RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8980
(355 letters)
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 127 bits (321), Expect = 6e-37
Identities = 73/85 (85%), Positives = 78/85 (91%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC ITVSQVSNWFGNKRIRYK
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 287 KNIGKAQEEANLYAAKKAAGASPYS 311
KNIGK QEEAN+YAAK A A+ S
Sbjct: 61 KNIGKFQEEANIYAAKTAVTATNVS 85
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 122 bits (308), Expect = 3e-35
Identities = 67/73 (91%), Positives = 71/73 (97%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC ITVSQVSNWFGNKRIRYK
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 287 KNIGKAQEEANLY 299
KNIGK QEEAN+Y
Sbjct: 61 KNIGKFQEEANIY 73
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 110 bits (278), Expect = 5e-31
Identities = 51/62 (82%), Positives = 56/62 (90%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+ R+ +KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC ITVSQVSNWFGNKRIRYK
Sbjct: 3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
Query: 287 KN 288
KN
Sbjct: 63 KN 64
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 94.7 bits (236), Expect = 8e-25
Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 231 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNIG 290
F K A+ I+ + + HL++PYPSEE K++LA+ +T+ QV+NWF N R R + +
Sbjct: 2 SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI 61
Query: 291 KAQEEA 296
A
Sbjct: 62 DQSNRA 67
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 93.7 bits (233), Expect = 3e-24
Identities = 22/68 (32%), Positives = 41/68 (60%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
++++ N ++ +IL ++ Y H YPSEE K+ L+ K N+++ Q+SNWF N R R
Sbjct: 6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRI 65
Query: 286 KKNIGKAQ 293
++ + +
Sbjct: 66 LPDMLQQR 73
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 94.1 bits (234), Expect = 3e-24
Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 12/96 (12%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
K++ +IL ++ Y H N YPSE+ K L+++ +++ QV NWF N R R
Sbjct: 5 HHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLL 64
Query: 287 KNIGKAQEEANLYAAKKAAGASPYSMGPSSQGTPTP 322
+ + G P S +G
Sbjct: 65 PD------------MLRKDGKDPNQFTISRRGAKIS 88
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 93.2 bits (232), Expect = 4e-24
Identities = 21/63 (33%), Positives = 40/63 (63%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
+ KR K A+ ++ + + H+ +PYP+E+ K+++A + N+T+ QV+NWF N R R
Sbjct: 6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
Query: 286 KKN 288
++
Sbjct: 66 LQS 68
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 91.6 bits (228), Expect = 9e-24
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 229 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R R F+K+ IL +F ++ NPY + E L + +++ Q+ NW N+R + K
Sbjct: 1 RGHR-FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription
regulation, transcriptional repression, DNA- binding
protein; HET: DNA; 2.25A {Saccharomyces cerevisiae}
SCOP: a.4.1.1
Length = 87
Score = 91.8 bits (228), Expect = 2e-23
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+ F+K+ IL +F ++ NPY + E L + +++ Q+ NW N+R + K
Sbjct: 28 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 90.2 bits (224), Expect = 7e-23
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
+ F+K+ IL +F ++ NPY + E L + +++ Q+ NW +R +K
Sbjct: 3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARR-AKEK 61
Query: 288 NIGKAQEEANLYAAKKAAG 306
I A E A+L + + A
Sbjct: 62 TITIAPELADLLSGEPLAK 80
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 80.4 bits (197), Expect = 8e-18
Identities = 35/233 (15%), Positives = 70/233 (30%), Gaps = 38/233 (16%)
Query: 76 IKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAASGGPGQP 135
+KE L+ E+ +++ D A+ + G + G Q
Sbjct: 3 LKELQALNTEEAAEQRAEVDRMLSEDPWRAAKMIKGYMQQHNIPQREVVD---VTGLNQS 59
Query: 136 DN-AIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERM 194
+ K + +Y + K + +F V QS +++
Sbjct: 60 HLSQHLNKGTPMKTQKRAALYTWYVRKQREILRQFNQTV------QSSGNMTDKSSQDQL 113
Query: 195 VQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPY 254
+ + + + + + RR R + + +IL + +
Sbjct: 114 LFLFPEFSQQSHGPGQSDDACSEPTNKKM----RRNRFKWGPASQQILYQAY---DRQKN 166
Query: 255 PSEEAKEELARKCN---------------------ITVSQVSNWFGNKRIRYK 286
PS+E +E L +CN +T +V NWF N+R
Sbjct: 167 PSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor,
structural genomics, loop insertion, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 95
Score = 67.7 bits (165), Expect = 2e-14
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 18/85 (21%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITVS 272
R R + K+ ++ YF N YP E +EE+A CN +T
Sbjct: 8 RGSRFTWRKECLAVMESYFNE---NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64
Query: 273 QVSNWFGNKRIRYKKNIGKAQEEAN 297
+V NWF N+R K+ A +
Sbjct: 65 KVYNWFANRRKEIKRRANIAAILES 89
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 59.4 bits (144), Expect = 5e-12
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R +K+ L F L + +P + L + S++ WF + R R ++
Sbjct: 5 HHHHRKKTKEQIAHLKASF---LQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
Query: 288 NIGK 291
I
Sbjct: 62 GIVH 65
>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 = 65.6 bits (159), Expect = 8e-12
Identities = 62/363 (17%), Positives = 105/363 (28%), Gaps = 111/363 (30%)
Query: 1 MDDRMH---------PVGIMGQQQAYGLDHGTPTPDLEPRKQDIGEILQQIMNITDQCLD 51
MD ++ P ++ Q L + ++P + I +
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQK--LLY-----QIDPNWTSRSDHSSNI----KLRIH 228
Query: 52 EAQARKHTLNCHRMKP-SL--------------FSVLCEIKEKTVLSLRNTQ-------- 88
QA L + L F++ C K +L+ R Q
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC----KILLTTRFKQVTDFLSAA 284
Query: 89 -----EEEPPDPQLMRLDNM-LIAEGVAG------PEKGGGANAAASASAAAS--GGPGQ 134
+ L + L+ + P + N + A S G
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLK-YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 135 PDNAIEHSDYRAKLAQIRQIYHQELEKYE-----QACNEF------TTHVMNLLREQSRT 183
DN +H + KL I + LE E + F T +++L+
