RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3400
(417 letters)
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 239 bits (611), Expect = 1e-78
Identities = 141/164 (85%), Positives = 148/164 (90%)
Query: 199 APSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258
S+EDAP+SDDLE FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ
Sbjct: 1 GGEHSDEDAPSSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 60
Query: 259 LSFKNMCKLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHK 318
LSFKNMCKLKPLL KWLEE DS++GSPT++DKIAAQGRKRKKRTSIEV VKGALE+HF K
Sbjct: 61 LSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLK 120
Query: 319 QPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362
PKPSA EIT LADSLQLEKEVVRVWFCNRRQKEKRMTP G
Sbjct: 121 CPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAAGAG 164
>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 = 235 bits (600), Expect = 4e-77
Identities = 92/159 (57%), Positives = 114/159 (71%), Gaps = 8/159 (5%)
Query: 205 EDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNM 264
E+ ++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNM
Sbjct: 1 EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNM 60
Query: 265 CKLKPLLQKWLEEADSTTG--------SPTSIDKIAAQGRKRKKRTSIEVTVKGALETHF 316
KLKPLL+KWL +A++ S + I R+RKKRTSIE ++ ALE F
Sbjct: 61 SKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSF 120
Query: 317 HKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
+ KP++++IT +A+ L +EKEV+RVWF NRRQKEKR+
Sbjct: 121 MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159
>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 = 221 bits (563), Expect = 1e-71
Identities = 88/145 (60%), Positives = 107/145 (73%), Gaps = 2/145 (1%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
LE FA +FK RRIKLG+TQ +VG AL ++G+ FSQTTICRFE LQLSFKN CKLK +
Sbjct: 3 RALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAI 62
Query: 271 LQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTL 330
L KWLEEA+ +K+ A RKRK+RT+I + K ALE HF + KPS+QEI +
Sbjct: 63 LSKWLEEAEQVGAL--YNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRM 120
Query: 331 ADSLQLEKEVVRVWFCNRRQKEKRM 355
A+ L LEKEVVRVWFCNRRQ+EKR+
Sbjct: 121 AEELNLEKEVVRVWFCNRRQREKRV 145
>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 = 218 bits (555), Expect = 2e-70
Identities = 89/155 (57%), Positives = 109/155 (70%)
Query: 202 GSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSF 261
G+ + +LE FAK KQ+RI LG+TQADVGL LG L+G VFSQTTI RFEALQLS
Sbjct: 1 GAMDMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSL 60
Query: 262 KNMCKLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPK 321
KNM KL+PLL+KW+EEAD+ +++KRTSIE V+ +LET F K PK
Sbjct: 61 KNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPK 120
Query: 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
PS Q+IT +A+ L LEK+VVRVWF NRRQK KR +
Sbjct: 121 PSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155
>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 = 206 bits (524), Expect = 8e-66
Identities = 63/149 (42%), Positives = 83/149 (55%), Gaps = 3/149 (2%)
Query: 209 TSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLK 268
+++ FAK FK RR+ LG TQ VG A+ G +SQ+ I RFE L ++ K+ KLK
Sbjct: 2 NMEEIREFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLK 61
Query: 269 PLLQKWLEEADSTTGSPTSIDKI---AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQ 325
P+L+KWL EA+ +KRK+RTS AL +F K P P+ Q
Sbjct: 62 PVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQ 121
Query: 326 EITTLADSLQLEKEVVRVWFCNRRQKEKR 354
EIT +A L ++EVVRVWF NRRQ K
Sbjct: 122 EITEMAKELNYDREVVRVWFSNRRQTLKN 150
>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 = 72.0 bits (177), Expect = 3e-16
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
++ RT I L +F PS ++I +AD L ++V++ WF N KE+
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63
Query: 354 RMTP 357
+ P
Sbjct: 64 QSGP 67
>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 = 66.0 bits (161), Expect = 4e-14
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHK-QPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+ RT I + G L++ H P + I TL+ L L K + +F N+R K
Sbjct: 5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64
Query: 354 RMTP 357
P
Sbjct: 65 HSGP 68
>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 = 58.3 bits (141), Expect = 2e-11
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 281 TTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEV 340
++GS Q KR RT+I L + P+ + + +A + L+K V
Sbjct: 2 SSGSSGGTGGEEPQRDKRL-RTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRV 60
Query: 341 VRVWFCNRRQKEKRMTP 357
V+VWF N R +E++ P
Sbjct: 61 VQVWFQNTRARERKSGP 77
>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 = 57.5 bits (139), Expect = 4e-11
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 291 IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
+A +K+T ++ L+ F + P E+ L + L + ++ WF + R
Sbjct: 1 MAHHHHHHRKKTKEQIAH---LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY 57
Query: 351 KEKR 354
+ +R
Sbjct: 58 RCQR 61
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 57.4 bits (139), Expect = 5e-11
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+ K++ +++ L+ F + P E+ L L VR WF +RR +
Sbjct: 9 SIYKNKKSHEQLSA---LKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65
Query: 355 M 355
+
Sbjct: 66 L 66
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 59.9 bits (144), Expect = 5e-11
Identities = 24/155 (15%), Positives = 47/155 (30%), Gaps = 17/155 (10%)
Query: 212 DLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL- 270
+ + A++ + QA + SQ T+ + + +
Sbjct: 5 NTKEVAQRITTELKRYSIPQAIFAQRVLCR-----SQGTLSDLLRNPKPWSKLKSGRETF 59
Query: 271 --LQKWLEEADST---------TGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQ 319
+ KWL+E + +K R + L F +
Sbjct: 60 RRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKEN 119
Query: 320 PKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+PS + T++ L LE V +F N R++
Sbjct: 120 KRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
>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 = 56.8 bits (137), Expect = 7e-11
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
K K+R ++ LE+ F + P P +E+ L ++ + + WF RR+K
Sbjct: 9 TKYKERAPEQLRA---LESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 55.8 bits (135), Expect = 1e-10
Identities = 23/61 (37%), Positives = 31/61 (50%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G K+K RT AL+ F KQ S Q++ L+ L L + V+ WF N+R K KR
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 355 M 355
Sbjct: 61 W 61
>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 = 56.1 bits (135), Expect = 2e-10
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
+K K++T +V + LE F K P+ E+ L +L + + WF RR+ M
Sbjct: 15 QKFKEKTQGQVKI---LEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSM 71
Query: 356 --TPPNTLGGPQDGMMEG 371
+++G + G G
Sbjct: 72 EQAVLDSMGSGKSGPSSG 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 = 54.7 bits (132), Expect = 4e-10
Identities = 24/68 (35%), Positives = 32/68 (47%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G + + T LE F Q SA E LA +L+L + V++WF NRR K KR
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
Query: 355 MTPPNTLG 362
+ LG
Sbjct: 62 KQLSSELG 69
>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 = 53.9 bits (130), Expect = 7e-10
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
+ + RT + L T + P+P A L + L V+RVWF N+R K+K+
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 356 T 356
+
Sbjct: 62 S 62
>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 = 53.9 bits (130), Expect = 8e-10
Identities = 18/62 (29%), Positives = 25/62 (40%)
Query: 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKE 352
+ R RT L+ F P E L++ L L V+ VWF N RQK
Sbjct: 3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKA 62
Query: 353 KR 354
++
Sbjct: 63 RK 64
>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 = 54.2 bits (130), Expect = 9e-10
Identities = 12/72 (16%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
+K K++T+ ++ V L+ F + +E+ L +L + + WF +++ +
Sbjct: 13 QKFKEKTAEQLRV---LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK 69
Query: 356 TPPNTLGGPQDG 367
+ G
Sbjct: 70 EEKMEIDESNAG 81
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 53.1 bits (127), Expect = 1e-09
Identities = 13/46 (28%), Positives = 27/46 (58%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
L+ ++ +PSA+E++ +ADS+ L +VV+ WF + + +
Sbjct: 18 LKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQS 63
>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 = 51.8 bits (125), Expect = 4e-09
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+ + K ++SI + LE F ++ +++E +A + VRVWF N+R + K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 51.7 bits (124), Expect = 5e-09
Identities = 22/83 (26%), Positives = 38/83 (45%)
Query: 277 EADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQL 336
+ ++ + + + +K+K RT T L F +Q S Q++ L++ L L
Sbjct: 2 KQPTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 337 EKEVVRVWFCNRRQKEKRMTPPN 359
+ V+ WF N+R K KR N
Sbjct: 62 SYKQVKTWFQNQRMKSKRWQKNN 84
>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 = 51.3 bits (123), Expect = 8e-09
Identities = 20/74 (27%), Positives = 35/74 (47%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
++ ++ RTS + ++++F P A+++ LA L K V++VWF N R K
Sbjct: 2 SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
Query: 352 EKRMTPPNTLGGPQ 365
+R GG
Sbjct: 62 FRRNLLRQENGGVS 75
>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 = 50.9 bits (122), Expect = 9e-09
Identities = 23/71 (32%), Positives = 30/71 (42%)
Query: 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+KRK+R LE F +Q SA E LA ++L V++WF N R K K
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
Query: 354 RMTPPNTLGGP 364
R G
Sbjct: 66 RAQNEKGYEGH 76
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 50.3 bits (121), Expect = 1e-08
