RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14772
(191 letters)
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 97
Score = 118 bits (296), Expect = 5e-35
Identities = 71/89 (79%), Positives = 80/89 (89%)
Query: 14 QVTELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDN 73
+T D + Q LPLARIKKIMKLD+ VKMISAEAP+LF+KAA++FI ELT+RAWIHTEDN
Sbjct: 9 NLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDN 68
Query: 74 KRRTLQRNDIAMAITKYDMFDFLIDIVPR 102
KRRTLQRNDIAMAITK+D FDFLIDIVPR
Sbjct: 69 KRRTLQRNDIAMAITKFDQFDFLIDIVPR 97
>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_A
Length = 140
Score = 112 bits (280), Expect = 4e-32
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 21 KTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHT-EDNKRRTLQ 79
LPL+R++ IMK +I+ E L +K ELF+ L A+ L+
Sbjct: 16 AETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALK 75
Query: 80 RNDIAMAITKYDMFDFLIDIVPR 102
++ + K +FL+ IVP+
Sbjct: 76 YEHLSQVVNKNKNLEFLLQIVPQ 98
>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B,
tata-DNA, transcription initiation, NC2, negative
cofactor, structural genomics, PSI; 2.62A {Homo sapiens}
SCOP: a.22.1.3
Length = 98
Score = 106 bits (265), Expect = 2e-30
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
Query: 21 KTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQR 80
P ARIKKIM+ D+ + ++A P++ S+A ELF+ L +A T+ +T+
Sbjct: 8 YNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTT 67
Query: 81 NDIAMAITKYDMFDFLIDIVPREEVKTATGPHR 113
+ + I D + +E A +
Sbjct: 68 SHLKQCIELEG--DPAANKARKEAELAAATAEQ 98
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_B
Length = 128
Score = 79.6 bits (196), Expect = 9e-20
Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 10/109 (9%)
Query: 25 LPLARIKKIMK--LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRND 82
LP A I +++K L + + S EA ++AA +F +T + +T+ D
Sbjct: 10 LPNAVIGRLIKEALPESASV-SKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKD 68
Query: 83 IAMAITKYDMFDFLIDIVP------REEVKTATGPHRRDDATKTALNPD 125
I +T+ D F+ + + R+ VK + TA N +
Sbjct: 69 ILQTLTELD-FESFVPSLTQDLEVYRKVVKEKKESKASKKDSNTAENAN 116
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 93
Score = 76.4 bits (188), Expect = 7e-19
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 25 LPLARIKKIMKLD-DGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDI 83
LP+A + +IMK I+ +A + FI +T A KR+T+ DI
Sbjct: 9 LPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDI 68
Query: 84 AMAITKYDMFDFLIDIVPRE 103
A++ FD ++ +
Sbjct: 69 LFAMSTLG-FDSYVEPLKLY 87
>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone,
H2A/H2B, tata-DNA, transcription initiation, NC2,
negative cofactor, structural genomics, PSI; 2.62A {Homo
sapiens} SCOP: a.22.1.3
Length = 179
Score = 58.3 bits (140), Expect = 4e-11
Identities = 23/150 (15%), Positives = 46/150 (30%), Gaps = 4/150 (2%)
Query: 25 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 84
+P A I K++K ++ +A L FIH ++ A ++++T+ +
Sbjct: 16 IPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVI 75
Query: 85 MAITKYDMFDFLIDIVPREEVK---TATGPHRRDDATKTALNPDQVQYYFQLAQQHQAAL 141
A+ F I V + A + + P++ Q +A
Sbjct: 76 QALESLG-FGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQELFAKARQ 134
Query: 142 QQNNQGATTTSATPTLVVNGGNSGAQQIQT 171
QQ + A +
Sbjct: 135 QQAELAQQEWLQMQQAAQQAQLAAASASAS 164
>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A
{Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A
1a7w_A 1b6w_A 1bfm_A
Length = 68
Score = 55.0 bits (133), Expect = 6e-11
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 25 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 84
LP+A I +I+K + G + +S +A + +K E E+ A + R+T++ DI
Sbjct: 3 LPIAPIGRIIK-NAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIE 61
Query: 85 MAITKY 90
+A +
Sbjct: 62 LARKMF 67
