RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2491
(162 letters)
>2nwl_A GLTPH, glutamate symport protein; alpha helical, membrane protein,
helical hairpin, unwound RE transport protein; HET: PLM;
2.96A {Pyrococcus horikoshii} PDB: 2nww_A* 1xfh_A*
2nwx_A* 3v8g_A 3v8f_A 3kbc_A
Length = 422
Score = 43.8 bits (104), Expect = 7e-06
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 107 TMRQLSKFVATSIGGFLVYHLIVIQLIYFLFTRKNPYKYYVNFFPAILTAFATSS 161
+ +L+K A G + ++++ + +P + + A+LTAF T S
Sbjct: 224 VVGELAKVTAAVYVGLTL-QILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRS 277
>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 = 33.3 bits (75), Expect = 0.031
Identities = 23/154 (14%), Positives = 40/154 (25%), Gaps = 57/154 (37%)
Query: 6 VMW-------PMRDRN-LAGIKLLETKRHRKHQICDLGHMIQTGLAFFVSLSISPNLGHK 57
++W M N L L+E + K + I L + L ++
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVE--KQPKESTISI-PSIY--------LELKVKLENE 442
Query: 58 QTDLHRRYDSYYASAQQVCRHLYRRIPGLPSDCHPAHTSKLISIEDMTVTMRQLSKFVAT 117
LHR +Y + D P + D
Sbjct: 443 YA-LHRSIVDHYNIPKTFD----------SDDLIPPY-------LDQY------------ 472
Query: 118 SIGGFLVYHLIVIQLI--YFLFTRKNPYKYYVNF 149
+ +HL I+ LF +++F
Sbjct: 473 -FYSHIGHHLKNIEHPERMTLFRMV-----FLDF 500
>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 = 29.6 bits (66), Expect = 0.47
Identities = 23/176 (13%), Positives = 52/176 (29%), Gaps = 45/176 (25%)
Query: 27 RKHQICDLGHMIQTGLAFFVS--LS-------ISPNLGHKQTDLHRRYD---SYYASAQQ 74
++ ++ L F + L + L T L + + +Y +
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 75 VCRHLYRRIPGLPSDCHPAHTSKLISI-------------------------EDMTVTMR 109
R ++ ++L++I D+
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSA 192
Query: 110 Q-LSKFVATSIGGFLVYHLIVIQLIYFLFTRKN-PYKYYVNF----FPAI-LTAFA 158
+ LS+ + T++ V+ + ++ +L N P K Y+ P I + A
Sbjct: 193 ETLSELIRTTLDAEKVFTQ-GLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA 247
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock
protein, protein binding; 2.75A {Mus musculus}
Length = 320
Score = 29.2 bits (65), Expect = 0.60
Identities = 5/23 (21%), Positives = 8/23 (34%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
TG ++S L K+
Sbjct: 45 LTGRIVYISEQAGVLLRCKRDVF 67
>3gdi_A Period circadian protein homolog 2; tandem PAS domains,
biological rhythms, cytoplasm, nucleus, phosphoprotein,
transcription; 2.40A {Mus musculus}
Length = 309
Score = 28.8 bits (64), Expect = 0.76
Identities = 3/23 (13%), Positives = 9/23 (39%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
+G ++S ++ K+
Sbjct: 34 VSGKILYISNQVASIFHCKKDAF 56
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm,
protein binding; 2.50A {Mus musculus}
Length = 317
Score = 28.5 bits (63), Expect = 0.99
Identities = 5/23 (21%), Positives = 9/23 (39%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
+G +S + L K+ L
Sbjct: 45 LSGRLVHISEQAALILNSKRGFL 67
>3rty_A Period circadian protein; PAS domain, signalling, timeless,
circadian clock protein; 2.85A {Drosophila
melanogaster} PDB: 1wa9_A 3gec_A
Length = 339
Score = 28.1 bits (62), Expect = 1.4
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
G+ + + SI+ LG+ +
Sbjct: 12 HDGIVLYTTPSITDVLGYPRDMW 34
>3a1k_A Amidase; AS family enzyme, hydrolase; 2.17A {Rhodococcus SP} PDB:
3a1i_A
Length = 521
Score = 28.0 bits (63), Expect = 1.4
Identities = 4/18 (22%), Positives = 7/18 (38%), Gaps = 1/18 (5%)