Identities = 22/58 (37%), Positives = 29/58 (50%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
RK RT ALE F ++ S E + SL L + V++WF NRR K KR+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>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 = 50.6 bits (121), Expect = 1e-08
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 6/65 (9%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPK-PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
K + LE F K P + + L+ L ++ WF +RR ++K
Sbjct: 12 SPVNKVEPNDT-----LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66
Query: 355 MTPPN 359
P +
Sbjct: 67 SGPSS 71
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 50.4 bits (121), Expect = 1e-08
Identities = 21/60 (35%), Positives = 27/60 (45%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
+RK+R LE F +Q SA E LA + L V++WF N R K KR
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
>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 = 53.3 bits (127), Expect = 2e-08
Identities = 27/175 (15%), Positives = 48/175 (27%), Gaps = 36/175 (20%)
Query: 210 SDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCK--- 266
+D AK K + Q +V G +Q+ + + K +
Sbjct: 25 QEDPWRVAKMVKSYLQQHNIPQREVVDTTGL------NQSHLSQHLNKGTPMKTQKRAAL 78
Query: 267 ------LKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQP 320
+ + + A + R+ R + L + +Q
Sbjct: 79 YTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQK 138
Query: 321 KPSAQEITTLA---------------------DSLQLEKEVVRVWFCNRRQKEKR 354
PS +E TL S + + V WF NRR++E
Sbjct: 139 NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF 193
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 48.9 bits (117), Expect = 5e-08
Identities = 22/68 (32%), Positives = 32/68 (47%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
++ RK RT AL+ F K + E LA SL L + V++WF N+R K
Sbjct: 2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61
Query: 352 EKRMTPPN 359
K+ P +
Sbjct: 62 IKKSGPSS 69
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 48.4 bits (116), Expect = 5e-08
Identities = 22/57 (38%), Positives = 27/57 (47%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+RK R LE F +Q SA E LA L+L V++WF NRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 48.8 bits (115), Expect = 7e-08
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 293 AQGRKRKKRTSIEVTVKGALETHFHK----QPKPSAQEITTLADSLQLEKEVVRVWFCNR 348
+ RT L+ ++ ++I +A L ++ E+VR W NR
Sbjct: 4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNR 63
Query: 349 RQKEKRM---TPPNTLG 362
R+K + M + G
Sbjct: 64 RRKYRLMGIEVSGPSSG 80
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 47.7 bits (114), Expect = 8e-08
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
LE F +Q ++ E LA +L++ V+ WF NRR K +R T
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 46.8 bits (111), Expect = 4e-07
Identities = 23/63 (36%), Positives = 32/63 (50%)
Query: 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+++K RTS LE FHKQ ++ E LA L++ V+ WF NRR K +
Sbjct: 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWR 73
Query: 354 RMT 356
R T
Sbjct: 74 RQT 76
>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 = 46.3 bits (110), Expect = 5e-07
Identities = 22/76 (28%), Positives = 33/76 (43%)
Query: 282 TGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVV 341
+ + + + R+ RT LE F KQ S + LA+SL L + V
Sbjct: 2 SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61
Query: 342 RVWFCNRRQKEKRMTP 357
+ W+ NRR K K+ P
Sbjct: 62 KTWYQNRRMKWKKSGP 77
>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 = 44.3 bits (105), Expect = 2e-06
Identities = 20/63 (31%), Positives = 25/63 (39%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+ + LE F Q S E LA LQL + V+ WF NRR K +R
Sbjct: 5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Query: 355 MTP 357
P
Sbjct: 65 SGP 67
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 43.6 bits (103), Expect = 3e-06
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 311 ALETHFHKQPK-PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
LE +F+K K P + +A L +E + WF R + +R
Sbjct: 16 ILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 60
>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 = 44.2 bits (104), Expect = 3e-06
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 15/78 (19%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSL---------------QL 336
++ R R + +E++F++ P + +A++ ++
Sbjct: 2 SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 61
Query: 337 EKEVVRVWFCNRRQKEKR 354
V WF NRR++ KR
Sbjct: 62 TSLKVYNWFANRRKEIKR 79
>3ivp_A Putative transposon-related DNA-binding protein; APC62618,
clostridium diffic structural genomics, PSI-2, protein
structure initiative; HET: PG4; 2.02A {Clostridium
difficile}
Length = 126
Score = 44.8 bits (106), Expect = 4e-06
Identities = 22/122 (18%), Positives = 38/122 (31%), Gaps = 16/122 (13%)
Query: 212 DLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE--ALQLSFKNMCKLKP 269
D A K+ R K G T+ VG + + E S + + L
Sbjct: 9 DFRALGLAIKEARKKQGLTREQVGAMIE------IDPRYLTNIENKGQHPSLQVLYDLVS 62
Query: 270 LLQKWLEE---ADSTTGSPTSIDKIAA--QGRKRKKRTSIEVTVKGALETHFHKQPKPSA 324
LL ++E S+ T ++ +E G +++ K+ A
Sbjct: 63 LLNVSVDEFFLPASSQVKSTKRRQLENKIDNFTDADLVIMESVADGIVKS---KEVGEMA 119
Query: 325 QE 326
E
Sbjct: 120 GE 121
>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 = 42.3 bits (99), Expect = 1e-05
Identities = 11/63 (17%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
+ G K++T ++ + L++ F + ++ L L + + WF + R
Sbjct: 1 GSSGSSGKRKTKEQLAI---LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYA 57
Query: 352 EKR 354
K
Sbjct: 58 LKH 60
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPK-PSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
G T+ + LE F K P + + L+ L + ++ WF RR +EK
Sbjct: 1 GSSGSSGTAQPNAI---LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
Query: 354 RMTPPN 359
P +
Sbjct: 58 PSGPSS 63
>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 = 41.7 bits (97), Expect = 3e-05
Identities = 15/81 (18%), Positives = 25/81 (30%)
Query: 276 EEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQ 335
++G A + K L++ F + PS +E LA
Sbjct: 4 HHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESG 63
Query: 336 LEKEVVRVWFCNRRQKEKRMT 356
L + + WF + R K
Sbjct: 64 LARTDIVSWFGDTRYAWKNGN 84
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 43.1 bits (100), Expect = 6e-05
Identities = 18/107 (16%), Positives = 29/107 (27%), Gaps = 21/107 (19%)
Query: 269 PLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEIT 328
L + G + R+ R + L + +Q PS +E
Sbjct: 114 LFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEERE 173
Query: 329 TLA---------------------DSLQLEKEVVRVWFCNRRQKEKR 354
L S + + V WF NRR++E
Sbjct: 174 ALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAF 220
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 39.8 bits (93), Expect = 7e-05
Identities = 16/66 (24%), Positives = 28/66 (42%)
Query: 291 IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
++ RKKR LE + + + ++ + L + V +WF NRR
Sbjct: 1 MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
Query: 351 KEKRMT 356
KEK++
Sbjct: 61 KEKKVI 66
>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 = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G +R RT+ + LE HF + +A + L+ L L V++WF NRR++ K
Sbjct: 1 GPRRT-RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI 59
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 298 RKKRTSIEVTVKGALETHFHKQP---KPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
R+ RT+ G LE F+K+ +P E+ A L L + ++VWF NRR K+KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCEL---AAQLNLPESTIKVWFQNRRMKDKR 58
>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 = 39.3 bits (92), Expect = 1e-04
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRR-- 349
++ R++RT+ LE F K P +A + L + V+VWF NRR
Sbjct: 2 SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
Query: 350 -QKEKRMTPPNTLGGPQDG 367
+++++ GP G
Sbjct: 62 CRQQQQQQQNGGQSGPSSG 80
>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 = 39.0 bits (90), Expect = 1e-04
Identities = 11/51 (21%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRR--QKEKRMTPPNT 360
L+ ++ +P++ E+ ++ ++ L +E V+ WF R+ Q + P++
Sbjct: 20 LKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNSRSGPSS 70
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein,
xenobiotic response E family of transcriptional
regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae
PV}
Length = 83
Score = 39.3 bits (92), Expect = 1e-04
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 210 SDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ +A + R G TQ ++ LG Q+ + + E
Sbjct: 9 NARYQALLDLLLEARSAAGITQKELAARLGR------PQSFVSKTE 48
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
fold, OPPF, STRU genomics, oxford protein production
facility; 2.80A {Neisseria gonorrhoeae}
Length = 141
Score = 40.3 bits (94), Expect = 2e-04
Identities = 29/127 (22%), Positives = 48/127 (37%), Gaps = 23/127 (18%)
Query: 153 LQHHSAYHVNV-------MNGMLHHHQPSPQLHHSLRDIQAHSPSYSQSQHPDAPSGSEE 205
+ HH +H+ V +NG + +P + H ++P + +
Sbjct: 1 MAHHHHHHIPVTHIKCLRINGQIKCVKPISPNTTPAAEHIEHVR-----KNPRRKAAMDR 55
Query: 206 DAPTSDD---LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE--ALQLS 260
A D L+A + F R+K GFTQ+++ A G Q + R E L
Sbjct: 56 AAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGL------PQPYLSRIENSKQSLQ 109
Query: 261 FKNMCKL 267
K + KL
Sbjct: 110 DKTVQKL 116
>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain,
transcription; 2.25A {Enterococcus faecalis} SCOP:
a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A
2grl_A 2grm_A
Length = 317
Score = 41.5 bits (97), Expect = 3e-04
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 218 KQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEA--LQLSFKNMCKL 267
KQ R +L + Q D+ Y + S++ + EA +S + + K
Sbjct: 6 SVLKQIRQELNYHQIDL-------YSGIMSKSVYIKVEADSRPISVEELSKF 50