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 53.2 bits (128), Expect = 2e-10
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 25 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 84
LP+A + ++++ G + +S +A + ++ E + E+ +A R+T++ DI
Sbjct: 7 LPIAPVDRLIR-KAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65
Query: 85 MAI 87
+AI
Sbjct: 66 LAI 68
>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA
binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1
PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B
Length = 84
Score = 33.6 bits (77), Expect = 0.005
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 39 GVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAI 87
GVK IS ++F+ + A +TE KR+T+ D+ A+
Sbjct: 24 GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYAL 72
>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 = 35.2 bits (80), Expect = 0.012
Identities = 22/114 (19%), Positives = 40/114 (35%), Gaps = 32/114 (28%)
Query: 45 AEAPMLFSKAAELFIHELTIRAWIHTEDNKRR--------------TLQ-----RNDIAM 85
E LF +F L R ++ + K R TLQ + I
Sbjct: 487 PERMTLFRM---VF---LDFR-FL---EQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Query: 86 AITKYD-MFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQ 138
KY+ + + ++D +P+ E + D + AL + + + +Q Q
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKYT--DLLRIALMAEDEAIFEEAHKQVQ 588
Score = 31.4 bits (70), Expect = 0.21
Identities = 22/149 (14%), Positives = 43/149 (28%), Gaps = 37/149 (24%)
Query: 2 DTGEKEHVN------RVIQVTELDLK-TQALPLARIKKIMKLDDGVKMISAEAPMLFSKA 54
+ + N +++ +T + T L A I + + E L K
Sbjct: 252 NVQNAKAWNAFNLSCKIL-LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
Query: 55 AELFIHELTIRAWIHTEDNKRRTLQRNDIAMAITKYDMFDFLIDIVPREEVKTATG-PHR 113
+ +L R L N ++ +I R+ + T H
Sbjct: 311 LDCRPQDL-----------PREVLTTNPRRLS---------IIAESIRDGLATWDNWKHV 350
Query: 114 RDDATKTA-------LNPDQVQ-YYFQLA 134
D T L P + + + +L+
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Score = 26.0 bits (56), Expect = 9.4
Identities = 17/120 (14%), Positives = 31/120 (25%), Gaps = 25/120 (20%)
Query: 90 YDMFDFLIDIVPREEVKTATG-PHRR------------------DDATKTALNPDQVQYY 130
D+ D I+ +EE+ + L + Y
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN---YK 92
Query: 131 FQLAQQHQAALQQNNQGATTTSATPTLVVNGGNSGAQ-QIQTIPMLLPLRTT-YKLTQHK 188
F L + +Q + + N A+ + + L LR +L K
Sbjct: 93 F-LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK 151
>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 = 34.6 bits (79), Expect = 0.018
Identities = 29/177 (16%), Positives = 52/177 (29%), Gaps = 59/177 (33%)
Query: 43 ISAEAPMLFS------KAAELFIHELTIRAWIHTEDNKRRT--LQRNDIAM-AITKYDMF 93
I A L A ++F L I W+ N L I+ I +
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA 247
Query: 94 DFLI-----DIVP---REEVKTATGPHRRD-----------------DATKTALNPDQVQ 128
+++ P R +K ATG H + + + A+
Sbjct: 248 HYVVTAKLLGFTPGELRSYLKGATG-HSQGLVTAVAIAETDSWESFFVSVRKAI-----T 301
Query: 129 YYFQL---AQQH-------QAALQQ---NNQGATTTSATPTLVVNGGNSGAQQIQTI 172
F + + + L+ NN+G +P L ++ +Q+Q
Sbjct: 302 VLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV----PSPMLSISNLTQ--EQVQDY 352
Score = 31.6 bits (71), Expect = 0.16
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 10/49 (20%)
Query: 4 GEKEHVNRVIQVTELD-LKTQALPLARIKKIMKLDDGVKMISAEAPMLF 51
G+ ++ V V L+ +K Q + + ++K + L++ V+ LF
Sbjct: 1857 GDLRALDTVTNV--LNFIKLQKIDIIELQKSLSLEE-VE------GHLF 1896
>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 = 33.4 bits (75), Expect = 0.019
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 31 KKIMKLDDGVKMISAE-APMLFSKAA 55
+ + KL +K+ + + AP L KA
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKAT 45
>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B
3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B
3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...