Sbjct: 344 WDN-WKHVNCD-KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV-- 399
Query: 184 RPITPKEIERMVQIIHKKFSSIQMQLKQST-------------CEAVMILRSRFLDARRK 230
++ +V +HK S ++ Q K+ST E L +D
Sbjct: 400 ---IKSDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNI 455
Query: 231 RRNFSKQ--ASEILNEYFYS----HLSNPYPSEEAKEELARKC--NITVSQVSNWFGNKR 282
+ F L++YFYS HL N E + L R + + K
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE--RMTLFRMVFLDF------RFLEQK- 506
Query: 283 IRY 285
IR+
Sbjct: 507 IRH 509
Score = 43.3 bits (101), Expect = 1e-04
Identities = 41/324 (12%), Positives = 86/324 (26%), Gaps = 114/324 (35%)
Query: 27 DLEPRKQDIG--EILQQIMNITDQCLDEAQARKHTLNCHRMKPSLFSVLC--EIKEKTVL 82
D E + +IL A +C ++ S+L EI ++
Sbjct: 8 DFETGEHQYQYKDILSVFE----------DAFVDNFDCKDVQDMPKSILSKEEIDH--II 55
Query: 83 SLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAASGGPGQPDNAIEHS 142
+ +RL L+++ + +
Sbjct: 56 ------MSKDAVSGTLRLFWTLLSKQ-------------EEMVQKFVEEVLRIN------ 90
Query: 143 DYRAKLAQIRQIYHQ---ELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIH 199
Y+ ++ I+ Q Y + + R + + + R
Sbjct: 91 -YKFLMSPIKTEQRQPSMMTRMYIEQRD----------RLYNDNQVFAKYNVSR-----L 134
Query: 200 KKFSSIQ---MQLKQS-------------TCEAVMILRSRFLDARRKRR----NFSKQAS 239
+ + ++ ++L+ + T A+ + S + + + N S
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 240 -----EILNEYFY----------SHLSN-PYPSEEAKEELAR--------KCNITVSQVS 275
E+L + Y H SN + EL R C + + V
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 276 NW-----FGNK-RI----RYKKNI 289
N F +I R+K+
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVT 278
Score = 42.1 bits (98), Expect = 2e-04
Identities = 36/301 (11%), Positives = 88/301 (29%), Gaps = 82/301 (27%)
Query: 19 LDH--GTPTPDLEPR--------KQD------IGEILQQ----IMN-ITDQCLDEAQARK 57
+DH + KQ+ + E+L+ +M+ I + + +
Sbjct: 51 IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR 110
Query: 58 HTLNCH-RMK--PSLFSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNM--LIAEGVAGP 112
+ R+ +F+ + + L LR L+ L ++ +GV G
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA---------LLELRPAKNVLIDGVLG- 160
Query: 113 EKGGGANAAASASAAASGGPGQPDNAI-------EHSDYRAKLAQIRQIYHQELEKYEQA 165
G A + + D I +S L ++++ +Q +
Sbjct: 161 ---SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP-ETVLEMLQKLLYQIDPNWTSR 216
Query: 166 CNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILR---- 221
+ + + + Q+ R + + K + +++L
Sbjct: 217 SDHSSNIKLRIHSIQAELRRL----------LKSKPY-----------ENCLLVLLNVQN 255
Query: 222 SRFLDA-----R-----RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITV 271
++ +A + R ++ ++ H S +E K L + +
Sbjct: 256 AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP 315
Query: 272 S 272
Sbjct: 316 Q 316
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 58.6 bits (142), Expect = 1e-11
Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 3/68 (4%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
A + S + L F N +P + E L + ++ +V WF ++R
Sbjct: 7 GASIYKNKKSHEQLSALKGSF---CRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHC 63
Query: 286 KKNIGKAQ 293
+ G
Sbjct: 64 RNLKGSRS 71
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 71
Score = 57.9 bits (140), Expect = 2e-11
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R R S +A IL + H YP +EA L+ + ++ + +F N+R K
Sbjct: 8 PRSRTKISLEALGILQSFI--HDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65
Query: 288 N 288
+
Sbjct: 66 S 66
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding
proteins/DNA), complex, DNA- binding protein, DNA; HET:
DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB:
1f43_A 1yrn_A*
Length = 61
Score = 56.8 bits (138), Expect = 4e-11
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+ + + + S QA L E F + + KEE+A+KC IT QV WF NKR+R K
Sbjct: 5 SPKGKSSISPQARAFLEEVFRRK---QSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 55.4 bits (133), Expect = 1e-09
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 3/102 (2%)
Query: 186 ITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 245
ITPK +++ ++ K + +++ ++ + + R++R +F+ QA E LN Y
Sbjct: 52 ITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAY 111
Query: 246 FYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
F NP P+ + E+A++ N V WF N+R K
Sbjct: 112 F---EKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 53.7 bits (128), Expect = 2e-09
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 24/81 (29%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 268
RR R + + +IL + + PS+E +E L +CN
Sbjct: 10 RRNRFKWGPASQQILFQAYER---QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 66
Query: 269 --ITVSQVSNWFGNKRIRYKK 287
+T +V NWF N+R
Sbjct: 67 NLVTEVRVYNWFANRRKEEAF 87
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 52.6 bits (126), Expect = 2e-09
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
K + + + L F NP P +E + L + +T ++ +WF +R +
Sbjct: 7 GPTKYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVN 63
Query: 287 KNIGKAQEEAN 297
K ++
Sbjct: 64 AEETKKSGPSS 74
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 51.7 bits (124), Expect = 4e-09
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+ + ++ EIL F + N +P +A + +T Q WF + ++
Sbjct: 2 SAQTVSGPTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
Query: 287 KNIGKAQEEANL 298
++ G E ++
Sbjct: 60 RSEGLPSECRSV 71
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 54.9 bits (131), Expect = 4e-09
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 24/80 (30%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 268
RR R + + +IL + + PS+E +E L +CN
Sbjct: 116 RRNRFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 172
Query: 269 --ITVSQVSNWFGNKRIRYK 286
+T +V NWF N+R
Sbjct: 173 NLVTEVRVYNWFANRRKEEA 192
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 54.1 bits (129), Expect = 4e-09
Identities = 18/110 (16%), Positives = 45/110 (40%), Gaps = 5/110 (4%)
Query: 178 REQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQ 237
+ R + + + + ++ S++++ + + R ++ R F+
Sbjct: 50 SKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGN--TPKKPRLVFTDV 107
Query: 238 ASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
