RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10666
(240 letters)
>1rv3_A Serine hydroxymethyltransferase, cytosolic; one-carbon metabolism;
HET: GLY PLP; 2.40A {Oryctolagus cuniculus} SCOP:
c.67.1.4 PDB: 1rv4_A* 1rvu_A* 1rvy_A* 1ls3_A* 1cj0_A*
1bj4_A* 1eji_A*
Length = 483
Score = 170 bits (433), Expect = 1e-50
Identities = 67/126 (53%), Positives = 81/126 (64%), Gaps = 31/126 (24%)
Query: 11 EG----KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL--- 63
G +YYGG + IDE+E + Q+R+L+A+ LDP+ WG NVQPYSGSPANFAVYT L
Sbjct: 74 LGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEP 133
Query: 64 ------------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFK 99
KISATSIFFES+ YKVN +TG IDYD+L E+ARLF
Sbjct: 134 HGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFH 193
Query: 100 PRLIIA 105
P+LIIA
Sbjct: 194 PKLIIA 199
>2a7v_A Serine hydroxymethyltransferase; structural genomics, structural
genomics consortium, SGC; 2.04A {Homo sapiens} SCOP:
c.67.1.4 PDB: 3ou5_A
Length = 490
Score = 169 bits (431), Expect = 4e-50
Identities = 69/122 (56%), Positives = 85/122 (69%), Gaps = 28/122 (22%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL------- 63
GK YYGG + +DEIE++ Q+R+L+AF+LDP QWG NVQPYSGSPAN AVYT L
Sbjct: 88 GKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRI 147
Query: 64 --------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLI 103
+ISATSIFFES+PYK+N +TGLIDY++LA +ARLF+PRLI
Sbjct: 148 MGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLI 207
Query: 104 IA 105
IA
Sbjct: 208 IA 209
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 2w7f_A* 2w7d_A* 2w7e_A*
2w7g_A* 2w7h_A* 1yjz_A* 1yjy_A* 2vgu_A* 2vgs_A* 2vgt_A*
2vgv_A* 2vgw_A* ...
Length = 405
Score = 93.8 bits (234), Expect = 2e-22
Identities = 39/120 (32%), Positives = 63/120 (52%), Gaps = 33/120 (27%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
G+ YYGG +++D +E +A++R+ + F G NVQP+SG+ AN AVY
Sbjct: 57 GRRYYGGCEYVDIVEELARERAKQLF-------GAEHANVQPHSGAQANMAVYFTVLEHG 109
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G ++ + + + + Y V+ ET +IDYD + E ARL +P+LI+A
Sbjct: 110 DTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVA 169
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 92.2 bits (230), Expect = 5e-22
Identities = 35/120 (29%), Positives = 56/120 (46%), Gaps = 33/120 (27%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
G YYGG + ID +E +A +R+ F G NVQP+SGS AN AVY
Sbjct: 57 GARYYGGCEVIDRVESLAIERAKALF-------GAAWANVQPHSGSQANMAVYMALMEPG 109
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G +++ + ++ + Y V +T LID +++ A +P++I+A
Sbjct: 110 DTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVA 169
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 91.9 bits (229), Expect = 9e-22
Identities = 36/120 (30%), Positives = 58/120 (48%), Gaps = 33/120 (27%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
G+ YYGG + +D +E +A+ R+ F G NVQP+SG+ AN AV
Sbjct: 79 GRRYYGGCEHVDVVENLARDRAKALF-------GAEFANVQPHSGAQANAAVLHALMSPG 131
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G++++ + +E+ Y V+ T LID D + +A F+P++IIA
Sbjct: 132 ERLLGLDLANGGHLTHGMRLNFSGKLYENGFYGVDPATHLIDMDAVRATALEFRPKVIIA 191
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 91.9 bits (229), Expect = 1e-21
Identities = 42/120 (35%), Positives = 58/120 (48%), Gaps = 33/120 (27%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
GK YYGG +F DE+E +A +R + F NVQP+SG+ AN AV
Sbjct: 66 GKRYYGGCEFADEVEALAIERVKRLF-------NAGHANVQPHSGAQANGAVMLALAKPG 118
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G K + + +F +L Y V+ +T LIDYD++ A+ KP LIIA
Sbjct: 119 DTVLGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIA 178
>3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011,
serine hydroxymethyltransfera salmonella typhimurium.;
HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A*