Length = 103
Score = 31.1 bits (70), Expect = 0.064
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 17 ELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRR 76
L Q + I+++ + GVK IS ++F+ + A +TE KR+
Sbjct: 22 VLRDNIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK 80
Query: 77 TLQRNDIAMAI 87
T+ D+ A+
Sbjct: 81 TVTAMDVVYAL 91
>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA
interaction, nucleoprotein, supercoiled DNA; 3.10A
{Saccharomyces cerevisiae} SCOP: a.22.1.1
Length = 102
Score = 30.4 bits (68), Expect = 0.13
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 23 QALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRND 82
Q + I+++ + GVK IS + F+ + + +TE KR+T+ D
Sbjct: 27 QGITKPAIRRLAR-RGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLD 85
Query: 83 IAMAI 87
+ A+
Sbjct: 86 VVYAL 90
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding
protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP:
a.22.1.2
Length = 154
Score = 30.9 bits (69), Expect = 0.13
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 19 DLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTL 78
D + A +++I+K G++ S++A L++K EL +A + +++ R+T+
Sbjct: 77 DYDGELFGRATVRRILK-RAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTV 135
Query: 79 QRNDIAMAIT 88
Q D+ AIT
Sbjct: 136 QGEDVEKAIT 145
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 30.0 bits (67), Expect = 0.15
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 1/67 (1%)
Query: 21 KTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQR 80
Q + I+++ + GVK IS + F+ + A +TE KR+T+
Sbjct: 26 NIQGITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTS 84
Query: 81 NDIAMAI 87
D+ A+
Sbjct: 85 LDVVYAL 91
>1bed_A DSBA oxidoreductase; TCPG, protein disulfide isomerase, disulfide
oxidoreductase; 2.00A {Vibrio cholerae} SCOP: c.47.1.13
PDB: 2ijy_A
Length = 181
Score = 30.4 bits (68), Expect = 0.26
Identities = 7/81 (8%), Positives = 24/81 (29%), Gaps = 4/81 (4%)
Query: 84 AMAITKYDMF-DFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQ 142
+A+ D + + + R ++ + + + ++
Sbjct: 76 MIALEVEDKMVPVMFNRIHTLRKPPKDEQELRQIFLDEGIDAAKFDAAYN-GFAVDSMVR 134
Query: 143 QNNQGATT--TSATPTLVVNG 161
+ ++ + P +VVN
Sbjct: 135 RFDKQFQDSGLTGVPAVVVNN 155
>3l9s_A Thiol:disulfide interchange protein; thioredoxin-fold, DSBA,
thiol-disulfide oxidoreductase, DISU bond, redox-active
center; 1.58A {Salmonella enterica subsp} PDB: 1a23_A
1a24_A 1a2j_A 1a2l_A 1a2m_A 1dsb_A 1fvk_A 3dks_A 1bq7_A
1fvj_A 1acv_A 1u3a_A* 1ti1_A* 2hi7_A* 2leg_A* 2zup_A*
3e9j_B* 1ac1_A 2b6m_A 2b3s_A
Length = 191
Score = 29.9 bits (66), Expect = 0.34
Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 3/80 (3%)
Query: 84 AMAITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQQ 143
AMA+ D + ++ + R + + + + ++ + Q
Sbjct: 81 AMALGVEDKVTVPLFEAVQKTQTVQSAADIRKVFVDAGVKGEDYDAAWN-SFVVKSLVAQ 139
Query: 144 NNQGATTT--SATPTLVVNG 161
+ A P + VNG
Sbjct: 140 QEKAAADLQLQGVPAMFVNG 159
>1mj5_A 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase; LINB, haloalkane
dehalogenase, 1, 3, 4, 4-cyclohexadiene dehalogenase;
0.95A {Sphingomonas paucimobilis} SCOP: c.69.1.8 PDB:
1cv2_A 1d07_A 2bfn_A 1g42_A* 1g4h_A* 1g5f_A* 1iz7_A
1iz8_A* 1k5p_A 1k63_A 1k6e_A
Length = 302
Score = 29.4 bits (66), Expect = 0.59
Identities = 16/127 (12%), Positives = 36/127 (28%), Gaps = 4/127 (3%)
Query: 37 DDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAITKYDMFDFL 96
+ + EA + + A+ + + ++ + LQ N + + L