L+ F + PS+E + ++++ + +S VSN+F N R R
Sbjct: 108 QRRTLHAIFKEN---KRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 51.2 bits (123), Expect = 6e-09
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R R F+ +L ++F + N YP ++ E+L+ N+ + WF N R + +K
Sbjct: 8 RSSRTRFTDYQLRVLQDFFDA---NAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
Query: 288 N 288
+
Sbjct: 65 S 65
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 50.4 bits (121), Expect = 1e-08
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
+R R + +L +YF N PSEE +E+A K + + +WF N + ++
Sbjct: 8 KRPRTRITDDQLRVLRQYF---DINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64
Query: 288 N 288
+
Sbjct: 65 S 65
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU
domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP:
a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A
1oct_C* 1pou_A 1pog_A 1hdp_A
Length = 160
Score = 51.5 bits (123), Expect = 3e-08
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R+KR + L + F + N P+ E +A + N+ + WF N+R + K+
Sbjct: 102 RKKRTSIETNIRVALEKSF---MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein,
homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP:
a.4.1.1
Length = 66
Score = 48.9 bits (117), Expect = 3e-08
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 3/66 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R R +++ L + + NP P KE+L ++ + WF NKR + KK
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAA---NPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
Query: 288 NIGKAQ 293
+
Sbjct: 61 RSIMMK 66
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 51.1 bits (122), Expect = 4e-08
Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 8/102 (7%)
Query: 186 ITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 245
++ K ++ I+ K + + R R ++R S A + L +
Sbjct: 51 LSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKR-----KRRTTISIAAKDALERH 105
Query: 246 FYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
F + PS + +A + N+ V WF N+R R K+
Sbjct: 106 F---GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 50.5 bits (120), Expect = 6e-08
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
+RKR + + L F L +P PS + +A + + V WF N+R +
Sbjct: 95 ARKRKRTSIENRVRWSLETMF---LKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKG 151
Query: 286 KKN 288
K++
Sbjct: 152 KRS 154
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 47.9 bits (114), Expect = 8e-08
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 222 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGN 280
S L+ R+KR ++K Q E+ EY N + +++ + ++ N++ QV+ WF N
Sbjct: 2 SHMLEGRKKRVPYTKVQLKELEREYAT----NKFITKDKRRRISATTNLSERQVTIWFQN 57
Query: 281 KRIRYKKNIGKAQEEA 296
+R++ KK I K + +
Sbjct: 58 RRVKEKKVINKLKTTS 73
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 80
Score = 47.9 bits (114), Expect = 1e-07
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
+R R + + EIL + + L + P+ + + +A + + V WF N R R +K
Sbjct: 18 KRLRTTITPEQLEILYQKY---LLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
Query: 288 N 288
+
Sbjct: 75 S 75
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding
domain, transcription, structural genomics, NPPSFA; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 72
Score = 46.7 bits (111), Expect = 3e-07
Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 222 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNK 281
+ N + ++ L + F S YP E+ + L+++ + +V ++ WF ++
Sbjct: 4 GSSGGIKDSPVN-KVEPNDTLEKVFVSV--TKYPDEKRLKGLSKQLDWSVRKIQCWFRHR 60
Query: 282 RIRYKKN 288
R + K +
Sbjct: 61 RNQDKPS 67
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 48.9 bits (116), Expect = 3e-07
Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 6/102 (5%)
Query: 186 ITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 245
++ K + ++ +++K T + + R R+KR + L +
Sbjct: 61 LSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRK---RKKRTSIEVGVKGALESH 117
Query: 246 FYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
F L P PS LA + V WF N+R + K+
Sbjct: 118 F---LKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant,
DNA binding protein, developmental protein, disease
mutation, DNA-binding; NMR {Homo sapiens}
Length = 67
Score = 46.2 bits (110), Expect = 3e-07
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RR R F++ E+L F N YP + E+LA+K N+ + ++ WF N+R + K+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRV---NCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
Query: 288 NIGKAQ 293
+ ++Q
Sbjct: 59 SHRESQ 64
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor,
homeodomain, structural genomics, oxford production
facility, OPPF, transcription; 2.60A {Homo sapiens}
Length = 96
Score = 46.7 bits (110), Expect = 4e-07
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
K + + +L F + +PS E ++LA++ + + + +WFG+ R +K
Sbjct: 26 TGKICKKTPEQLHMLKSAF---VRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
Query: 288 N 288
Sbjct: 83 G 83
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 89
Score = 45.7 bits (108), Expect = 8e-07
Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
A +K + ++ +IL + F L + +P++ + L + ++ ++ +WF +R
Sbjct: 13 APQKFKEKTQGQVKILEDSF---LKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRD 69
Query: 287 KNIGKAQEEANLYAAKKAAG 306
+ + ++G
Sbjct: 70 SMEQAVLDSMGSGKSGPSSG 89
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA
complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P
2lkx_A* 2l7m_P
Length = 68
Score = 45.0 bits (107), Expect = 8e-07
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RR+R +F+ Q + L F N YP +EE+A N+T ++V WF N+R +++K
Sbjct: 4 RRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 288 N 288
Sbjct: 61 R 61
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA
binding helix- turn-helix motif, structural genomics,
NPPSFA; NMR {Mus musculus}
Length = 80
Score = 45.1 bits (107), Expect = 1e-06
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RR+R F++ ++L F YP +EE+A K N+ S+V WF N+R + ++
Sbjct: 8 RRERTTFTRAQLDVLEALF---AKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64
Query: 288 N 288