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 39.0 bits (90), Expect = 3e-04
Identities = 17/81 (20%), Positives = 27/81 (33%), Gaps = 21/81 (25%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLA---------------------DSL 334
+ R+ R + L + +Q PS +E TL S
Sbjct: 8 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67
Query: 335 QLEKEVVRVWFCNRRQKEKRM 355
+ + V WF NRR++E
Sbjct: 68 LVTEVRVYNWFANRRKEEAFR 88
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 19/57 (33%), Positives = 25/57 (43%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
G +R++RT LE F + P +A L + VRVWF NRR K
Sbjct: 1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 57
>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 = 37.5 bits (87), Expect = 5e-04
Identities = 16/65 (24%), Positives = 27/65 (41%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
RKKR LE + + + ++ + L + + +WF NRR KEK+
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 355 MTPPN 359
P +
Sbjct: 65 SGPSS 69
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 311 ALETHF---HKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
LE +F +K P P+ + +A L +E + WF R + +R
Sbjct: 15 ILEYNFNKVNKHPDPTTLCL--IAAEAGLTEEQTQKWFKQRLAEWRR 59
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 20/60 (33%), Positives = 26/60 (43%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
++ R+ RT ALE F + P LA + L +E V VWF NRR K
Sbjct: 2 SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 37.0 bits (86), Expect = 8e-04
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRR-- 349
++ ++ RTS ALE F + P LA + L + ++VWF NRR
Sbjct: 2 SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61
Query: 350 -QKEKRMTPPNTLGGPQDG 367
++E+++ GP G
Sbjct: 62 WRREEKLRNQRRQSGPSSG 80
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 39.0 bits (90), Expect = 0.001
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 331 ADSLQLEKEVVRVWFCNRRQKEKRM 355
AD L E E +R W R ++ KR+
Sbjct: 77 ADRLTQEPESIRKW---REEQRKRL 98
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus
thuringiensis serovar ISRAELE35646}
Length = 293
Score = 39.8 bits (92), Expect = 0.001
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 212 DLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLL 271
E + K+ R+ G TQ L N+ Q+ + R E + +M L+ +
Sbjct: 2 QAEKLGSEIKKIRVLRGLTQKQ-------LSENICHQSEVSRIE-SGAVYPSMDILQGIA 53
Query: 272 QKW 274
K
Sbjct: 54 AKL 56
>4ghj_A Probable transcriptional regulator; structural genomics, niaid,
national institute of allergy AN infectious diseases;
HET: MSE; 1.75A {Vibrio vulnificus}
Length = 101
Score = 37.2 bits (86), Expect = 0.001
Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 18/100 (18%)
Query: 168 LHHHQPSPQLHHSLRDIQAHSPSYSQSQHPDAPSGSEEDAPTSDDLEAFAKQFKQRRIKL 227
+HHH HHS Y QS + + E + KQ R+
Sbjct: 1 MHHHH-----HHSSGVDLGTENLYFQSNAMKHVTAAA-------LAEEIGDRLKQARLNR 48
Query: 228 GFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKL 267
TQ++V G ++ T+ E ++ M +
Sbjct: 49 DLTQSEVAEIAGI------ARKTVLNAEKGKVQLDIMIAI 82
>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 = 36.1 bits (84), Expect = 0.001
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
R+ RT+ LE F P + LA L LE + +++WF NRR K KR
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein
structure initiative, midwest center for structural
genomic binding; 1.80A {Silicibacter pomeroyi}
Length = 86
Score = 36.8 bits (85), Expect = 0.001
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 210 SDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + ++ +Q R+ G TQAD+ L Q+ + + E
Sbjct: 9 TPEHVYLCQRLRQARLDAGLTQADLAERLDK------PQSFVAKVE 48
>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 = 34.6 bits (80), Expect = 0.004
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 298 RKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
R R + E ++ + P + + L + L + ++ W NRR+KEK +
Sbjct: 1 RGHRFTKENVRILESWFAKNIEN-PYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
Query: 356 T 356
T
Sbjct: 60 T 60
>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 = 35.6 bits (82), Expect = 0.004
Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 4/81 (4%)
Query: 276 EEADSTTGSPTSIDKIAAQGR-KRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLAD 332
+ AD + + D I + R R + E ++ + P + + L
Sbjct: 7 KSADGLVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIEN-PYLDTKGLENLMK 65
Query: 333 SLQLEKEVVRVWFCNRRQKEK 353
+ L + ++ W NRR+KEK
Sbjct: 66 NTSLSRIQIKNWVSNRRRKEK 86
>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 = 35.2 bits (81), Expect = 0.004
Identities = 18/59 (30%), Positives = 25/59 (42%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
RKKR LE F + +A L L + V++WF NRR K K++
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
>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 = 34.6 bits (80), Expect = 0.004
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 312 LETHFHKQ---PKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
L+ F++ + Q++ + L L + +++WF N+R K K+
Sbjct: 18 LKREFNENRYLTERRRQQL---SSELGLNEAQIKIWFKNKRAKIKK 60
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 34.7 bits (80), Expect = 0.004
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQP---KPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
G ++ RT+ LE F +P E+ A L L + +++WF NRR K
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVEL---AVMLNLTERHIKIWFQNRRMK 57
Query: 352 EKR 354
K+
Sbjct: 58 WKK 60
>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA
binding protein, transcription regulator; HET: CME;
1.95A {Enterobacteria phage P2}
Length = 84
Score = 35.2 bits (81), Expect = 0.004
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 210 SDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + R + +Q+++ + LG SQ+ I + E
Sbjct: 5 DHRYRCLVQLLTKLRKEASLSQSELAIFLGL------SQSDISKIE 44
>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 = 34.5 bits (80), Expect = 0.005
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 6/41 (14%)
Query: 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + + K +RI+LG QA++ +GT +Q +I + E
Sbjct: 1 SISSRVKSKRIQLGLNQAELAQKVGT------TQQSIEQLE 35
>1zug_A Phage 434 CRO protein; gene regulating protein, transcription
regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A
3cro_L*
Length = 71
Score = 34.2 bits (79), Expect = 0.006
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 213 LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
++ +++ K+RRI L TQ ++ G Q +I E
Sbjct: 1 MQTLSERLKKRRIALKMTQTELATKAGV------KQQSIQLIE 37
>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 = 34.8 bits (80), Expect = 0.007
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 3/75 (4%)
Query: 296 RKRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
R R + E ++ + P + + L + L + ++ W RR KEK
Sbjct: 3 PYRGHRFTKENVRILESWFAKNIEN-PYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEK 61
Query: 354 RMTPPNTLGGPQDGM 368
+T L G
Sbjct: 62 TITIAPELADLLSGE 76
>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 = 34.4 bits (79), Expect = 0.007
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 290 KIAAQGRKRKKRTSIEVTVKGALETHFHKQP---KPSAQEITTLADSLQLEKEVVRVWFC 346
G +R+ R + LE FH + E+ A +L L + +++WF
Sbjct: 13 IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEM---AHALSLTERQIKIWFQ 69
Query: 347 NRRQKEKRMT 356
NRR K K+
Sbjct: 70 NRRMKLKKEI 79
>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 = 33.9 bits (78), Expect = 0.007
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQP---KPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+++ R + LE FH + EI A +L L + +++WF NRR K K
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEI---AHALSLTERQIKIWFQNRRMKWK 58
Query: 354 RMT 356
+
Sbjct: 59 KEN 61
>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 = 33.9 bits (78), Expect = 0.010
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 287 SIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKP--SAQEITTLADSLQLEKEVVRVW 344
S IA + ++R+ RT+ + LE F + P +E LA L + ++VW
Sbjct: 8 SEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTRE--ELAQRTNLTEARIQVW 65
Query: 345 FCNRRQK 351
F NRR +
Sbjct: 66 FQNRRAR 72
>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 = 33.7 bits (78), Expect = 0.010
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 212 DLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + ++ + RR KL QA +G +G S I ++E
Sbjct: 2 NTQLMGERIRARRKKLKIRQAALGKMVGV------SNVAISQWE 39
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 36.6 bits (84), Expect = 0.012
Identities = 22/110 (20%), Positives = 29/110 (26%), Gaps = 4/110 (3%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSP 107
HHHHH V S + G+ A P G H
Sbjct: 2 AHHHHHHVDDDD----KMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPIS 57
Query: 108 VDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHS 157
P M PHS P + +G+ +SP+ S
Sbjct: 58 TLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVS 107
Score = 34.7 bits (79), Expect = 0.049
Identities = 18/114 (15%), Positives = 29/114 (25%), Gaps = 2/114 (1%)
Query: 101 HHHQQSPVDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAYH 160
HH VD + + S P + P S +
Sbjct: 2 AHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSS 61
Query: 161 VNVMNGMLHHHQPSPQLHHSLRDIQAHSPSYSQSQHPDAPSGSEEDAPTSDDLE 214
G SP HS+ +P+ S S +S+D++
Sbjct: 62 PINGMGPPFSVISSPMGPHSMS--VPTTPTLGFSTGSPQLSSPMNPVSSSEDIK 113
Score = 34.3 bits (78), Expect = 0.062
Identities = 18/115 (15%), Positives = 28/115 (24%)
Query: 43 YQHHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHH 102
+ HH S P + P + G G I P +
Sbjct: 5 HHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPIN 64
Query: 103 HQQSPVDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHS 157
P + P + S +P +SS P +S P +
Sbjct: 65 GMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLN 119
Score = 29.7 bits (66), Expect = 2.0
Identities = 16/89 (17%), Positives = 23/89 (25%), Gaps = 4/89 (4%)
Query: 126 MGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAYHVNVMNGMLHHHQPSPQLHHSLRD-- 183