Sbjct: 123 ERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPL 182
Query: 97 IDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQQNNQGATTTSATPT 156
+ E+ P + Q A+ ++ G + S P
Sbjct: 183 SE----AEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPK 238
Query: 157 LVVNGGN 163
L +N
Sbjct: 239 LFINAEP 245
>3hd5_A Thiol:disulfide interchange protein DSBA; protein structure
initiative II(PSI II), NYSGXRC, structural genomics;
2.35A {Bordetella parapertussis}
Length = 195
Score = 28.4 bits (63), Expect = 1.1
Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 3/80 (3%)
Query: 84 AMAITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQQ 143
A+ + D+ + + E + + A ++ + F + Q +Q+
Sbjct: 81 LQALERPDLHPKVFTAIHTERKRLFDKKAMGEWAASQGVDRAKFDSVFD-SFSVQTQVQR 139
Query: 144 NNQGATTT--SATPTLVVNG 161
+Q A TP V G
Sbjct: 140 ASQLAEAAHIDGTPAFAVGG 159
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 28.5 bits (63), Expect = 1.3
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 11/54 (20%)
Query: 97 IDIVPREEVKTATGPHRRDDATKTALN-------PDQVQYYFQL----AQQHQA 139
I++ P E + + ++ LN YY Q A+Q QA
Sbjct: 176 IELPPNEILFSENNDMDNNNDGVDELNKKCTFWDAISKLYYVQFFFKQAEQEQA 229
>2rem_A Disulfide oxidoreductase; disulfide oxidoreductase, DSBA,
thioredoxin fold, redox- active center; 1.90A {Xylella
fastidiosa}
Length = 193
Score = 28.2 bits (62), Expect = 1.3
Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 8/70 (11%)
Query: 114 RDDATKTALNPDQVQYYFQLAQQHQAALQQNNQGATTT--SATPTLVVNG-----GNSGA 166
+ PD+ F + + Q A TPT+VVNG G+
Sbjct: 115 AVFYAGYGVQPDRFVATFN-GPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFE 173
Query: 167 QQIQTIPMLL 176
++ L+
Sbjct: 174 DTLRITDYLV 183
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA
binding prote; 1.70A {Xenopus laevis}
Length = 77
Score = 26.8 bits (59), Expect = 1.5
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 25 LPLAR-IKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDI 83
LP R +++I + + A M +A+E ++ L + KR T+ DI
Sbjct: 7 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDI 66
Query: 84 AMA 86
+A
Sbjct: 67 QLA 69
>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi
anemia, DNA repair, DNA BI protein; 2.40A
{Saccharomyces cerevisiae}
Length = 88
Score = 26.9 bits (59), Expect = 1.9
Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 27 LARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMA 86
L +I + + +K I+ E + K ++FI E +R+ +D ++ + ++
Sbjct: 7 LIKILSQNEGGNDMK-IADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELS 65
Query: 87 IT 88
Sbjct: 66 HQ 67
>3gyk_A 27KDA outer membrane protein; APC61738.2, silicibacter pomeroyi
DSS-3, thioredoxin-like, oxidoreductase, structural
genomics, PSI-2; HET: MSE; 1.76A {Silicibacter pomeroyi}
Length = 175
Score = 26.9 bits (60), Expect = 2.9
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 7/65 (10%)
Query: 114 RDDATKTALNPDQVQYYFQLAQQHQAALQQNNQGATTT--SATPTLVVNG----GNSGAQ 167
A + L+ +Q+Q + A + A + Q+ A + TP+ VV G
Sbjct: 104 LRIAREVGLDTEQLQRDME-APEVTAHIAQSMALAQKLGFNGTPSFVVEDALVPGFVEQS 162
Query: 168 QIQTI 172
Q+Q
Sbjct: 163 QLQDA 167
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 25.7 bits (56), Expect = 3.5
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 25 LPLAR-IKKIMK--LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRN 81
LP +R ++I A+A + +AAE F+ L A++ T R TL
Sbjct: 7 LPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPK 66
Query: 82 DIAMA 86
D+ +A
Sbjct: 67 DVQLA 71