Sbjct: 65 Q 65
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain,
transcription factor, leucine zipper- containing factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 76
Score = 44.6 bits (105), Expect = 1e-06
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 229 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKN 288
+ +K+ IL +F L + E ++L + + ++ WFG+ R K
Sbjct: 5 SSGKRKTKEQLAILKSFF---LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61
>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 = 49.3 bits (117), Expect = 1e-06
Identities = 73/459 (15%), Positives = 129/459 (28%), Gaps = 161/459 (35%)
Query: 24 PTP------DLEPRKQDIGEILQQIMNITDQCLDEAQARKHTLNCHRMKPSLFSVLCEIK 77
P P D EP E++ + + ++ ++ + L L E
Sbjct: 42 PEPTEGFAADDEP--TTPAELVGKFLGYVSSLVEPSKV-------GQFDQVLNLCLTEF- 91
Query: 78 EKTVLSLRN----TQEEEPPDPQLMRLDNMLI-----AEGVAGPEKGGGANAA---ASAS 125
E L + + + + LI A +A +N+A A
Sbjct: 92 ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE 151
Query: 126 AAAS-----GGPGQPDNAIEHSDYRAKLAQIRQIYH-----------------QELEKYE 163
A GG G D DY ++R +Y EL +
Sbjct: 152 GNAQLVAIFGGQGNTD------DY---FEELRDLYQTYHVLVGDLIKFSAETLSELIRTT 202
Query: 164 QACNEFTTHVMNL---LREQSRTR--------PITPKEIERMVQIIH---------KKFS 203
+ T +N+ L S T PI+ I ++Q+ H
Sbjct: 203 LDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG-VIQLAHYVVTAKLLGFTPG 261
Query: 204 SIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFY----SHLSNP------ 253
++ LK +T + ++ + + +F + + F+ + + P
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 254 ------------YPS---------EEAKEELARKCN--------ITVSQVSNWFGNKRIR 284
PS +E ++ K N + +S V N
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV-----NGA-- 374
Query: 285 YKKNI---GKAQEEANLYA------AKKAAGASPYSMGPSSQ------------GTP--T 321
KN+ G Q LY KA S P S+ +P +
Sbjct: 375 --KNLVVSGPPQS---LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHS 429
Query: 322 PMMSPAPPGGPQDSMGYSVNMNGD------YSSPMSGYD 354
++ PA +D + +V+ N Y G D
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVY-DTFDGSD 467
Score = 36.6 bits (84), Expect = 0.015
Identities = 40/227 (17%), Positives = 69/227 (30%), Gaps = 96/227 (42%)
Query: 14 QQAYGL--------------DHGTPTPDLEPRKQDIGEILQQIM-NITDQCLDEAQARKH 58
+AY + G P+P M +I++ L + Q + +
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEGVPSP----------------MLSISN--LTQEQVQDY 352
Query: 59 --TLNCHRMKPSLFSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKG- 115
N H P+ ++ +SL N N++ V+GP +
Sbjct: 353 VNKTNSH--LPA--------GKQVEISLVNGA------------KNLV----VSGPPQSL 386
Query: 116 GGANAAASASAAASGGPGQ-----------------PDNAIEHSDYRAKLAQIRQIYHQE 158
G N + A S G Q P + HS L + +++
Sbjct: 387 YGLNLTLRKAKAPS-GLDQSRIPFSERKLKFSNRFLPVASPFHSHL---LVPASDLINKD 442
Query: 159 LEKYEQACN--EFTTHVMNL-----LREQSRTRPITPKEIERMVQII 198
L K + N + V + LR S + I+ R+V I
Sbjct: 443 LVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGS--ISE----RIVDCI 483
Score = 30.4 bits (68), Expect = 1.1
Identities = 23/180 (12%), Positives = 54/180 (30%), Gaps = 52/180 (28%)
Query: 143 DYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIH--- 199
D + ++ + + + F+ +++++ P + IH
Sbjct: 1634 DLYKTSKAAQDVW-NRADNHFKDTYGFS--ILDIVINN-------PVNL-----TIHFGG 1678
Query: 200 KKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEA 259
+K I+ E +D + K K+ +E Y +
Sbjct: 1679 EKGKRIRENYSAMIFET-------IVDGKLKTEKIFKEINEHSTSYTFRS---E------ 1722
Query: 260 KEELARKCN----ITVSQVSNWFGNKRIRYKKNIGKAQEEANL-------YAAKKA-AGA 307
K L+ +T+ + + + + ++ K G +A YAA + A
Sbjct: 1723 KGLLSATQFTQPALTLMEKAAF---EDLKSK---GLIPADATFAGHSLGEYAALASLADV 1776
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 44.4 bits (105), Expect = 2e-06
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
+R R +F + YF N P + ++LA+K +T + WF N R ++++
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAI---NHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
Query: 288 NIGKAQ 293
N+ + +
Sbjct: 65 NLLRQE 70
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac
development, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 72
Score = 44.3 bits (105), Expect = 2e-06
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
++ EIL F + N +P +A + +T Q WF + ++
Sbjct: 1 GSEGAATMTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
Query: 287 KN 288
++
Sbjct: 59 RS 60
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 44.3 bits (105), Expect = 2e-06
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 228 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
RR R F+ + E L F + YP +E+LARK ++ +V WF N+R +++
Sbjct: 8 RRHRTIFTDEQLEALENLFQETK----YPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
Query: 287 KN 288
++
Sbjct: 64 RS 65
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 44.6 bits (105), Expect = 2e-06
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 224 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRI 283
F + K + + + +L F L++ ++E L + +T ++ WF K
Sbjct: 10 FTPQKFKEK--TAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEK-- 62
Query: 284 RYKKNIGKAQEEANLYAAKKAAGASP 309
+ K + + + E + A ++G S
Sbjct: 63 KKSKALKEEKMEIDESNAGSSSGPSS 88
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation,
helix-turn-helix, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 70
Score = 43.7 bits (103), Expect = 2e-06
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 222 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGN 280
S R+KR +SK Q E+ EY N + +++ + +++ +++ Q++ WF N
Sbjct: 2 SSGSSGRKKRIPYSKGQLRELEREYAA----NKFITKDKRRKISAATSLSERQITIWFQN 57
Query: 281 KRIRYKK 287
+R++ KK
Sbjct: 58 RRVKEKK 64
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 43.5 bits (103), Expect = 4e-06
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RR R FS + L F YP +EELA++ N+T +++ WF N+R R +K
Sbjct: 19 RRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex,
HOX hexapeptide, TALE homeodomain, homeodomain
interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB:
1san_A
Length = 77
Score = 43.3 bits (102), Expect = 4e-06
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 226 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