M H H + NS SP S ++ + QLH +
Sbjct: 1 MAHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLS 60
Query: 184 --IQAHSPSYSQSQHPDAPSGSEEDAPTS 210
I P +S P P +
Sbjct: 61 SPINGMGPPFSVISSPMGPHSMSVPTTPT 89
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria
phage P22} SCOP: a.35.1.2
Length = 76
Score = 33.4 bits (77), Expect = 0.013
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 212 DLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + ++ + RR KL QA +G +G S I ++E
Sbjct: 2 NTQLMGERIRARRKKLKIRQAALGKMVGV------SNVAISQWE 39
>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 = 36.4 bits (83), Expect = 0.017
Identities = 43/312 (13%), Positives = 86/312 (27%), Gaps = 85/312 (27%)
Query: 123 HGGMGSPHSWHTPVVSS------------HYIPSGNSGAASPLQHHSAYHVNVMNGMLHH 170
G +GS +W V ++ N + + + ++ +L+
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV-------LEMLQKLLYQ 208
Query: 171 HQPSPQLHHSLRDIQAHSPSYSQSQH--PDAPSG--SEEDAPTS----DD------LEAF 216
P+ S D HS + H + + AF
Sbjct: 209 IDPN---WTSRSD---HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF 262
Query: 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRF--EALQLSFKNMCKLKPLLQKW 274
K+ T + + S T + ++ ++K LL K+
Sbjct: 263 NLS-----CKILLTTRFKQVT------DFLSAATTTHISLDHHSMTL-TPDEVKSLLLKY 310
Query: 275 L--------EEADSTTGSPTSIDKIAAQGRKRKKR-------------TSIEVTVKGALE 313
L E T +P + IA R T IE ++ LE
Sbjct: 311 LDCRPQDLPREV--LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN-VLE 367
Query: 314 THFHKQPKPSAQEITTLADSLQLEKEV-VRVWFCNRRQKEKRMTPPNTLGGPQDGMMEGQ 372
+++ ++ S + + +WF + + N L + ++E Q
Sbjct: 368 PAEYRK---MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV--NKL--HKYSLVEKQ 420
Query: 373 LGMHGYHHPDLH 384
P ++
Sbjct: 421 PKESTISIPSIY 432
Score = 35.6 bits (81), Expect = 0.036
Identities = 28/198 (14%), Positives = 59/198 (29%), Gaps = 61/198 (30%)
Query: 155 HHSAYHVNVMNGMLHHHQPSPQLHHSLRDIQAHSPSYSQSQHPDAPSGSEEDAPTSDDLE 214
HH +H++ G + + +DI S +
Sbjct: 1 HHHHHHMDFETG---------EHQYQYKDI------------------------LSVFED 27
Query: 215 AFAKQFKQRRI----KLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCK--LK 268
AF F + + K ++ ++ + + + S T F L + M + ++
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEIDHIIMS--KDAVSGTLRL-FWTLLSKQEEMVQKFVE 84
Query: 269 PLLQK---WLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETH---FHKQPKP 322
+L+ +L + I + R+ T + + + L F K
Sbjct: 85 EVLRINYKFL------------MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 323 SAQEITTLADSL-QLEKE 339
Q L +L +L
Sbjct: 133 RLQPYLKLRQALLELRPA 150
Score = 31.7 bits (71), Expect = 0.53
Identities = 21/148 (14%), Positives = 45/148 (30%), Gaps = 46/148 (31%)
Query: 265 CK-----LKPLLQKWLEEADSTTGSPTSIDKIAAQGR------KRKKRTSIEVTVKGALE 313
CK K +L K EE D S ++ K+ ++ V+ L
Sbjct: 35 CKDVQDMPKSILSK--EEIDHIIMSKDAVSGT----LRLFWTLLSKQEEMVQKFVEEVLR 88
Query: 314 THF----------HKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLGG 363
++ +QP + D L + +V + +R Q ++
Sbjct: 89 INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL-------- 140
Query: 364 PQDGMMEGQLGMHGYHHPD--LHGSPMG 389
+ ++E + + + G +
Sbjct: 141 -RQALLELR------PAKNVLIDG--VL 159
Score = 29.4 bits (65), Expect = 2.5
Identities = 6/6 (100%), Positives = 6/6 (100%)
Query: 45 HHHHHH 50
HHHHHH
Sbjct: 1 HHHHHH 6
>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 = 32.6 bits (75), Expect = 0.020
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 311 ALETHFHKQPKP--SAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
LE F + P +E LA + L + ++VWF NRR K ++
Sbjct: 13 ELEKAFSRTHYPDVFTRE--ELAMKIGLTEARIQVWFQNRRAKWRK 56
>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding,
nucleotide-binding, membrane, transmembrane, transport
protein; 3.00A {Methanosarcina acetivorans} SCOP:
f.58.1.1
Length = 295
Score = 35.1 bits (81), Expect = 0.037
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 44 QHHHHHHHHHQVPSSPSPNGH--PVSLSAAHNPWVSLQPG 81
HHHHHHHHH + GH + ++
Sbjct: 3 HHHHHHHHHHSSGENLYFQGHMKAKNRKTRKFEPLTFVFS 42
Score = 29.3 bits (66), Expect = 2.3
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 95 HNHHHPHHHQQSPVDIKPPPDMHRTSHQH 123
H+HHH HHH S ++ M + +
Sbjct: 3 HHHHHHHHHHSSGENLYFQGHMKAKNRKT 31
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 34.7 bits (80), Expect = 0.039
Identities = 15/42 (35%), Positives = 18/42 (42%)
Query: 44 QHHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGAD 85
HHHHHHHHH + H V L+AA Q +
Sbjct: 3 HHHHHHHHHHSSGHIDDDDKHMVGLTAAGGGSGDAQSSQSSG 44
Score = 27.7 bits (62), Expect = 7.6
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 93 GIHNHHHPHHHQQSPVD 109
G H+HHH HHH +D
Sbjct: 2 GHHHHHHHHHHSSGHID 18
>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein,
helix-turn-H restriction-modification, transcription;
2.00A {Citrobacter SP} PDB: 3lis_A
Length = 98
Score = 32.5 bits (74), Expect = 0.043
Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 216 FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
++ K R++ G +Q +G+ G + + ++E
Sbjct: 2 LIRRLKDARLRAGISQEKLGVLAG--IDEASASARMNQYE 39
>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 = 32.6 bits (74), Expect = 0.044
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 273 KWLEEADSTTGSP-TSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQP---KPSAQEIT 328
W++ + + S + + R T+ ++T LE FH + EI
Sbjct: 12 DWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLT---ELEKEFHFNKYLSRARRVEI- 67
Query: 329 TLADSLQLEKEVVRVWFCNRRQKEKR 354
A +L+L + V++WF NRR K+K+
Sbjct: 68 --AATLELNETQVKIWFQNRRMKQKK 91
>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 = 32.8 bits (75), Expect = 0.049
Identities = 5/40 (12%), Positives = 12/40 (30%), Gaps = 6/40 (15%)
Query: 216 FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
FA+ + + + G + L T+ +
Sbjct: 10 FAENLSRLKKEHGLKNHQIAELLNV------QTRTVAYYM 43
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 32.1 bits (73), Expect = 0.054
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 274 WLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQP---KPSAQEITTL 330
W++ T + A G +++RTS LE FH + EI
Sbjct: 11 WMKRVHLGTSTVN------ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEI--- 61
Query: 331 ADSLQLEKEVVRVWFCNRRQKEKR 354
A +L L + +++WF NRR K K+
Sbjct: 62 AHALSLTERQIKIWFQNRRMKWKK 85
>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 = 32.0 bits (73), Expect = 0.063
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 16/87 (18%)
Query: 216 FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEA--LQLSFKNMCKLKPLLQK 273
K +Q R G TQ D+ + I +E+ + + + K++ +
Sbjct: 14 VGKVIQQGRQSKGLTQKDLATKINE------KPQVIADYESGRAIPNNQVLGKIERAIGL 67
Query: 274 WLEEADSTTGSPTSIDKIAAQGRKRKK 300
L D I K +G + K
Sbjct: 68 KLRGKD--------IGKPIEKGPRAKS 86
>2jmr_A FIMF; protein, cell adhesion; NMR {Escherichia coli}
Length = 179
Score = 33.2 bits (76), Expect = 0.082
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 41 LKYQHHHHHHHHHQVPSSPSPNGH 64
L+YQ +HHHHHH Q S+ + G+
Sbjct: 152 LEYQDNHHHHHHKQADSTITIRGY 175
>3f1y_A Mannosyl-3-phosphoglycerate synthase; GT-A type
glycosyltransferase, GT-81, mannosyl-3-phosphoglyc
synthase, GDP-mannose, transferas; 2.20A {Rubrobacter
xylanophilus} PDB: 3kia_A* 3o3p_A*
Length = 387
Score = 33.7 bits (76), Expect = 0.10
Identities = 17/77 (22%), Positives = 28/77 (36%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSP 107
HHHHHH P +G + +A P G D +M I + +H++
Sbjct: 2 HHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEFMSTYHERPL 61
Query: 108 VDIKPPPDMHRTSHQHG 124
+ S+ +G
Sbjct: 62 GPASAAEWFRQRSYDYG 78
>2es4_D Lipase chaperone; protein-protein complex, steric chaperone,
triacylglycerol hydrolase, all alpha helix protein, A/B
hydrolase fold; 1.85A {Burkholderia glumae} SCOP:
a.137.15.1
Length = 332
Score = 33.6 bits (76), Expect = 0.11
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 44 QHHHHHHHHHQ--------VPSSPSPNGHPVSLS--AAHNPWVSLQPGAGADPWSSSMPG 93
HHHHHHHHH +P++PSP AA P + A P +++PG
Sbjct: 2 HHHHHHHHHHSSGHIEGRHMPAAPSPAPAGAVAGGPAAGVPAAASGAAEAAMPLPAALPG 61
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, HEL helix motif,
transcription regulator; 3.20A {Streptococcus
pneumoniae}
Length = 158
Score = 32.6 bits (74), Expect = 0.11
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 6/40 (15%)
Query: 216 FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
K K R TQ + +G S+ ++ R+E
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGI------SRNSLSRYE 35
>3rce_A Oligosaccharide transferase to N-glycosylate PROT;
oligosaccharyltransferase, membrane protein, helical
bundle, glycosylation, acceptor peptide, plasma
membrane; HET: PPN; 3.40A {Campylobacter lari}
Length = 724
Score = 33.5 bits (75), Expect = 0.13
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 42 KYQHHHHHHHHH 53
++ HHHHHHHHH
Sbjct: 713 EFHHHHHHHHHH 724
Score = 33.5 bits (75), Expect = 0.13
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 40 ELKYQHHHHHHHHHQ 54
LK + HHHHHHHH
Sbjct: 709 RLKREFHHHHHHHHH 723
Score = 28.1 bits (61), Expect = 6.4
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 40 ELKYQHHHHHHH 51
E + HHHHHHH
Sbjct: 713 EFHHHHHHHHHH 724
>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional
regulator, transcription regulator; 1.69A {Aeromonas
hydrophila} SCOP: a.35.1.3
Length = 74
Score = 30.7 bits (70), Expect = 0.14
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 8/66 (12%)
Query: 204 EEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSF 261
+ DL F ++ ++ R G +Q + G ++ + E Q +S
Sbjct: 2 QSHHDHYADLVKFGQRLRELRTAKGLSQETLAFLSG------LDRSYVGGVERGQRNVSL 55
Query: 262 KNMCKL 267
N+ KL
Sbjct: 56 VNILKL 61
>2x4f_A Myosin light chain kinase family member 4; LUNG, breast cancer,
transferase, serine/threonine-protein kinase,
nucleotide-binding; HET: 16X 1PE; 2.67A {Homo sapiens}
Length = 373
Score = 33.1 bits (76), Expect = 0.14
Identities = 16/69 (23%), Positives = 21/69 (30%), Gaps = 1/69 (1%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQ 105