>3h93_A Thiol:disulfide interchange protein DSBA; disulfide bond,
redox-active center, transcription regulator; HET: MSE
GOL; 1.50A {Pseudomonas aeruginosa PAO1}
Length = 192
Score = 27.1 bits (59), Expect = 3.6
Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 83 IAMAITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQ 142
+ ++D+ + + + + +E K AT D ++ ++ + + + ++
Sbjct: 81 LESMGVEHDVHNAVFEAIHKEHKKLATPEEMADFLAGKGVDKEKFLSTYN-SFAIKGQME 139
Query: 143 QNNQGATT--TSATPTLVVNG 161
+ + A + PT+VVNG
Sbjct: 140 KAKKLAMAYQVTGVPTMVVNG 160
>2znm_A Thiol:disulfide interchange protein DSBA; thioredoxin fold,
DSBA-like, oxidoreductase; 2.30A {Neisseria meningitidis
serogroup B} PDB: 3dvx_A
Length = 195
Score = 26.4 bits (57), Expect = 5.3
Identities = 7/80 (8%), Positives = 25/80 (31%), Gaps = 3/80 (3%)
Query: 84 AMAITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQQ 143
+ + ++ + ++ + ++ + + + AA +
Sbjct: 80 LSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYD-SPEAAAAALK 138
Query: 144 NNQGATT--TSATPTLVVNG 161
+ +TPT++V G
Sbjct: 139 MQKLTEQYRIDSTPTVIVGG 158
>2qvb_A Haloalkane dehalogenase 3; RV2579, alpha-beta hydrolase protei
structural genomics consortium, TBSGC, hydrolase; 1.19A
{Mycobacterium tuberculosis} PDB: 2o2i_A 2o2h_A
Length = 297
Score = 26.6 bits (59), Expect = 5.5
Identities = 15/123 (12%), Positives = 29/123 (23%), Gaps = 4/123 (3%)
Query: 41 KMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAITKYDMFDFLIDIV 100
+ EA + A+ + + + L+ N + + L D
Sbjct: 126 GIAFMEAIVTPMTWADWPPAVRGVFQGFRSPQGEPMALEHNIFVERVLPGAILRQLSD-- 183
Query: 101 PREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQAALQQNNQGATTTSATPTLVVN 160
EE+ P + AL + + P L +N
Sbjct: 184 --EEMNHYRRPFVNGGEDRRPTLSWPRNLPIDGEPAEVVALVNEYRSWLEETDMPKLFIN 241
Query: 161 GGN 163
Sbjct: 242 AEP 244
>3hz8_A Thiol:disulfide interchange protein DSBA; thiol-oxidoreductase,
disulfide bond; 1.45A {Neisseria meningitidis MC58} PDB:
3dvw_A 3a3t_A
Length = 193
Score = 25.9 bits (56), Expect = 8.2
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 117 ATKTALNPDQVQYYFQLAQQHQAALQQNNQGATTT--SATPTLVVNG-----GNSGAQQI 169
+TA + +V ++ + + QA + + T PT++V G +
Sbjct: 117 GEQTAFDGKKVLAAYE-SPESQARADKMQELTETFQIDGVPTVIVGGKYKVEFADWESGM 175
Query: 170 QTIPMLL 176
TI +L
Sbjct: 176 NTIDLLA 182
>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex,
MERR-family transcription activator, MU binding protein;
HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3
d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A*
3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A*
3d6y_A* 1bow_A 2bow_A*
Length = 278
Score = 25.9 bits (57), Expect = 8.8
Identities = 15/89 (16%), Positives = 25/89 (28%), Gaps = 12/89 (13%)
Query: 18 LDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRT 77
LK PL +KK L+ A E IR + +T
Sbjct: 57 KSLKYIGTPLEEMKKAQDLEM------------EELFAFYTEQERQIREKLDFLSALEQT 104
Query: 78 LQRNDIAMAITKYDMFDFLIDIVPREEVK 106
+ M + ++ EE++
Sbjct: 105 ISLVKKRMKRQMEYPALGEVFVLDEEEIR 133
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 0.130 0.365
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,740,411
Number of extensions: 155121
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 46
Length of query: 191
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 103
Effective length of database: 4,244,745
Effective search space: 437208735
Effective search space used: 437208735
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: 54 (24.8 bits)