R+KR ++K Q E+ E+ + N Y + + + E+AR N+T QV WF N+R++
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLF----NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
Query: 285 YKK 287
KK
Sbjct: 68 MKK 70
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 42.8 bits (101), Expect = 7e-06
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 228 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+R R +F+++ E L + F +H YP A+E LA K ++ +++ WF N+R +++
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTH----YPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 287 KN 288
+
Sbjct: 64 RE 65
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA
binding protein/DNA), transcription/DNA complex; HET:
DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB:
1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A
1du0_A* 1ztr_A 1enh_A 2p81_A
Length = 61
Score = 41.9 bits (99), Expect = 7e-06
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 225 LDARRKRRNFS-KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRI 283
+ +R R FS +Q + + E+ N Y +E +++L+ + + +Q+ WF NKR
Sbjct: 1 MAEKRPRTAFSSEQLARLKREFNE----NRYLTERRRQQLSSELGLNEAQIKIWFKNKRA 56
Query: 284 RYKKN 288
+ KK+
Sbjct: 57 KIKKS 61
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 102
Score = 41.4 bits (96), Expect = 3e-05
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 24/77 (31%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------ 268
+ R R + + +IL + + PS+E +E L +CN
Sbjct: 6 SGRNRFKWGPASQQILYQAYDR---QKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 62
Query: 269 ---ITVSQVSNWFGNKR 282
+T +V NWF N+R
Sbjct: 63 SNLVTEVRVYNWFANRR 79
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 40.0 bits (94), Expect = 5e-05
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 228 RRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
RRKRR FS+ L F Y S +E LA ++T +QV WF N R + K
Sbjct: 2 RRKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
Query: 287 KNIGKAQEE 295
+ +
Sbjct: 59 RQAKDKAAQ 67
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 64
Score = 39.8 bits (93), Expect = 5e-05
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 230 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKR 282
+ + Q + IL E ++ +P E+ E L+++ + V + WF +R
Sbjct: 3 SGSSGTAQPNAIL-EKVFTA-ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 53
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 39.5 bits (93), Expect = 6e-05
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 227 ARRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
RRK R FS+ L F Y S +++LA +T +QV WF N+R +
Sbjct: 1 GRRKPRVLFSQAQVYELERRF---KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKS 57
Query: 286 K 286
K
Sbjct: 58 K 58
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix,
helix-turn-helix; NMR {Drosophila melanogaster} SCOP:
a.4.1.1
Length = 68
Score = 39.7 bits (93), Expect = 7e-05
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 228 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
RR R F+ Q +E+ + Y + +L+ K + +QV WF N+R R+K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQ----GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
Query: 287 KNIGKAQEEA 296
+ ++++
Sbjct: 59 IQSDQHKDQS 68
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A
1hom_A 1ftz_A
Length = 68
Score = 39.3 bits (92), Expect = 7e-05
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 228 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+R R+ +++ Q E+ E+ + N Y + + E+A ++T Q+ WF N+R+++K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
Query: 287 K 287
K
Sbjct: 59 K 59
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 38.8 bits (91), Expect = 1e-04
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R+ R F+ L F Y S + E + ++T +QV WF N+R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQ---KQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex,
DNA-binding protein, protein/DNA complex; HET: DNA;
2.35A {Homo sapiens} SCOP: a.4.1.1
Length = 97
Score = 39.9 bits (93), Expect = 1e-04
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 207 MQLKQSTCEAVMILRSRFLDARRKRRNF-SKQASEILNEYFYSHLSNPYPSEEAKEELAR 265
M++K++ + + R NF ++Q +E+ E+ + N Y S + E+A
Sbjct: 14 MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHF----NKYLSRARRVEIAA 69
Query: 266 KCNITVSQVSNWFGNKRIRYKK 287
+ +QV WF N+R++ KK
Sbjct: 70 TLELNETQVKIWFQNRRMKQKK 91
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 38.5 bits (90), Expect = 1e-04
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 228 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
RR R F++ Q + E++ Y S + ELA + N+ S + WF N+R++ K
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYK----ENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
Query: 287 K 287
+
Sbjct: 58 R 58
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 38.4 bits (90), Expect = 1e-04
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 231 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKN 288
F+ E L + F YP +EELA K +T +++ WF N+R +++K
Sbjct: 3 HMTFTSFQLEELEKAFSR---THYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 38.5 bits (90), Expect = 2e-04
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 226 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
+R R +++ Q E+ E+ + N Y S + ELA N+T + WF N+R++
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLF----NKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
Query: 285 YKK 287
+KK
Sbjct: 58 WKK 60
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 38.5 bits (90), Expect = 2e-04
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
R+ R +S L F Y + + ELA +T +QV WF NKR + KK
Sbjct: 8 RKPRTIYSSFQLAALQRRFQK---TQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 37.6 bits (88), Expect = 3e-04
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
++ R FS+ L + F Y S + +EL+ N++ QV WF N+R++ K+
Sbjct: 4 QKMRTVFSQAQLCALKDRFQK---QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 38.4 bits (88), Expect = 3e-04
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 227 ARRKRRNFSKQASEILNEYFYSHLSN-PYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