3g8m_A* 1eqb_A*
Length = 420
Score = 90.0 bits (224), Expect = 4e-21
Identities = 41/120 (34%), Positives = 63/120 (52%), Gaps = 34/120 (28%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
GK YYGG +++D +E +A R+ + F G NVQP+SGS ANFAVYT
Sbjct: 64 GKRYYGGCEYVDVVEQLAIDRAKELF-------GADYANVQPHSGSQANFAVYTALLQPG 116
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G ++ + + +PY ++ E+G IDYD++A+ A+ KP++II
Sbjct: 117 DTVLGMNLAQGGHLTHGSPVNFSGKLYNIVPYGID-ESGKIDYDEMAKLAKEHKPKMIIG 175
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 86.1 bits (214), Expect = 8e-20
Identities = 45/120 (37%), Positives = 59/120 (49%), Gaps = 34/120 (28%)
Query: 12 GK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYT------ 61
GK YYGG +F+DEIE +A +R K F C NVQP SGS AN VY
Sbjct: 59 GKRYYGGCEFVDEIETLAIERCKKLF-------NCKFANVQPNSGSQANQGVYAALINPG 111
Query: 62 ----------------GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G K+S++ +ES Y V + G IDY+K+ E A+ KP+LI+
Sbjct: 112 DKILGMDLSHGGHLTHGAKVSSSGKMYESCFYGVELD-GRIDYEKVREIAKKEKPKLIVC 170
>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 = 37.1 bits (85), Expect = 0.004
Identities = 30/175 (17%), Positives = 58/175 (33%), Gaps = 38/175 (21%)
Query: 77 YKVNTETGLIDY---DKLAESARLFKPRLIIAETIEDLKLLTKVLLEETSKWRIKHNREI 133
+ ++ ETG Y D L+ F + ++D+ K +L EI
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKD-VQDM---PKSILS---------KEEI 51
Query: 134 RDLYNEPDVVGEIKSGRLRW------AGHVQRREEDS---NIRSIWEH-QPEGRRPRGRP 183
+ D V RL W VQ+ E+ N + + + E R+P
Sbjct: 52 DHIIMSKDAVSGTL--RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP-SMM 108
Query: 184 KNRWKDQVRKDMTILNLTTEDSFNRALWRQKVGEAKYLL-----GNYLLLK-MSG 232
+ +Q + + + + +R Q + + L +L+ + G
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNVSR---LQPYLKLRQALLELRPAKNVLIDGVLG 160
Score = 36.4 bits (83), Expect = 0.008
Identities = 25/160 (15%), Positives = 46/160 (28%), Gaps = 29/160 (18%)
Query: 27 VAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGLKISATSIFFESLPY-KVNTETGL 85
V ++ AFNL C + + + + S+ S+ ++ L
Sbjct: 253 VQNAKAWNAFNL-----SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 86 -----IDYDKLAESARLFKPRLI--IAETIED-------LKLLTKVLLEETSKWRIKH-- 129
L PR + IAE+I D K + L + +
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367
Query: 130 NREIRDLYNE----PDVVGEIKSGRLR--WAGHVQRREED 163
E R +++ P I + L W ++
Sbjct: 368 PAEYRKMFDRLSVFPPSA-HIPTILLSLIWFDVIKSDVMV 406
Score = 32.1 bits (72), Expect = 0.19
Identities = 33/241 (13%), Positives = 61/241 (25%), Gaps = 83/241 (34%)
Query: 77 YKVNTETGL-IDYDKLAES--ARLFKPRLIIAETIEDLKLL--TKVLLEETSKWRIKHNR 131
+ E L I+Y L +P ++ IE L + + + R++
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL 138
Query: 132 EIRD-LYN---EPDVV-----GEIKS-----------------GRLRWA--GHVQRREED 163
++R L +V+ G K+ ++ W + E
Sbjct: 139 KLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 164 --------SNIRSIWEHQPEGRRPRGRPKNRWKDQVRK------------------DMTI 197
I W + + + + ++R+ +
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258
Query: 198 LN---------LTTEDS----FNRALWRQKV-----------GEAKYLLGNYLLLKMSGL 233
N LTT F A + E K LL YL + L
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
Query: 234 R 234
Sbjct: 319 P 319
>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 = 34.2 bits (77), Expect = 0.017
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 90 KLAESARLFK----PRLIIAETIE 109
KL S +L+ P L I T+E
Sbjct: 24 KLQASLKLYADDSAPALAIKATME 47
>3ha2_A NADPH-quinone reductase; structural genomics, PSI-2, protein
structure initiative, no structural genomics,
consortium, NESG; HET: MSE; 1.80A {Pediococcus
pentosaceus atcc 25745}
Length = 177
Score = 29.4 bits (66), Expect = 0.76
Identities = 5/45 (11%), Positives = 9/45 (20%), Gaps = 5/45 (11%)
Query: 113 LLTKVLLEETSKWRIKHNREIRDLYNEPDVVGEIKSGRLRWAGHV 157
+ N L + +V E L +
Sbjct: 16 NTQPFFKAAIENF---SNVTWHPLVADFNVEQEQS--LLLQNDRI 55