HHHHHH V ++ S A + WS++
Sbjct: 3 HHHHHHSSGVDLGTENLYFQSMKNSGDQDSRSGHNEA-KEVWSNADLTERMPVKSKRTSA 61
Query: 106 SPVDIKPPP 114
VDI PP
Sbjct: 62 LAVDIPAPP 70
>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription
complex, serine kinase, DNA-bindin mercury derivative,
repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B*
3hzi_B*
Length = 88
Score = 30.9 bits (70), Expect = 0.14
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 213 LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEA 256
A K R + G+TQ+++ +G Q TI FE
Sbjct: 10 PTQLANAMKLVRQQNGWTQSELAKKIGI------KQATISNFEN 47
>1uoz_A Putative cellulase; hydrolase, glycoside hydrolase, family 6;
HET: GLC SSG; 1.10A {Mycobacterium tuberculosis} SCOP:
c.6.1.1 PDB: 1up3_A* 1up0_A* 1up2_A*
Length = 315
Score = 32.7 bits (74), Expect = 0.19
Identities = 11/32 (34%), Positives = 12/32 (37%), Gaps = 7/32 (21%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWV 76
HHHHHHHHH + NP
Sbjct: 3 HHHHHHHHHHSSG-------HIEGRHMANPLA 27
>3qrp_A Putative uncharacterized protein TTHB192; RAMP domain, protein-RNA
complex, RNA binding protein-RNA CO; HET: PGP U5P; 2.35A
{Thermus thermophilus HB8} PDB: 3qrq_A 3qrr_A*
Length = 267
Score = 32.5 bits (73), Expect = 0.20
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 5/86 (5%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSP 107
HHHHHH P +G + +A P G D +M I + + +
Sbjct: 2 HHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSENLYFQMWLTK 61
Query: 108 VDIKPPPDMHRTSHQHGGMGSPHSWH 133
+ + P + + +P+ H
Sbjct: 62 LVLNP-----ASRAARRDLANPYEMH 82
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 29.2 bits (66), Expect = 0.31
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 293 AQGRKRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
+ G + + + T + +H P PS + LA + V WF N+R
Sbjct: 1 SSGHIEGRHMNKQATEILNEYFYSHLSN-PYPSEEAKEELAKKCGITVSQVSNWFGNKRI 59
Query: 351 KEKR 354
+ K+
Sbjct: 60 RYKK 63
>3odm_A Pepcase, PEPC, phosphoenolpyruvate carboxylase; beta-barrel,
lyase; 2.95A {Clostridium perfringens}
Length = 560
Score = 32.4 bits (73), Expect = 0.33
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 44 QHHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 3 HHHHHHHHHHS 13
Score = 29.3 bits (65), Expect = 2.5
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 93 GIHNHHHPHHHQQSPVD-----IKPPPDMHRTSHQH 123
G H+HHH HHH +D +K P M QH
Sbjct: 2 GHHHHHHHHHHSSGHIDDDDKHMKIPCSM---MTQH 34
Score = 28.5 bits (63), Expect = 4.3
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 41 LKYQHHHHHHHH 52
+ + HHHHHHHH
Sbjct: 1 MGHHHHHHHHHH 12
>3rj1_B Mediator of RNA polymerase II transcription subun; RNA polymeras
II, POL II, head module, head, regulator, helical
bundle; 4.30A {Saccharomyces cerevisiae}
Length = 583
Score = 31.8 bits (71), Expect = 0.40
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 45 HHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 2 HHHHHHHHHH 11
Score = 29.5 bits (65), Expect = 2.3
Identities = 10/11 (90%), Positives = 10/11 (90%)
Query: 44 QHHHHHHHHHQ 54
HHHHHHHHHQ
Sbjct: 2 HHHHHHHHHHQ 12
Score = 28.3 bits (62), Expect = 5.2
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 94 IHNHHHPHHHQQ 105
+H+HHH HHH Q
Sbjct: 1 MHHHHHHHHHHQ 12
>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding,
HOST-virus interaction, metal-binding, nucleus,
receptor, transcription, transcription regulation,
zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo
sapiens} PDB: 3dzu_D* 3e00_D* 2env_A
Length = 419
Score = 32.0 bits (72), Expect = 0.41
Identities = 10/50 (20%), Positives = 15/50 (30%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNH 97
HHHHH V + + A P+ S + P +
Sbjct: 2 AHHHHHHVDDDDKMYQSAIKVEPASPPYYSEKTQLYNKPHEEPSNSLMAI 51
>1d1d_A Protein (capsid protein); two independent domains helical
bundles, virus/viral protein; NMR {Rous sarcoma virus}
SCOP: a.28.3.1 a.73.1.1
Length = 262
Score = 31.3 bits (70), Expect = 0.45
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 44 QHHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQP 80
HHHHHHHHH + PV + W L+P
Sbjct: 2 HHHHHHHHHHSSGHIEGRHNMPVVIKTEGPAWTPLEP 38
>2fgy_A Carboxysome shell polypeptide; beta class of carbonic anhydrase,
lyase; 2.20A {Halothiobacillus neapolitanus}
Length = 542
Score = 31.6 bits (71), Expect = 0.49
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 22/77 (28%)
Query: 45 HHHHHHHHHQVPSSPSPNGH-----------------PVSLSAAHNPWVSL-----QPGA 82
+HHHHHH + +P++ + P +S++ P + L P
Sbjct: 4 YHHHHHHDYDIPTTENLYFQGAMGSMNTRNTRSKQRAPCGVSSSVKPRLDLIEQAPNPVY 63
Query: 83 GADPWSSSMPGIHNHHH 99
P ++P H
Sbjct: 64 DRHPACITLPERTCRHP 80
>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 = 31.7 bits (72), Expect = 0.49
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 9/65 (13%)
Query: 289 DKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNR 348
AA + + E F ++ +++E +A + VRVWF N+
Sbjct: 366 TAAAAAISPQARAFL---------EQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINK 416
Query: 349 RQKEK 353
R + K
Sbjct: 417 RMRSK 421
>2y7j_A Phosphorylase B kinase gamma catalytic chain, testis/liver isoform;
transferase; HET: B49; 2.50A {Homo sapiens} PDB: 1h0t_A
1lp1_B 1q2n_A 2spz_A 3mzw_B* 1ss1_A 2jwd_A 1bdc_A 1bdd_A
1fc2_C* 2b87_A 2b88_A 1h0t_B 1lp1_A 2b87_B 2b89_A 3s1k_A
Length = 365
Score = 30.8 bits (70), Expect = 0.73
Identities = 15/98 (15%), Positives = 26/98 (26%), Gaps = 1/98 (1%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQ 105
HHHHHH V + + H P ++ + P + +
Sbjct: 2 HHHHHHSSGVDNKFNKERRRARREIRHLPNLNREQRRAFIRSLRDDPSQSANLLAEAKKL 61
Query: 106 SPVDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIP 143
+ K +++ S P Y P
Sbjct: 62 NDAQPKGTENLYFQSMGPED-ELPDWAAAKEFYQKYDP 98
>3tyj_A BCLA protein; exosporium, protein binding; 2.15A {Bacillus
anthracis} PDB: 3twi_A
Length = 155
Score = 30.2 bits (67), Expect = 0.76
Identities = 15/41 (36%), Positives = 19/41 (46%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGAD 85
HHHHHH + PS G P L A ++ +SL G
Sbjct: 5 HHHHHHENLYFQGGPSGLGLPAGLYAFNSGGISLDLGINDP 45
>2hdi_B Colicin-IA; outer membrane, iron transport, TONB BOX, signal
transductio colicin I receptor, receptor ligand,
membrane protein; HET: LDA; 2.50A {Escherichia coli}
Length = 113
Score = 29.3 bits (65), Expect = 0.78
Identities = 17/39 (43%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 45 HHHHHHHHHQVPSSP---SPNGHPVSLSAAHNPWVSLQP 80
HHHHHHHH P SP P S H+ VS P
Sbjct: 2 HHHHHHHHKNTPDGKTIVSPEKFPGRSSTNHSIVVSGDP 40
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix,
transcription/DNA complex; HET: DNA; 1.80A
{Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A
1rio_A 1lli_A*
Length = 92
Score = 28.8 bits (64), Expect = 0.87
Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLK 268
+D +++++ +LG +Q V +G Q+ + L+ N L
Sbjct: 13 EDARRLKAIYEKKKNELGLSQESVADKMG------MGQSGVGALFNGINALNAYNAALLA 66
Query: 269 PLLQ 272
+L+
Sbjct: 67 KILK 70
>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET:
DNA; 2.10A {Enterobacter SP} PDB: 3clc_A*
Length = 82
Score = 28.4 bits (64), Expect = 0.88
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 210 SDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKL 267
S L + K+ R++ G TQ D+ +T I E L+ K++ +
Sbjct: 6 SFLLSKVSFVIKKIRLEKGMTQEDLAYKSN------LDRTYISGIERNSRNLTIKSLELI 59
>3uau_A JLPA, surface-exposed lipoprotein; adhesin, bacterial cell
surface, cell adhesion; 2.70A {Campylobacter jejuni
subsp}
Length = 379
Score = 30.5 bits (68), Expect = 0.88
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 30.5 bits (68), Expect = 0.88
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 45 HHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 28.6 bits (63), Expect = 4.0
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 41 LKYQHHHHHHHH 52
+ + HHHHHHHH
Sbjct: 1 MGHHHHHHHHHH 12
>2c07_A 3-oxoacyl-(acyl-carrier protein) reductase; oxidoreductase, FABG,
short-chain alcohol reductase, fatty acid biosynthesis,
apicoplast; 1.5A {Plasmodium falciparum} SCOP: c.2.1.2
Length = 285
Score = 30.6 bits (70), Expect = 0.89
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 45 HHHHHHHHHQVPS 57
HHHHHHHHH
Sbjct: 3 HHHHHHHHHHSSG 15
Score = 30.2 bits (69), Expect = 0.95
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 28.3 bits (64), Expect = 4.0
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 46 HHHHHHHHQVPSSPSPNGH 64
HHHHHHHH S H
Sbjct: 3 HHHHHHHHHHSSGHIEGRH 21
Score = 28.3 bits (64), Expect = 4.4
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 41 LKYQHHHHHHHH 52
+ + HHHHHHHH
Sbjct: 1 MGHHHHHHHHHH 12
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
caldolyticus} SCOP: a.35.1.3
Length = 77
Score = 28.4 bits (64), Expect = 0.90
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE--ALQLSFKNMCKL 267
+ F + K+ R + G +Q ++ G +T I E +S N+ K+
Sbjct: 6 EIKRKFGRTLKKIRTQKGVSQEELADLAG------LHRTYISEVERGDRNISLINIHKI 58
>3u61_A DNA polymerase accessory protein 62; AAA+, ATP hydrolase, clamp
loader, sliding clamp, primer-TEM DNA, DNA binding
protein-DNA complex; HET: DNA ADP 08T; 3.20A
{Enterobacteria phage T4} PDB: 3u5z_A* 3u60_A*
Length = 199
Score = 29.9 bits (67), Expect = 1.0
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 44 QHHHHHHHHHQ 54
+HHHHHHHHH
Sbjct: 189 EHHHHHHHHHH 199
Score = 28.7 bits (64), Expect = 2.4
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 41 LKYQHHHHHHHH 52
L++ HHHHHHHH
Sbjct: 188 LEHHHHHHHHHH 199
>3r3h_A O-methyltransferase, SAM-dependent; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.65A {Legionella pneumophila subsp}
Length = 242
Score = 30.3 bits (69), Expect = 1.0
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 18 DGMNIVNTSIGYPSPRSVPDSGELKYQHHHHHHHHHQ 54
DGM +V + + ++ + HHHHH H Q
Sbjct: 212 DGMFLV---------QPIAENLYFQSHHHHHHWSHPQ 239
>3nc3_A Cytochrome P450 CYPX; cytochrome P450 oxidase, HAEM protein,
oxidoreductase; HET: HEM; 2.66A {Bacillus subtilis} PDB:
3nc5_A* 3nc6_A* 3nc7_A*
Length = 441