A + R FS + L +Y+ + +++ E E +A + N+ V W GN+R +Y
Sbjct: 8 ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67
Query: 286 KK 287
+
Sbjct: 68 RL 69
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 37.4 bits (87), Expect = 4e-04
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 226 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
+ + FS Q E+ ++ Y S ++ LA+ ++ QV WF N+R +
Sbjct: 6 SGKGGQVRFSNDQTIELEKKFET----QKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
Query: 285 YKK 287
+++
Sbjct: 62 WRR 64
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA
binding, homeodomain, homeotic proteins, development,
specificity; HET: DNA; 2.40A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 9ant_A*
Length = 81
Score = 37.5 bits (87), Expect = 5e-04
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 226 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
RR R+ +++ Q E+ E+ N Y + + E+A ++T Q+ WF N+R++
Sbjct: 19 LRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 285 YKK 287
KK
Sbjct: 75 LKK 77
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 37.5 bits (87), Expect = 5e-04
Identities = 17/63 (26%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 226 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIR 284
+ +R+R ++++ Q E+ E+ + N Y + + E+A ++T Q+ WF N+R++
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Query: 285 YKK 287
+KK
Sbjct: 83 WKK 85
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 37.5 bits (87), Expect = 6e-04
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
++ R FS +LN+ F Y S + +EL+ N++ QV WF N+R++ K+
Sbjct: 23 QKTRTVFSSTQLCVLNDRFQR---QKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic
development, complex (homeodomain/DNA); HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P*
1vnd_A 1qry_A
Length = 77
Score = 37.0 bits (86), Expect = 6e-04
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 228 RRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYK 286
+RKRR F+K + L F Y S +E LA +T +QV WF N R + K
Sbjct: 9 KRKRRVLFTKAQTYELERRF---RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
Query: 287 KNIGKAQEEAN 297
+ + E +
Sbjct: 66 RAQNEKGYEGH 76
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 37.1 bits (86), Expect = 0.001
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
++ R +F++ L + F Y + + LAR +T +QV WF N+R ++++
Sbjct: 18 KKPRTSFTRIQVAELEKRF---HKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 288 NIGKAQEEANLYAAKK 303
+ EA AA +
Sbjct: 75 Q-TAEEREAERQAANR 89
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 35.4 bits (82), Expect = 0.002
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
+ S L F Y S + LA+ +T +QV WF N+R + K+
Sbjct: 5 HHHHSHMSHTQVIELERKFSH---QKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 35.5 bits (82), Expect = 0.002
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 228 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
RR R F++ L + F Y S + +LA ++ QV W+ N+R+++KK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEK---QKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 33.4 bits (77), Expect = 0.007
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 251 SNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKK 287
Y + + LA+ +T +QV WF N+R ++++
Sbjct: 18 RQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 31.5 bits (71), Expect = 0.047
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 4/62 (6%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
+ S +L Y+ N PS E ++A N+ + V WF +
Sbjct: 3 SGSSGQPPLKNLLS-LLKAYY---ALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQ 58
Query: 286 KK 287
Sbjct: 59 IS 60
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage,
structural evolution, transcription; 1.40A {Xylella
fastidiosa}
Length = 79
Score = 31.1 bits (70), Expect = 0.087
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 262 ELARKCNITVSQVSNWFGNKRI 283
LA + S +SNW R+
Sbjct: 16 ALAASLGVRQSAISNWRARGRV 37
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 32.7 bits (74), Expect = 0.19
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 306 GASPYSMGP----SSQGTPTP-MMSPAPPGGPQDSMGYSVNMNGDYSSPMSGYDS 355
+PY P G+P SP GG + G+ +SP G S
Sbjct: 1482 AGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQS 1536
Score = 29.7 bits (66), Expect = 1.8
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 306 GASPYSMGPSSQGTPTPMMSPAPPGGPQDSMGYSVNMNGDYSSPM 350
ASPY G S G +P S PG S YS + G +SP
Sbjct: 1527 AASPYK-GVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPA 1570
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 29.8 bits (66), Expect = 0.23
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 230 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKN 288
N K +L Y+ N P+ + +++ + V WF +++ N
Sbjct: 8 SPINPYKDHMSVLKAYY---AMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSN 63
>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 = 29.9 bits (66), Expect = 0.82
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 4/24 (16%)
Query: 286 KKNIGKAQEEANLYAAKKAAGASP 309
K+ + K Q LYA A P
Sbjct: 19 KQALKKLQASLKLYADDSA----P 38
>1t95_A Hypothetical protein AF0491; shwachman-bodian-diamond syndrome
protein orthologue, unknown function; 1.90A
{Archaeoglobus fulgidus} SCOP: a.5.8.1 d.235.1.2
d.58.11.3 PDB: 1p9q_C
Length = 240
Score = 29.9 bits (67), Expect = 1.00
Identities = 25/183 (13%), Positives = 48/183 (26%), Gaps = 23/183 (12%)
Query: 70 FSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAAS 129
F VL L+ +E +++L AE V K G A+
Sbjct: 25 FEVLV--DPYLARDLKEGKEVN--------FEDLLAAEEVFKDAKKG--ERASVDELRKI 72
Query: 130 GGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPK 189
G +++ Q E E + + + P P
Sbjct: 73 FGTDDVFEIARK---IILEGEVQITAEQRREMLEAKRKQIINFISRNTIDPRTNAPHPPS 129
Query: 190 EIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR-------NFSKQASEIL 242
IER ++ + ++ + V L+ + + +A L
Sbjct: 130 RIERALEEAKVHIDIFK-SVEAQVKDIVKALKPILPLKFEEMEIAIKIPPEHTGRAISAL 188
Query: 243 NEY 245
+
Sbjct: 189 YNF 191
>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha,
helix-turn-helix, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.35.1.12
Length = 91
