKGRIEQE 336
T W ++ +KL I L L+ ++
Sbjct: 342 ATW------DNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase,
membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio
marinus} PDB: 3ayy_A 3ayz_A 3rgw_L
Length = 596
Score = 33.3 bits (75), Expect = 0.12
Identities = 18/113 (15%), Positives = 30/113 (26%), Gaps = 12/113 (10%)
Query: 168 KKLLTPQPRLRTGFFSVLDSSMLSPSTIN-------EACTSVGVAKYGKQIGLDEIIKVD 220
+ L + D STI E+ + + I D
Sbjct: 436 NRFNAVCRLLDPNHKDITDLKAFLGSTIGRTLARALESEYCGDMMLDDFNQLISNIKNGD 495
Query: 221 LIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLV 273
+ +P + KG G G L + I+ + +YQ V
Sbjct: 496 SSTANTDKWDPSSWPEHAKGVGTVAAPRGALAHWIVIEKGK-----IKNYQCV 543
>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 561
Score = 32.9 bits (74), Expect = 0.18
Identities = 19/113 (16%), Positives = 34/113 (30%), Gaps = 9/113 (7%)
Query: 197 EACTSVGVAKYGKQIGLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGA 256
E+ V + + + D P + +G G E G L +
Sbjct: 436 ESKILVDAMQGWYDGLIANVKSGDTKTFNETLWEPSSWPSRAQGVGIMEAPRGALGHWIV 495
Query: 257 IDDST-----PVVTSVHDYQLVDDI----PVEKLLIHDVPVDIICTPTQVIFT 300
I+D VV S + D E L + + + P +++ T
Sbjct: 496 IEDGRIANYQAVVPSTWNAGPRDGRGQAGAYEAALQDNHQLVDVKQPIEILRT 548
>1vp6_A CNBD, cyclic-nucleotide binding domain of mesorhizobium LOTI CNG
potassium channel; dimer helical bundle beta barrel core
with cyclic AMP bound; HET: CMP; 1.70A {Mesorhizobium
loti} SCOP: b.82.3.2 PDB: 3cl1_A* 2k0g_A* 2kxl_A 3clp_A*
1u12_A 3co2_A
Length = 138
Score = 29.6 bits (67), Expect = 0.78
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 221 LIVIGSVAVNPKTGARLGKGEGFAEL 246
+V GSV+V LG G F E+
Sbjct: 57 FVVEGSVSVATPNPVELGPGAFFGEM 82
>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_L* 3use_L*
Length = 582
Score = 29.8 bits (66), Expect = 1.4
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 5/77 (6%)
Query: 197 EACTSVGVAKYGKQIGLDEIIKVDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGA 256
EA + G +Y + + +L + P T +G GF E G L + A
Sbjct: 458 EAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAPRGALGHWAA 517
Query: 257 IDDSTPVVTSVHDYQLV 273
I D + YQ V
Sbjct: 518 IRDGK-----IDLYQCV 529
>2d7i_A Polypeptide N-acetylgalactosaminyltransferase 10; beta trefoil,
rossmann fold; HET: NAG NGA UDP; 2.50A {Homo sapiens}
PDB: 2d7r_A*
Length = 570
Score = 29.8 bits (66), Expect = 1.8
Identities = 28/124 (22%), Positives = 42/124 (33%), Gaps = 7/124 (5%)
Query: 47 NNKARNGVAFDESAYEAERLSMDAKARDLMAETSKRETESGAEDDPKSWKWIIRKRIWDL 106
N K V DE A + + + +++ S + KS+KW + K WDL
Sbjct: 356 NLKRVAEVWMDEYAEYIYQRRPEYRHLSAGDVAVQKKLRS--SLNCKSFKWFMTKIAWDL 413
Query: 107 MEVQNIAQNPRPVHHRIPNFVGAS--VAAKNLTGLEEFRVAGCV--KVNPDSPQKQVRLL 162
+ + P I N VG K+ R+ GCV + QV
Sbjct: 414 PKFYPPVEPPAAAWGEIRN-VGTGLCADTKHGALGSPLRLEGCVRGRGEAAWNNMQVFTF 472
Query: 163 TLSG 166
T
Sbjct: 473 TWRE 476
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 2.8
Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 62 EAERLSMDAKARDLMAETSKRETESGAEDDPKSWKWIIRKRIWDLMEVQNIAQN 115
+ +RL + D ++ ++E A+ D + W +R + +E +N N
Sbjct: 94 QRKRL----QELDAASKVMEQEWREKAKKDLEEWN----QRQSEQVE-KNKINN 138
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1
Length = 498
Score = 28.8 bits (64), Expect = 3.3
Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 219 VDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLV 273
+ + G+ +G GF E G L + I D + +YQ+V
Sbjct: 396 LKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKK-----IENYQIV 445
>1qgi_A Protein (chitosanase); hydrolase, chitosan degradation; HET: GCS
NAG; 1.60A {Bacillus circulans} SCOP: d.2.1.7 PDB:
2d05_A
Length = 259
Score = 28.2 bits (62), Expect = 3.8
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 4/69 (5%)
Query: 38 PFTLSFKLGNNKARNGVAFDESAYEAERLSMDAKARDLMAETSKRETESGAEDDPKSWKW 97
S L AR+G + +E + + R L+ +T+K ++ K W
Sbjct: 179 ATGGSDTLQGLLARSGSSSNEKTF----MKNFHAKRTLVVDTNKYNKPPNGKNRVKQWDT 234
Query: 98 IIRKRIWDL 106
++ +L
Sbjct: 235 LVDMGKMNL 243
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron
transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans}
SCOP: e.18.1.1
Length = 542
Score = 28.2 bits (62), Expect = 4.7
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 219 VDLIVIGSVAVNPKTGARLGKGEGFAELEYGMLRYMGAIDDSTPVVTSVHDYQLV 273
+ IV V +G GFA++ G L + I+D + ++QLV
Sbjct: 440 ENNIVKDKQIVEDYAVPTSARGVGFADVSRGGLSHWMTIEDGK-----IDNFQLV 489
>2faf_A Phosphoenolpyruvate carboxykinase; pepck, phosphoryl transfer,
lyase; HET: 20S EPE 1PE; 1.70A {Gallus gallus} PDB:
2fah_A* 2qzy_A*
Length = 608
Score = 27.4 bits (60), Expect = 8.3
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 287 PVDIICTPTQVIFTNTTIPKPQGIYWDKLSPEKLGQIRILRELKGRIEQETGKE------ 340
P + IFTN + G+YWD L + L + +
Sbjct: 331 PNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNS 390
Query: 341 QTCGPSEKLPPMA 353
+ C P+++ P M
Sbjct: 391 RFCAPADQCPIMD 403
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
0.316 0.134 0.389
Gapped
Lambda K H
0.267 0.0470 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,565,512
Number of extensions: 346916
Number of successful extensions: 646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 637
Number of HSP's successfully gapped: 21
Length of query: 357
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 262
Effective length of database: 4,049,298
Effective search space: 1060916076
Effective search space used: 1060916076
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 (21.6 bits)
S2: 58 (26.8 bits)