Score = 30.4 bits (69), Expect = 1.1
Identities = 14/67 (20%), Positives = 18/67 (26%), Gaps = 6/67 (8%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQ 104
HHHHHH VP Q S N+ + + Q
Sbjct: 5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMSQSIKLFSVLS---DQFQNNPYAYFSQ 61
Query: 105 ---QSPV 108
+ PV
Sbjct: 62 LREEDPV 68
>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning,
protein-DNA complex, heilx-turn- helix motif,
transcription factor; HET: BRU; 2.20A {Escherichia coli}
SCOP: a.4.14.1
Length = 178
Score = 29.8 bits (67), Expect = 1.1
Identities = 18/160 (11%), Positives = 42/160 (26%), Gaps = 33/160 (20%)
Query: 211 DDL----EAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCK 266
++L A F R + G + D+ +G S I + L
Sbjct: 34 NELTPREIA---DFIGRELAKGKKKGDIAKEIGK------SPAFITQHVTLL-------D 77
Query: 267 LKPLLQKWLEEADSTTG------------SPTSIDKIAAQGRKRKKRTSIEVTVKGALET 314
L + P ++ + R ++++ ++ L+
Sbjct: 78 LPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKL-LREFLDE 136
Query: 315 HFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
A T A+ + ++ K+ +
Sbjct: 137 KGRDPNTVDAFNGQTDAERDAEAGDGQDGEDGDQDGKDAK 176
>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2,
protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} PDB:
3p5j_B 3puf_B 3p56_B
Length = 332
Score = 30.2 bits (67), Expect = 1.2
Identities = 16/47 (34%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 47 HHHHHHHQVPSS-------PSPNGHPVSLSAAHNPWVSLQPGAGADP 86
HHHHHH Q P+S P G A V L P D
Sbjct: 5 HHHHHHSQDPNSLEVLFQGPMAGGRD-RGDLAARQLVFLLPEHLKDA 50
>2w1i_A JAK2; chromosomal rearrangement, nucleotide-binding,
tyrosine-protein kinase, proto-oncogene,
phosphoprotein, disease mutation, SH2 domain; HET: PTR
L0I; 2.60A {Homo sapiens}
Length = 326
Score = 30.0 bits (68), Expect = 1.2
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 45 HHHHHHHHHQVPSSPS--PNGHPVSLSAAHNPWV 76
+HHHHHH + +P++ + G S +P
Sbjct: 4 YHHHHHHDYDIPTTENLYFQGAMGSAFEDRDPTQ 37
>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic
aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo
sapiens} PDB: 2xiq_A* 3bic_A
Length = 762
Score = 30.4 bits (69), Expect = 1.3
Identities = 9/49 (18%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 6 YLPASSVVASDLDGMNIVNTSIGYPSPRSVPDSGELKYQHHHHHHHHHQ 54
+ P + + + + ++ + + + + L +Q HHHHHH ++
Sbjct: 712 FGPGTRIPKAAVQVLDDIEKCLEK---KQQSVAENLYFQSHHHHHHDYK 757
>1svj_A Potassium-transporting ATPase B chain; alpha-beta sandwich,
hydrolase; NMR {Escherichia coli} SCOP: d.220.1.1 PDB:
1u7q_A 2a00_A* 2a29_A*
Length = 156
Score = 29.4 bits (66), Expect = 1.3
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 29.4 bits (66), Expect = 1.3
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 45 HHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 27.5 bits (61), Expect = 6.0
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 41 LKYQHHHHHHHH 52
+ + HHHHHHHH
Sbjct: 1 MGHHHHHHHHHH 12
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide
binding, hydrogenase maturation factor transferase; HET:
ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A*
3ttf_A* 3ttd_A 3tsq_A
Length = 657
Score = 30.1 bits (68), Expect = 1.5
Identities = 4/10 (40%), Positives = 4/10 (40%)
Query: 44 QHHHHHHHHH 53
HHH H
Sbjct: 385 LHHHAHAAAC 394
>3ga4_A Dolichyl-diphosphooligosaccharide-protein glycosyltransferase
subunit OST6; oxidoreductase, active site loop, redox
state, membrane; HET: PG4; 1.30A {Saccharomyces
cerevisiae} PDB: 3g7y_A 3g9b_A*
Length = 178
Score = 29.2 bits (65), Expect = 1.5
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 22 IVNTSIGYPSPRSVPDSGELKYQHHHHHHHH 52
I+N SI P + E + HHHHHHHH
Sbjct: 151 ILNISITVPQA---FNVQEEFHHHHHHHHHH 178
>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine
kinase domain, signaling protein, transferase, inner
membrane, membrane; 2.50A {Escherichia coli}
Length = 299
Score = 29.6 bits (67), Expect = 1.6
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 29.6 bits (67), Expect = 1.9
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 45 HHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
Score = 27.7 bits (62), Expect = 6.9
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 41 LKYQHHHHHHHH 52
+ + HHHHHHHH
Sbjct: 1 MGHHHHHHHHHH 12
>3u4j_A NAD-dependent aldehyde dehydrogenase; PSI-biology, nysgrc,
structural genomics, NEW YORK structura genomics
research consortium, tetramer; 2.00A {Sinorhizobium
meliloti}
Length = 528
Score = 29.8 bits (68), Expect = 1.6
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 23 VNTSIGYPSPRSVPDSGELKYQHHHHHHH 51
V+ ++G P+P + L +Q HHHHHH
Sbjct: 494 VHVTLGRPAP--WFTAENLYFQSHHHHHH 520
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 29.8 bits (66), Expect = 1.7
Identities = 13/158 (8%), Positives = 23/158 (14%), Gaps = 5/158 (3%)
Query: 63 GHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSPVDIKPPPDMHRTSHQ 122
P+ + A + G + Q
Sbjct: 79 DKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQ 138
Query: 123 HGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAYHVNVMNGMLHHHQPSPQLHHSLR 182
G P P + H + + Q
Sbjct: 139 GPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQM--- 195
Query: 183 DIQAHSPSYSQSQHPDAPSGSEEDAPTSDDLEAFAKQF 220
P + + + L QF
Sbjct: 196 --PPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQF 231
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 29.7 bits (66), Expect = 1.7
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 47 HHHHHHHQVPSSPSPN------GHPVSLSAAHNPWVSL 78
HHHHHH Q P+S +L++ W S+
Sbjct: 4 HHHHHHSQDPNSMPARALLPRRMGHRTLASTPALWASI 41
>2r5o_A Putative ATP binding component of ABC- transporter;
immunoglobulin fold, carbohydrate binding, domain
swapping, O antigen export; HET: PG4; 1.30A
{Escherichia coli}
Length = 188
Score = 29.2 bits (65), Expect = 1.7
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVS 67
HHHHHHHHH + S+ + +
Sbjct: 2 HHHHHHHHHHISSASGESQMSLD 24
>1v8p_A Hypothetical protein PAE2754; PIN-domain, tetramer, structural
genomics, unknown function; 2.52A {Pyrobaculum
aerophilum} SCOP: c.120.1.1 PDB: 1v8o_A
Length = 158
Score = 28.9 bits (64), Expect = 1.7
Identities = 7/14 (50%), Positives = 12/14 (85%)
Query: 45 HHHHHHHHHQVPSS 58
+HHHHHH + +P++
Sbjct: 4 YHHHHHHDYDIPTT 17
>2fe1_A Conserved hypothetical protein PAE0151; PIN domain, structural
genomics, unknown function; 2.20A {Pyrobaculum
aerophilum} SCOP: c.120.1.1
Length = 156
Score = 28.9 bits (64), Expect = 1.8
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 45 HHHHHHHHHQVPSSPS 60
+HHHHHH + +P++ +
Sbjct: 4 YHHHHHHDYDIPTTEN 19
>4af8_A Metacaspase MCA2; hydrolase, cysteine peptidase, caspase/hemoglobin
fold; 1.40A {Trypanosoma brucei} PDB: 4afp_A 4afv_A
4afr_A
Length = 367
Score = 29.6 bits (65), Expect = 1.9
Identities = 15/78 (19%), Positives = 21/78 (26%), Gaps = 3/78 (3%)
Query: 47 HHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQS 106
HHHHHH + + ++ G G SS P + Q
Sbjct: 5 HHHHHHSSGLVPGGSHMCSLITQLCDAGQLADYVGLGWLNAVSSQPYLVQ---ALGLQPP 61
Query: 107 PVDIKPPPDMHRTSHQHG 124
P + HG
Sbjct: 62 PRRVDVDAAFRDAKGLHG 79
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding,
transcription, transcription regulation; 1.64A
{Enterobacteria phage lambda}
Length = 80
Score = 27.7 bits (61), Expect = 1.9
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 8/64 (12%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLK 268
+D +++++ +LG + V +G Q+ + L+ N L
Sbjct: 8 EDARRLKAIWEKKKNELGLSYESVADKMG------MGQSAVAALFNGINALNAYNAALLA 61
Query: 269 PLLQ 272
+L+
Sbjct: 62 KILK 65
>4fl4_A Glycoside hydrolase family 9; structural genomics,
montreal-kingston bacterial structural initiative,
BSGI, dockerin; 2.80A {Clostridium thermocellum} PDB:
3p0d_A
Length = 88
Score = 27.6 bits (62), Expect = 1.9
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 46 HHHHHHHHQVPSSPSPN 62
HHHHHHHH S
Sbjct: 3 HHHHHHHHHHSSGHIEG 19
Score = 27.3 bits (61), Expect = 2.9
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 45 HHHHHHHHHQVPSSPS 60
HHHHHHHHH
Sbjct: 3 HHHHHHHHHHSSGHIE 18
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 29.8 bits (66), Expect = 2.0
Identities = 16/157 (10%), Positives = 29/157 (18%)
Query: 52 HHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSPVDIK 111
HH+ P + P S +
Sbjct: 3 HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62
Query: 112 PPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAYHVNVMNGMLHHH 171
P S + H V + +
Sbjct: 63 TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122
Query: 172 QPSPQLHHSLRDIQAHSPSYSQSQHPDAPSGSEEDAP 208
QPS + ++R + P ++ P + P
Sbjct: 123 QPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPP 159
Score = 29.4 bits (65), Expect = 2.8
Identities = 17/163 (10%), Positives = 31/163 (19%), Gaps = 13/163 (7%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVS--------LSAAHNPWVSLQPGAGADPWSSSMPGIHNH 97
HH + Q N P+ A Q G SM
Sbjct: 3 HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62
Query: 98 HHPHHHQQSPVDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHS 157
+D + P + + Q +
Sbjct: 63 TPAQEQLHQQIDQATTS-----MNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117
Query: 158 AYHVNVMNGMLHHHQPSPQLHHSLRDIQAHSPSYSQSQHPDAP 200
A + + + + + + P + P P
Sbjct: 118 APAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 30.0 bits (67), Expect = 2.1
Identities = 10/62 (16%), Positives = 12/62 (19%), Gaps = 1/62 (1%)
Query: 350 QKEKRMTPPNTLGGPQDGMMEGQLGMHGYHHPDLHGSPMGPHSHSHSHSPPMLSPSHQSM 409
+ + M G P SPM S SP Q
Sbjct: 1454 DMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTP-YERSPMVDSGFVGSPDAAAFSPLVQGG 1512
Query: 410 QS 411
Sbjct: 1513 SE 1514
Score = 27.7 bits (61), Expect = 8.3
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 124 GGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAYHVNVMNGMLHHHQPSPQLHHSLRD 183
G G+P+ +P+V S ++ S ++ A SPL + SP +
Sbjct: 1480 EGAGTPYE-RSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASP---YKGVQ 1535
Query: 184 IQAHSPSYSQSQHPDAPSGSEEDAPTS 210