Score = 28.2 bits (63), Expect = 1.2
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 261 EELARKCNITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMGPSSQGTP 320
++LA K N ++++ + I + +GK + L K G P GP ++ P
Sbjct: 30 KDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKDIGK-PIEKGPRAKSGP 88
Query: 321 T 321
+
Sbjct: 89 S 89
>2wbm_A MTHSBDS, ribosome maturation protein SDO1 homolog;
shwachman-bodian-diamond syndrome protein; 1.75A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 252
Score = 29.2 bits (65), Expect = 1.6
Identities = 21/183 (11%), Positives = 51/183 (27%), Gaps = 22/183 (12%)
Query: 70 FSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAAS 129
F VL R + ++++L + V + G + A+ +
Sbjct: 39 FEVLV--DPDLAAEFRREDSDVS-------VEDVLAVQEVFRDARKG--DKASEEAMRKV 87
Query: 130 GGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPK 189
P + I+ Q + E + + P PK
Sbjct: 88 FETADPLEVTPV---ILRRGTIQLTAEQRRQMIEDKRLKIINKIAREAINPQNGLPHPPK 144
Query: 190 EIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR-------NFSKQASEIL 242
IE+ ++ + + + + +R++ K R + A ++
Sbjct: 145 RIEKAMEEARVHVDPFK-TVDEQVNIVLKAIRTKIPIKFEKVRVAIKIPGEMAGSAYGVI 203
Query: 243 NEY 245
+ +
Sbjct: 204 SNF 206
>2kdo_A Ribosome maturation protein SBDS; SBDS protein, protein structure,
RNA-interacting protein mutation, phosphoprotein,
ribosome biogenesis; NMR {Homo sapiens} PDB: 2l9n_A
Length = 252
Score = 29.2 bits (65), Expect = 1.6
Identities = 34/164 (20%), Positives = 54/164 (32%), Gaps = 18/164 (10%)
Query: 70 FSVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVA-GPEKGGGANAAASASAAA 128
F + C + V+ R+ E++ LD +L V KG A SA
Sbjct: 29 FEIAC--YKNKVVGWRSGVEKD--------LDEVLQTHSVFVNVSKGQVAKKEDLISA-- 76
Query: 129 SGGPGQPDNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITP 188
D+ E +++ + + EQ + T V + RP T
Sbjct: 77 ----FGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTV 132
Query: 189 KEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR 232
IER ++ IH KQ E + L+ + R R
Sbjct: 133 ILIERAMKDIHYSV-KTNKSTKQQALEVIKQLKEKMKIERAHMR 175
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding
cooperativity, maltose binding protein, MBP, sugar
binding, DNA binding protein; 2.10A {Escherichia coli}
SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A
Length = 421
Score = 29.8 bits (67), Expect = 1.6
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 226 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRY 285
A+ + E + + + KEE+A+KC IT QV WF NKR+R
Sbjct: 363 AAQTAAAAAISPQARAFLEQVF--RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 420
Query: 286 K 286
K
Sbjct: 421 K 421
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 29.3 bits (65), Expect = 2.2
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 304 AAGASPY---SMGPSSQGTPTPMMSPAPPGGPQDSMGYSVNMNGDYSSPMSG 352
A G + Y G ++ +P PG S G+S SP S
Sbjct: 1505 AGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPT--YSPTSP 1554
Score = 29.3 bits (65), Expect = 2.5
Identities = 16/50 (32%), Positives = 17/50 (34%), Gaps = 3/50 (6%)
Query: 307 ASPYSMGPSSQGTPT-PMMSPAPPGGPQDSMGYSVNMNGDYSSPMSGYDS 355
SP S +PT P SP P S YS SP S S
Sbjct: 1545 TSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPS--YSPTSPSYS 1592
Score = 28.5 bits (63), Expect = 3.9
Identities = 14/48 (29%), Positives = 16/48 (33%), Gaps = 4/48 (8%)
Query: 308 SPYSMGPSSQG--TPTPMMSPAPPGGPQDSMGYSVNMNGDYSSPMSGY 353
Y P+S G +P SP P S YS SP S
Sbjct: 1524 GAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYS--PTSPSYSPTSPS 1569
Score = 27.8 bits (61), Expect = 7.0
Identities = 15/51 (29%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 307 ASPYSMGPSSQGTPT-PMMSPAPPGGPQDSMGYSVNMNG-DYSSPMSGYDS 355
SP S +PT P SP P S YS +SP S
Sbjct: 1636 TSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTS 1686
>1u4q_A Spectrin alpha chain, brain; alpha spectrin, three repeats of
spectrin, alpha-helical linker region, 3-helix
coiled-coil, structural protein; 2.50A {Gallus gallus}
SCOP: a.7.1.1 a.7.1.1 a.7.1.1
Length = 322
Score = 29.1 bits (65), Expect = 2.3
Identities = 14/95 (14%), Positives = 31/95 (32%), Gaps = 9/95 (9%)
Query: 149 AQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQ 208
Q + H+ LE A V++ ++ S I +EI++ + + ++
Sbjct: 144 VQNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQL 203
Query: 209 LKQSTCEAVMILRSRFLDARRKRRNFSKQASEILN 243
R + L+ + + F E
Sbjct: 204 AAA---------RGQRLEESLEYQQFVANVEEEEA 229
>3iz5_V 60S ribosomal protein L17 (L22P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_V
Length = 171
Score = 27.6 bits (61), Expect = 2.4
Identities = 6/40 (15%), Positives = 8/40 (20%), Gaps = 3/40 (7%)
Query: 104 LIAEG---VAGPEKGGGANAAASASAAASGGPGQPDNAIE 140
G A A + S P + I
Sbjct: 54 HKQAIPFRRYCGGVGRTAQAKSRHSNGQGRWPAKSARFIL 93
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 29.5 bits (66), Expect = 2.4
Identities = 23/116 (19%), Positives = 38/116 (32%), Gaps = 23/116 (19%)
Query: 189 KEIERMVQIIHKKFSSIQMQ--LKQSTCEAVMILRS----RFLDARRKRRNFSKQ----- 237
EI ++ I + QM LK + +I F+ R K+
Sbjct: 295 GEI---LEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQY 351
Query: 238 ASEILNEYFYSHLSNPYPSEEAKEEL----ARK---CNITVSQVSNW--FGNKRIR 284
A +IL + F H++ E K + C + + FG KR+
Sbjct: 352 AKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 407
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 29.1 bits (65), Expect = 2.9
Identities = 20/116 (17%), Positives = 42/116 (36%), Gaps = 23/116 (19%)
Query: 189 KEIERMVQIIHKKFSSIQMQ--LKQSTCEAVMILRSR----FLDARRKRRNFSKQ----- 237
++I ++ I + QM +K EA +I ++ R +++
Sbjct: 281 RDI---LEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLRY 337
Query: 238 ASEILNEYFYSHLSNPYPSEEAKE----ELARK---CNITVSQVSNW--FGNKRIR 284
A +IL + H++ E K + + C + + + FG KR+
Sbjct: 338 AHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLD 393
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 26.5 bits (59), Expect = 3.0
Identities = 5/22 (22%), Positives = 7/22 (31%)
Query: 261 EELARKCNITVSQVSNWFGNKR 282
L + + VS W N
Sbjct: 25 LWLTETLDKNKTTVSKWCTNDV 46
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, HEL helix motif,
transcription regulator; 3.20A {Streptococcus