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 2.3
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 12/71 (16%)
Query: 120 EETSKWRIKHNREIRDLYNEPDVVGEIKSGRLRWAGHVQRREEDSNIRSIWEHQPEGRRP 179
E KWR + + ++ E D ++ W ++ E+ W + +
Sbjct: 85 ESIRKWREEQRKRLQ----ELDAASKVM--EQEWREKAKKDLEE------WNQRQSEQVE 132
Query: 180 RGRPKNRWKDQ 190
+ + NR D+
Sbjct: 133 KNKINNRIADK 143
Score = 26.7 bits (58), Expect = 6.9
Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 154 AGHVQRREEDSNIRSIW-EHQPEGRRPRG----RPKNRWKDQVRKDMTILNLTTEDSFNR 208
A + +E +IR W E Q + + + W+++ +KD+ N + +
Sbjct: 75 AQADRLTQEPESIRK-WREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEK 133
Query: 209 ALWRQKVGEAKYL 221
++ + +
Sbjct: 134 NKINNRIADKAFY 146
>3jxe_A Tryptophanyl-tRNA synthetase; adenosine triphosphate, rossmann
fold, crystallography, X-RAY, P. horikoshii,
aminoacyl-tRNA synthetase; HET: TYM; 3.00A {Pyrococcus
horikoshii}
Length = 392
Score = 27.4 bits (61), Expect = 4.4
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 76 PYKVNTETGLIDYDKLAESARLFKPRLIIAETIEDLKLLTK 116
P++V G++DYDKL + F + + +E LTK
Sbjct: 9 PWEV---EGVVDYDKLIKH---FGTSPLTEDLLEKTAELTK 43
>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 = 27.7 bits (61), Expect = 4.7
Identities = 22/145 (15%), Positives = 45/145 (31%), Gaps = 52/145 (35%)
Query: 2 NRAEMSSDEEGKYYGGNQF------------IDEIEIVAQQRSLKAFNLDPEQWGCNVQP 49
+R S E K N+F + +++ + + + + V
Sbjct: 405 SRIPFS---ERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-- 459
Query: 50 YSGSPANFAVYTG--LKISATSIFFESL-------PYKVN-------TETGLIDYDKLAE 93
+ + G L++ + SI E + P V T ++D+
Sbjct: 460 -------YDTFDGSDLRVLSGSIS-ERIVDCIIRLP--VKWETTTQFKATHILDFGPGGA 509
Query: 94 S--ARLFKP-------RLIIAETIE 109
S L R+I+A T++
Sbjct: 510 SGLGVLTHRNKDGTGVRVIVAGTLD 534
Score = 27.3 bits (60), Expect = 6.3
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 11/58 (18%)
Query: 131 REIRDLYNE-PDVVGE-IKSGRLRWAGHVQRREEDS-------NIRSIWEHQPEGRRP 179
E+RDLY +VG+ IK + ++ + NI W P P
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE-WLENPS-NTP 226
>3hv0_A Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-binding,
aminoacyl-tRNA synthetase, ligase, nucleotide-binding;
HET: TRP; 2.42A {Cryptosporidium parvum iowa II}
Length = 393
Score = 26.4 bits (58), Expect = 8.4
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 76 PYKVNTE-TGLIDYDKLAESARLFKPRLIIAETIEDLKLLTK 116
P++V + IDY+KL + F +LI + IE ++ LT
Sbjct: 6 PWEVKADNAYGIDYNKLIDK---FGCKLITKDMIERMERLTG 44
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens} PDB: 3n9v_A
Length = 313
Score = 26.3 bits (58), Expect = 9.3
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 194 DMTILNLTTEDSFNRALWRQKVGEAKYLLGNYLLLK---MSGL 233
D++ D+ W + V E + Y +K + G+
Sbjct: 48 DLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGI 90
>1lar_A Protein (LAR); tyrosine phosphatease, LAR protein, hydrolase; 2.00A
{Homo sapiens} SCOP: c.45.1.2 c.45.1.2 PDB: 2fh7_A
2nv5_A
Length = 575
Score = 26.5 bits (59), Expect = 9.5
Identities = 8/74 (10%), Positives = 16/74 (21%), Gaps = 3/74 (4%)
Query: 116 KVLLEETSKWRIKHNREIRDLYNEPDVVGEIKSGRLRWAGHVQRREEDSNIRSIWEHQPE 175
+ LLE H + ++ ++
Sbjct: 270 EALLE---AATCGHTEVPARNLYAHIQKLGQVPPGESVTAMELEFKLLASSKAHTSRFIS 326
Query: 176 GRRPRGRPKNRWKD 189
P + KNR +
Sbjct: 327 ANLPCNKFKNRLVN 340
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
0.317 0.134 0.397
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,727,488
Number of extensions: 219520
Number of successful extensions: 517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 502
Number of HSP's successfully gapped: 36
Length of query: 240
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,160,982
Effective search space: 619986318
Effective search space used: 619986318
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: 56 (25.3 bits)