++ +S + P S +P+S
Sbjct: 1536 SPGYTSPFSSAMSPGYGLTSPSYSPSS 1562
>1v58_A Thiol:disulfide interchange protein DSBG; reduced DSBG, redox
protein, protein disulfide isomerase, thioredoxin fold;
1.70A {Escherichia coli} SCOP: c.47.1.9 d.17.3.1 PDB:
1v57_A 2h0i_A 2h0h_A 2h0g_A 2iy2_A
Length = 241
Score = 29.2 bits (65), Expect = 2.1
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 18 DGMNIVNTSIGYPSPRSVPDSGELKYQHHHHHHHH 52
N + ++G P +++ K QHHHHHHHH
Sbjct: 207 SKENTLQQAVGLPDQKTLNIIMGNKLQHHHHHHHH 241
>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 = 30.0 bits (67), Expect = 2.1
Identities = 29/173 (16%), Positives = 45/173 (26%), Gaps = 74/173 (42%)
Query: 4 TTYLPASSVVASDLDGMNIVNTSIGYPSP----RSVPDSGELKYQHHHHHHHHHQVPSSP 59
T LP S + S + + G PSP ++ Y + + H +P+
Sbjct: 316 NTSLPPSILEDS-------LENNEGVPSPMLSISNLTQEQVQDYVNKTNSH----LPAGK 364
Query: 60 --------SPN-----GHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQS 106
G P SL ++L + P QS
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYG-----LNLT--------------LRKAKAPSGLDQS 405
Query: 107 PVDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGAASPLQHHSAY 159
+ P S S+ ++P ASP HS
Sbjct: 406 RI--------------------PFSERKLKFSNRFLP-----VASPF--HSHL 431
>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription
factor, DNA binding protein; 1.88A {Neisseria
meningitidis}
Length = 114
Score = 28.3 bits (63), Expect = 2.1
Identities = 9/57 (15%), Positives = 18/57 (31%), Gaps = 6/57 (10%)
Query: 199 APSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ E D A + R+ G++Q ++ G +T + E
Sbjct: 5 KLTLPAELPDEQDLRAVLAYNMRLFRVNKGWSQEELARQCG------LDRTYVSAVE 55
>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 = 27.3 bits (61), Expect = 2.2
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 6/66 (9%)
Query: 295 GRKRKKRTSIEVTV--KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKE 352
R++++ + + T +H P PS + LA + V WF N+R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSN-PYPSEEAKEELAKKCGITVSQVSNWFGNKR--- 56
Query: 353 KRMTPP 358
R
Sbjct: 57 IRYKKN 62
>3tjj_A Peroxiredoxin-4; thioredoxin fold, sulfenylation, endoplasmic
reticulum, oxidoreductase; HET: CSO; 1.91A {Homo
sapiens} PDB: 3tjk_A 3tjb_A 3tjf_A 3tjg_A 3tkq_A 3tkp_A
3tks_A 3tkr_A 3tks_C
Length = 254
Score = 29.3 bits (66), Expect = 2.3
Identities = 16/71 (22%), Positives = 22/71 (30%), Gaps = 3/71 (4%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQ 104
HHHHHH Q P P + AG + + H H
Sbjct: 3 SSHHHHHHSQDPLVPRGSWETEERPRTREE--ECHFYAGGQVYPGEASRVSVADHSLHLS 60
Query: 105 QSPVDIKPPPD 115
++ + KP P
Sbjct: 61 KAKIS-KPAPY 70
>3oc3_A Helicase MOT1, MOT1; regulation of transcription,
hydrolase-transc complex; HET: MES; 3.10A
{Encephalitozoon cuniculi}
Length = 800
Score = 29.5 bits (65), Expect = 2.4
Identities = 9/9 (100%), Positives = 9/9 (100%)
Query: 45 HHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHH 11
Score = 29.1 bits (64), Expect = 3.1
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding,
helix-turn-helix, zinc binding, GE regulation; 2.70A
{Mycobacterium tuberculosis}
Length = 131
Score = 28.3 bits (64), Expect = 2.5
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 37 DSGELKYQHHHHHHHHH 53
D+GE Y+ HHHHH
Sbjct: 67 DTGESVYRRCSEHHHHH 83
>3qtc_A Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP B
O-methyl tyrosine binding, magnesium binding,
aminoacylatio esterification; HET: 0A1 ANP; 1.75A
{Methanosarcina mazei} PDB: 2q7e_A* 2q7g_A* 2q7h_A*
2zim_A* 2zin_A* 2e3c_A* 2zcd_A* 2zce_A* 2zio_A*
Length = 290
Score = 29.1 bits (65), Expect = 2.5
Identities = 10/31 (32%), Positives = 12/31 (38%)
Query: 44 QHHHHHHHHHQVPSSPSPNGHPVSLSAAHNP 74
HHHHHHH VP P + +
Sbjct: 3 HHHHHHHHGGLVPRGSHGASAPALTKSQTDR 33
>2p0u_A Stilbenecarboxylate synthase 2; polyketide synthase, PKS type
transferase; 1.90A {Marchantia polymorpha}
Length = 413
Score = 29.2 bits (65), Expect = 2.5
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 44 QHHHHHHHHHQVPSSPSPNGHPVSLSAAHNP 74
+HHHHHHHH + S G S A
Sbjct: 2 KHHHHHHHHGGLVPRGSHGGSSRSRLIAQAV 32
>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 = 27.9 bits (61), Expect = 2.6
Identities = 21/102 (20%), Positives = 34/102 (33%), Gaps = 26/102 (25%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEV----------- 340
+ G + R + L + +Q PS +E L + + +
Sbjct: 1 GSSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 60
Query: 341 --------VRV--WFCNRRQKEKR-----MTPPNTLGGPQDG 367
VRV WF NRR++E M ++ GP G
Sbjct: 61 LGSNLVTEVRVYNWFANRRKEEAFRQKLAMDAYSSNSGPSSG 102
>2oay_A C1-inhibitor, plasma protease C1 inhibitor, C1 INH, C1INH; latent
serpin, RCL insertion, immune system,hydrolase inhibi;
HET: NAG; 2.35A {Homo sapiens}
Length = 390
Score = 29.1 bits (66), Expect = 2.6
Identities = 10/30 (33%), Positives = 11/30 (36%)
Query: 43 YQHHHHHHHHHQVPSSPSPNGHPVSLSAAH 72
Y HHHHHH P + S S
Sbjct: 1 YVHHHHHHTGSFCPGPVTLCSDLESHSTEA 30
>2bgs_A Aldose reductase; holoenzyme, aldo/keto reductase,
oxidoreductase; HET: NDP; 1.64A {Hordeum vulgare} PDB:
2bgq_A* 2vdg_A*
Length = 344
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/36 (36%), Positives = 15/36 (41%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQP 80
HHHHHHHHH + H + SA Q
Sbjct: 3 HHHHHHHHHSSGHIDDDDKHMLEASAKATMGQGEQD 38
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural
genomics, PSI-2, protein structure initiative; NMR
{Eubacterium rectale atcc 33656}
Length = 94
Score = 27.4 bits (61), Expect = 2.8
Identities = 7/42 (16%), Positives = 14/42 (33%), Gaps = 6/42 (14%)
Query: 214 EAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
F++ K TQ ++ ++G S T +
Sbjct: 8 AIFSENLNSYIAKSEKTQLEIAKSIG------VSPQTFNTWC 43
>3b9f_I Protein C inhibitor; michaelis complex, acute phase, blood
coagulation, cleavage of basic residues, disease
mutation; HET: NAG FUC SGN IDS; 1.60A {Homo sapiens}
PDB: 2ol2_A*
Length = 395
Score = 29.1 bits (66), Expect = 3.1
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAA 71
HHHHHHHHH + H V + A
Sbjct: 4 HHHHHHHHHSSGHIDDDDKHMVGATVA 30
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 28.7 bits (65), Expect = 3.2
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 37 DSGELKYQHHHHHHHHHQVP 56
S E Y HHHHHH P
Sbjct: 301 QSAENLYFQSHHHHHHWSHP 320
>3s3u_A Cysteine transferase; autoproteolytic, carbapenem, biosynthesis,
DOM-fold, amidohy transferase; 1.60A {Streptomyces
cattleya}
Length = 419
Score = 29.1 bits (64), Expect = 3.2
Identities = 11/51 (21%), Positives = 16/51 (31%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHN 96
HHHHHH P + + + + +PG HN
Sbjct: 3 SSHHHHHHSSGLVPRGSHMDPEAGSRARGLKGVHRVSANSGGIGGVPGPHN 53
>3tla_A MCCF; serine protease, hydrolase; 1.20A {Escherichia coli} PDB:
3tle_A* 3tlg_A 3tlb_A* 3tlc_A* 3tlz_A* 3tly_A
Length = 371
Score = 29.0 bits (65), Expect = 3.3
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 41 LKYQHHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWV--SLQPG 81
+ + HHHHHHHHH + + +P + L G
Sbjct: 1 MGHHHHHHHHHHHHSSGHIDDDDKHMLEMIQSHPLLAAPLAVG 43
>1zxj_A MPN555, hypothetical protein Mg377 homolog; mostly alpha helical
protein, TRI-lobal structure, structural genomics, PSI;
2.80A {Mycoplasma pneumoniae}
Length = 218
Score = 28.6 bits (63), Expect = 3.4
Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 46 HHHHHHHHQVPSSPS--PNGH 64
HHHHHH + +P++ + GH
Sbjct: 5 HHHHHHDYDIPTTENLYFQGH 25
>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-BIND protein; HET: CYS GOL;
1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A
Length = 283
Score = 28.5 bits (64), Expect = 3.5
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 45 HHHHHHHHHQ 54
HHHHHHHHH
Sbjct: 3 HHHHHHHHHH 12
>3f4s_A Alpha-DSBA1, putative uncharacterized protein; thioredoxin-fold,
oxidoreductase; HET: PGE; 1.55A {Wolbachia pipientis}
PDB: 3f4r_A* 3f4t_A*
Length = 226
Score = 28.3 bits (63), Expect = 3.5
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 39 GELKYQHHHHHHHH 52
+K +HHHHHHHH
Sbjct: 213 AIVKLEHHHHHHHH 226
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
a.4.1.1
Length = 80
Score = 26.9 bits (59), Expect = 3.7
Identities = 8/67 (11%), Positives = 22/67 (32%), Gaps = 4/67 (5%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQ----PKPSAQEITTLADSLQLEKEVVRVWFCN 347
++ G ++ RT K + + K + + ++V+++W N
Sbjct: 12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71
Query: 348 RRQKEKR 354
+
Sbjct: 72 NKNSGPS 78
>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 = 26.6 bits (59), Expect = 3.9
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 6/69 (8%)
Query: 293 AQGRKRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
+ G+ ++ T ++ L H P P+ E +A L V WF N R
Sbjct: 5 SSGKNKRGVLPKHATNVMRSWLFQHIGH-PYPTEDEKKQIAAQTNLTLLQVNNWFINAR- 62
Query: 351 KEKRMTPPN 359
+R+
Sbjct: 63 --RRILQSG 69
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 27.1 bits (60), Expect = 3.9
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 4/68 (5%)
Query: 291 IAAQGRKRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCN- 347
+ E ++ L H + PS QE L+ L V WF N
Sbjct: 1 MGHHHHHHSHMLPKESVQILRDWLYEHRYN-AYPSEQEKALLSQQTHLSTLQVCNWFINA 59
Query: 348 RRQKEKRM 355
RR+ M
Sbjct: 60 RRRLLPDM 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 = 26.6 bits (59), Expect = 4.1
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 293 AQGRKRKKRTSIEVT--VKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
+ G+KRK E ++ + H K PS +E L++ L + WF N R
Sbjct: 5 SSGKKRKGNLPAESVKILRDWMYKHRFK-AYPSEEEKQMLSEKTNLSLLQISNWFINAR- 62
Query: 351 KEKRMTPP 358
+R+ P
Sbjct: 63 --RRILPD 68
>3hzu_A Thiosulfate sulfurtransferase SSEA; niaid, ssgcid, infectious
disease, transferase structural genomics; 2.10A
{Mycobacterium tuberculosis} PDB: 3p3a_A
Length = 318
Score = 28.4 bits (64), Expect = 4.1
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 49 HHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADP 86
HHHHH + + + P S+ +P +L A +
Sbjct: 3 HHHHHHMGTLEAQTQGPGSMPLPADPSPTLSAYAHPER 40