pneumoniae}
Length = 158
Score = 28.0 bits (62), Expect = 3.2
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 261 EELARKCNITVSQVSNW 277
E AR I+ + +S +
Sbjct: 18 LEFARIVGISRNSLSRY 34
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics,
PSI-2, protein structure initiative; HET: MSE; 1.65A
{Bacteroides fragilis}
Length = 76
Score = 26.5 bits (59), Expect = 3.2
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 261 EELARKCNITVSQVSNWFGNKR 282
LA + + + +S W NK
Sbjct: 27 RWLAEQMGKSENTISRWCSNKS 48
>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434}
SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A
2r63_A 1sq8_A
Length = 69
Score = 26.4 bits (59), Expect = 3.4
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 261 EELARKCNITVSQVSNW 277
ELA+K T +
Sbjct: 18 AELAQKVGTTQQSIEQL 34
>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix,
DNA-binding, transcription, transcription regulation;
1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB:
3jxb_C 3jxc_L 3jxd_L
Length = 68
Score = 26.4 bits (59), Expect = 3.8
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 261 EELARKCNITVSQVSNW 277
L + ++ +S W
Sbjct: 22 AALGKMVGVSNVAISQW 38
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria
phage P22} SCOP: a.35.1.2
Length = 76
Score = 26.1 bits (58), Expect = 4.7
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 261 EELARKCNITVSQVSNW 277
L + ++ +S W
Sbjct: 22 AALGKMVGVSNVAISQW 38
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 28.0 bits (62), Expect = 4.8
Identities = 7/34 (20%), Positives = 10/34 (29%)
Query: 261 EELARKCNITVSQVSNWFGNKRIRYKKNIGKAQE 294
E +A K + S V F N +
Sbjct: 34 ESVADKMGMGQSGVGALFNGINALNAYNAALLAK 67
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class
I, activator, RNA polymeras holoenzyme, sigma70, open
complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia
coli k-12}
Length = 613
Score = 28.1 bits (62), Expect = 4.8
Identities = 22/145 (15%), Positives = 48/145 (33%), Gaps = 13/145 (8%)
Query: 88 QEEEPPDPQLMRLDNMLIAEGVAGPEKGGGANAAASASAAASGGPGQPDNAIEHSDYRAK 147
EE P + + L E + E + ++ DN+I+ R K
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADD--------DNSIDPELAREK 220
Query: 148 LAQIRQIYHQELEKYEQACNEFTTHVMNL--LREQSRTRPITPKEIERMVQIIHKKFSSI 205
A++R Y + + T + L E + + PK+ + +V + +
Sbjct: 221 FAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRV 280
Query: 206 QM---QLKQSTCEAVMILRSRFLDA 227
+ + + E + + F+
Sbjct: 281 RTQERLIMKLCVEQCKMPKKNFITL 305
>3go9_A Insulinase family protease; IDP00573, structural genomics, for
structural genomics of infectious diseases, csgid, HYDR;
HET: MSE; 1.62A {Yersinia pestis}
Length = 492
Score = 28.3 bits (63), Expect = 4.8
Identities = 21/159 (13%), Positives = 49/159 (30%), Gaps = 27/159 (16%)
Query: 179 EQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQA 238
R ++ E + ++ + + S L A R +
Sbjct: 353 AALRANGLSQAEFDALMTQKNDQLSK--------------------LFATYARTDTDILM 392
Query: 239 SEILNEYFYSHLSNPYPSEEAKEELARKCNITVSQVSNWFGNKRIRYKKNI----GKAQE 294
S+ L S + + P + K A +T+++++ +++ + K +
Sbjct: 393 SQRLR-SQQSGVVDIAPEQYQKLRQAFLSGLTLAELNREL-KQQLSQDTTLVLMQPKGEP 450
Query: 295 EANLYAAKKA-AGASPYSMGPSSQGTPTPMMSPAPPGGP 332
E N+ A ++ G + P + AP
Sbjct: 451 EVNVKALQEIYNGIMAPQTVAEEEVAPAEAVETAPVMPT 489
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural
genomics, PSI-2, protein structure initiative; NMR
{Eubacterium rectale atcc 33656}
Length = 94
Score = 26.6 bits (59), Expect = 5.1
Identities = 4/23 (17%), Positives = 9/23 (39%)
Query: 261 EELARKCNITVSQVSNWFGNKRI 283
E+A+ ++ + W I
Sbjct: 26 LEIAKSIGVSPQTFNTWCKGIAI 48
>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure
initiative, MI center for structural genomics, MCSG,
transcription regulat; HET: MSE; 1.90A {Listeria
innocua}
Length = 114
Score = 26.7 bits (59), Expect = 5.2
Identities = 3/23 (13%), Positives = 9/23 (39%)
Query: 261 EELARKCNITVSQVSNWFGNKRI 283
++A N+ V+ + +
Sbjct: 26 HQIAELLNVQTRTVAYYMSGETK 48
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 27.3 bits (60), Expect = 7.5
Identities = 8/34 (23%), Positives = 10/34 (29%)
Query: 305 AGASPYSMGPSSQGTPTPMMSPAPPGGPQDSMGY 338
G S M P +GT + A Y
Sbjct: 135 GGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQY 168
>3i8b_A Xylulose kinase; strain ATCC 15703 / DSM 20083, 11200J,,
transferase, structural genomics, PSI-2; 2.00A
{Bifidobacterium adolescentis ATCC15703}
Length = 515
Score = 27.3 bits (61), Expect = 7.9
Identities = 7/43 (16%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 115 GGGANAAASASAAASGGPGQPDNAIEHSDYRAKLAQIRQIYHQ 157
G A G+P A+ + Y + +H
Sbjct: 474 SGETEPPAWQLTIDGVETGEPTEAV-YEAYAKARGEGHHHHHH 515
>3t76_A VANU, transcriptional regulator vanug; structural genomics, center
for structural genomics of infec diseases, csgid; HET:
MSE; 1.12A {Enterococcus faecalis} PDB: 3t75_A* 3tyr_A*
3tys_A*
Length = 88
Score = 25.5 bits (56), Expect = 9.7
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 260 KEELARKCNITVSQVSNWFGNKRIRYK 286
K EL ++ S + N+ +
Sbjct: 40 KGELREAVGVSKSTFAKLGKNENVSLT 66
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 27.5 bits (61), Expect = 9.8
Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 15/107 (14%)
Query: 186 ITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 245
EI+ + ++ SSI +A+ + SR +KR N ++A +I+++Y
Sbjct: 246 SLDPEIQNELFPSLEQASSIANVD-----DALDFIGSRV-AIGQKRENRIEKAQQIIDKY 299
Query: 246 FYSHLSNPYPSEEAKEEL----ARK---CNITVSQVSNW--FGNKRI 283
F HL K K + + + + NKR+
Sbjct: 300 FLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRL 346
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
0.313 0.129 0.371
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,415,668
Number of extensions: 324420
Number of successful extensions: 932
Number of sequences better than 10.0: 1
Number of HSP's gapped: 897
Number of HSP's successfully gapped: 126
Length of query: 355
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 260
Effective length of database: 4,049,298
Effective search space: 1052817480
Effective search space used: 1052817480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.4 bits)