Query: 65 YDSYYASAQQVCRHLYRR 82
+ Y A+ + L R
Sbjct: 392 GGASYGKARNL-VPLARA 408
>3kfu_E Glutamyl-tRNA(Gln) amidotransferase subunit A; ASPRS, gatcab,
ATP-binding, aminoacyl-tRNA synthetase, ligas
nucleotide-binding, protein biosynthesis, ligase-RNA
comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Length = 471
Score = 27.9 bits (63), Expect = 1.8
Identities = 6/18 (33%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 65 YDSYYASAQQVCRHLYRR 82
Y++YY AQ R +
Sbjct: 354 YEAYYGRAQAF-RRRLKA 370
>3ip4_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, ATP-binding, nucleotide-bindi protein
biosynthesis; 1.90A {Staphylococcus aureus subsp} PDB:
2df4_A 2dqn_A* 2g5h_A 2g5i_A* 2f2a_A
Length = 485
Score = 27.9 bits (63), Expect = 1.8
Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 65 YDSYYASAQQVCRHLYRR 82
YD+YY +Q+V R L +
Sbjct: 371 YDAYYKKSQKV-RTLIKN 387
>3h0l_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, protein biosynthesis; HET: ADP; 2.30A
{Aquifex aeolicus} PDB: 3h0m_A 3h0r_A*
Length = 478
Score = 27.9 bits (63), Expect = 1.9
Identities = 9/18 (50%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 65 YDSYYASAQQVCRHLYRR 82
YD+YY AQ+V R L
Sbjct: 364 YDAYYLKAQKV-RRLITN 380
>2gi3_A Glutamyl-tRNA(Gln) amidotransferase subunit A; TM1272, structural
genomics, joint center for structura genomics, JCSG;
HET: MSE MPD; 1.80A {Thermotoga maritima} SCOP:
c.117.1.1 PDB: 3al0_A*
Length = 476
Score = 27.5 bits (62), Expect = 1.9
Identities = 5/18 (27%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 65 YDSYYASAQQVCRHLYRR 82
Y++Y+ A +V R
Sbjct: 357 YEAYFNKAMKV-RRKISD 373
>2frg_P TREM-like transcript-1; immunoglobulin-like, beta-sandwich, cell
surface receptor, triggering receptor, platelet
receptor, ITIM, immune system; 1.19A {Homo sapiens}
Length = 106
Score = 26.8 bits (59), Expect = 1.9
Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 22/65 (33%)
Query: 64 RYDSYYASAQQV-CRHLYRRIPGLPSDCHPAHTSKL--------ISIED------MTVTM 108
Y AQ+V CR LP C P +S + + + V M
Sbjct: 20 HYRLQDVKAQKVWCR-------FLPEGCQPLVSSAVDRRAPAGRRTFLTDLGGGLLQVEM 72
Query: 109 RQLSK 113
L +
Sbjct: 73 VTLQE 77
>1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered double
layers of alpha helices on TOP and bottom, hydrolase;
HET: EPE; 1.40A {Stenotrophomonas maltophilia} SCOP:
c.117.1.1 PDB: 1m21_A*
Length = 503
Score = 27.2 bits (61), Expect = 3.2
Identities = 5/18 (27%), Positives = 6/18 (33%)
Query: 65 YDSYYASAQQVCRHLYRR 82
D Y A+ R L
Sbjct: 381 ADPAYIRARSDARRLAGP 398
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 26.5 bits (58), Expect = 4.2
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
G +VS S++ L H +DL
Sbjct: 104 TDGSIIYVSESVTSLLEHLPSDL 126
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 25.7 bits (56), Expect = 8.2
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 39 QTGLAFFVSLSISPNLGHKQTDL 61
G FVS S+ L + Q DL
Sbjct: 105 DRGKILFVSESVFKILNYSQNDL 127
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
0.329 0.140 0.431
Gapped
Lambda K H
0.267 0.0557 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,415,765
Number of extensions: 127254
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 18
Length of query: 162
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,300,587
Effective search space: 326844612
Effective search space used: 326844612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.6 bits)