>3tkt_A Cytochrome P450; aromatic hydrocarbon binding of P450 E
oxidoreductase; HET: HEM; 2.20A {Novosphingobium
aromaticivorans}
Length = 450
Score = 28.5 bits (64), Expect = 4.1
Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 1/44 (2%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQ-PGAGADPW 87
HHHHHH VP + P+ + + + G
Sbjct: 5 HHHHHHSSGLVPRGSHMDSIPMVPAEVGRAVIDPKSYGTWEPLL 48
>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP
binding, structure function project, S2F, unknown
function; 2.00A {Escherichia coli} SCOP: c.37.1.10
d.237.1.1
Length = 318
Score = 28.3 bits (64), Expect = 4.2
Identities = 2/19 (10%), Positives = 5/19 (26%)
Query: 36 PDSGELKYQHHHHHHHHHQ 54
+ + + H Q
Sbjct: 203 LEENVVSTKPRFHFIADKQ 221
Score = 27.9 bits (63), Expect = 5.6
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSA 70
H + + S +PV +S
Sbjct: 214 FHFIADKQNDISSIVVELDYPVDISE 239
>3tr9_A Dihydropteroate synthase; biosynthesis of cofactors, prosthetic
groups, and carriers, transferase; HET: PT1; 1.90A
{Coxiella burnetii}
Length = 314
Score = 28.3 bits (64), Expect = 4.3
Identities = 9/10 (90%), Positives = 9/10 (90%)
Query: 44 QHHHHHHHHH 53
HHHHHHHHH
Sbjct: 305 HHHHHHHHHH 314
Score = 27.6 bits (62), Expect = 7.4
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 31 SPRSVPDSGELKYQHHHHHHHHHQ 54
S ++ + HHHHHHHHH
Sbjct: 291 SVDTIEEENLYFQGHHHHHHHHHH 314
>2g0q_A AT5G39720.1 protein; structural genomics, protein structure
initiative, center for eukaryotic structural genomics,
CESG, unknown function; NMR {Arabidopsis thaliana}
Length = 173
Score = 28.0 bits (62), Expect = 4.3
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 48 HHHHHHQVPSSPSPNGHPV 66
HHHHHH SS S H V
Sbjct: 2 HHHHHHLECSSDSLQLHNV 20
>3qrz_A Abscisic acid receptor PYL5; crystal, hormone receptor; 2.60A
{Arabidopsis thaliana}
Length = 223
Score = 28.3 bits (62), Expect = 4.4
Identities = 22/122 (18%), Positives = 32/122 (26%), Gaps = 22/122 (18%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAH-----NPWVSLQPGAGADPWSSSMPGIHNHHHP-- 100
HHHHH + + H N + +LQP D + H P
Sbjct: 5 HHHHHSSGENLYFQGHMRSPVQLQHGSDATNGFHTLQPHDQTDGPIKRVCLTRGMHVPEH 64
Query: 101 ----HHHQQSP--------VDIKPPPDMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSG 148
H H P I PP+ +P + + I G+
Sbjct: 65 VAMHHTHDVGPDQCCSSVVQMIHAPPE--SVWALVRRFDNPKVYK-NFIRQCRIVQGDGL 121
Query: 149 AA 150
Sbjct: 122 HV 123
>4ets_A Ferric uptake regulation protein; metal binding protein,
transcription factor; 2.10A {Campylobacter jejuni subsp}
Length = 162
Score = 27.7 bits (62), Expect = 4.5
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 37 DSGELKYQHHHHHHHHHQV 55
S KY+ + HH H +
Sbjct: 91 GSAGKKYELANKPHHDHMI 109
>2d2a_A SUFA protein; iron-sulfur cluster, iron, ISCA, YADR, metal
transport; 2.70A {Escherichia coli}
Length = 145
Score = 27.7 bits (62), Expect = 4.6
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 93 GIHNHHHPHHHQQSPVD 109
G H+HHH HHH +D
Sbjct: 2 GHHHHHHHHHHSSGHID 18
Score = 26.6 bits (59), Expect = 8.9
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 45 HHHHHHHHHQVPSSPSPN 62
HHHHHHHHH +
Sbjct: 3 HHHHHHHHHHSSGHIDDD 20
>2i68_A Protein EMRE; transmembrane protein, small-multidrug resistance,
transporter, homodimer, dual topology, transport
protein; NMR {Escherichia coli}
Length = 137
Score = 27.4 bits (61), Expect = 4.6
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 19 GMNIVNTSIGYP----SPRSVPDSGELKYQHHHHHHHH 52
+N+++ S + + + +L HHHHHH
Sbjct: 100 IINLLSRSTPHEFEAYVEQKLISEEDLNSAVDHHHHHH 137
>1o13_A Probable NIFB protein; ribonuclease H-like motif fold, structural
genomics, joint C structural genomics, JCSG, protein
structure initiative; 1.83A {Thermotoga maritima} SCOP:
c.55.5.1 PDB: 1t3v_A
Length = 136
Score = 27.6 bits (61), Expect = 4.7
Identities = 11/20 (55%), Positives = 12/20 (60%), Gaps = 4/20 (20%)
Query: 38 SGELKY----QHHHHHHHHH 53
SG+LK H HHHH HH
Sbjct: 117 SGQLKDSDYEVHDHHHHEHH 136
>3sam_A 62 kDa protein, rifampicin resistance protein; double-barrel,
jelly-roll, scaffolding protein, structural P
rifampicin-resistance protein; 2.55A {Vaccinia virus}
PDB: 3saq_A 2ygc_A* 2ygb_A
Length = 576
Score = 28.5 bits (63), Expect = 4.7
Identities = 7/14 (50%), Positives = 12/14 (85%)
Query: 45 HHHHHHHHHQVPSS 58
+HHHHHH + +P++
Sbjct: 4 YHHHHHHDYDIPTT 17
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain,
coiled-coil domain, DNA and cleavage, nucleus; HET: DNA
EVP; 2.16A {Homo sapiens}
Length = 803
Score = 28.6 bits (63), Expect = 4.7
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 35 VPDSGELKYQHHHHHHHHH 53
P + HHHHHHHHH
Sbjct: 785 APGFSSISAHHHHHHHHHH 803
>4e1r_A Protein LSR2; anti-parallel beta sheet, dimer, DNA binding
protein; 2.04A {Mycobacterium tuberculosis}
Length = 86
Score = 26.8 bits (59), Expect = 4.7
Identities = 7/14 (50%), Positives = 12/14 (85%)
Query: 45 HHHHHHHHHQVPSS 58
+HHHHHH + +P++
Sbjct: 4 YHHHHHHDYDIPTT 17
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 28.4 bits (64), Expect = 4.8
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVS 67
HHHHHHHHH ++
Sbjct: 3 HHHHHHHHHHSSGHIEGRHMDIN 25
>3c3r_A Programmed cell death 6-interacting protein; ALIX BRO1 CHMP4C
amphipathic-helix, apoptosis, HOST-virus interaction,
protein transport, transport; 2.02A {Homo sapiens} PDB:
2oew_A 3c3o_A 3c3q_A
Length = 380
Score = 28.3 bits (62), Expect = 5.1
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 45 HHHHHHHHHQVPSSPSPNGH 64
HHHHHHHHH + GH
Sbjct: 2 HHHHHHHHHHSGQNLYFQGH 21
Score = 27.9 bits (61), Expect = 7.0
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 44 QHHHHHHHHHQVPSSPS 60
HHHHHHHHH +
Sbjct: 2 HHHHHHHHHHSGQNLYF 18
>2cnt_A Modification of 30S ribosomal subunit protein S18; N-alpha
acetylation, GCN5-N-acetyltransferase, ribosomal Pro
acetyltransferase, GNAT; HET: COA; 2.4A {Salmonella
typhimurium} PDB: 2cnm_A* 2cns_A*
Length = 160
Score = 27.6 bits (62), Expect = 5.2
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 41 LKYQHHHHHHHHH 53
+K HHHHHHHHH
Sbjct: 148 MKLHHHHHHHHHH 160
>3ubk_A Glutathione transferase; GSH binding; 1.95A {Leptospira interrogans
serovar lai} PDB: 3ubl_A*
Length = 242
Score = 28.1 bits (63), Expect = 5.4
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 40 ELKYQHHHHHHH 51
L +Q HHHHHH
Sbjct: 223 NLYFQSHHHHHH 234
>3qre_A Enoyl-COA hydratase, ECHA12_1; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, tuberculosis; 2.40A {Mycobacterium marinum M}
Length = 298
Score = 28.0 bits (63), Expect = 5.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 49 HHHHHQVPSSPSPNGHPVSLSAA 71
HHHHH + + + P S+SAA
Sbjct: 3 HHHHHHMGTLEAQTQGPGSMSAA 25
>3lgd_A Adenosine deaminase CECR1; TIM barrel, dimerization and receptor
binding domains, glyco hydrolase, growth factor,
secreted; HET: NAG; 2.00A {Homo sapiens} PDB: 3lgg_A*
Length = 508
Score = 28.4 bits (63), Expect = 5.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 31 SPRSVPDSGELKYQHHHHHHHH 52
S + D+ ++ + H HHHHHH
Sbjct: 487 SLHHILDAQKMVWNHRHHHHHH 508
>1wuf_A Hypothetical protein LIN2664; structural genomics, unknown
function, nysgxrc target T2186, superfamily, protein
structure initiative, PSI; 2.90A {Listeria innocua}
SCOP: c.1.11.2 d.54.1.1
Length = 393
Score = 28.0 bits (63), Expect = 5.8
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 46 HHHHHHHHQVPSSP 59
HHHHHHHH P
Sbjct: 2 HHHHHHHHHHGLVP 15
Score = 27.3 bits (61), Expect = 9.3
Identities = 9/9 (100%), Positives = 9/9 (100%)
Query: 45 HHHHHHHHH 53
HHHHHHHHH
Sbjct: 2 HHHHHHHHH 10
>2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane
protein; 3.10A {Archaeoglobus fulgidus} SCOP: f.58.1.1
Length = 284
Score = 28.1 bits (63), Expect = 5.9
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 45 HHHHHHHHHQVPSSP 59
HHHHHHHHH
Sbjct: 3 HHHHHHHHHHSSGEN 17
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 25.7 bits (57), Expect = 5.9
Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358
L H P PS ++ LA L V WF N R +R+ P
Sbjct: 17 LFQHLTH-PYPSEEQKKQLAQDTGLTILQVNNWFINAR---RRIVQP 59
>3pqa_A Lactaldehyde dehydrogenase; structural genomics, protein structure
initiative, nysgrc, P biology, oxidoreductase; 1.50A
{Methanocaldococcus jannaschii} PDB: 3rhd_A*
Length = 486
Score = 28.3 bits (64), Expect = 6.0
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 38 SGELKYQHHHHHHH 51
+ L +Q HHHHHH
Sbjct: 465 AENLYFQSHHHHHH 478
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA
binding motif, transcriptional regulator, bacter
antitoxin, Zn binding protein, transcription
regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB:
3gn5_A* 3gn5_B* 2kz8_A
Length = 133
Score = 27.0 bits (59), Expect = 6.1
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 6/39 (15%)
Query: 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ + R KL TQ + G R+E
Sbjct: 73 PEFIVKVRKKLSLTQKEASEIFGG------GVNAFSRYE 105
>3sgw_A Ribose 5-phosphate isomerase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, valley fever; 1.70A {Coccidioides immitis} PDB:
3sdw_A 3qd5_A*
Length = 184
Score = 27.6 bits (62), Expect = 6.6
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 49 HHHHHQVPSSPSPNGHPVSLSAAHNP 74
HHHHH + + + P S++A P
Sbjct: 3 HHHHHHMGTLEAQTQGPGSMAATPLP 28
>3r24_A NSP16, 2'-O-methyl transferase; methyltransferase, zinc-finger,
transferase, viral protein; HET: SAM; 2.00A {Sars
coronavirus}
Length = 344
Score = 27.8 bits (61), Expect = 6.6
Identities = 14/58 (24%), Positives = 18/58 (31%), Gaps = 3/58 (5%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHH 102
HHHHHH VP +G + +A P G D +M
Sbjct: 2 HHHHHHSSGLVPRG---SGMKETAAAKFERQHMDSPDLGTDDDDKAMAASQAWQPGVA 56
>1pq4_A Periplasmic binding protein component of AN ABC T uptake
transporter; ZNUA, loop, metal-binding, metal binding
protein; 1.90A {Synechocystis SP} SCOP: c.92.2.2 PDB:
2ov3_A 2ov1_A
Length = 291
Score = 27.8 bits (62), Expect = 6.7
Identities = 9/44 (20%), Positives = 12/44 (27%), Gaps = 2/44 (4%)
Query: 95 HNHHHPHHHQQSPVDIKPPPDMHRTSHQHGGMGS--PHSWHTPV 136
H+H H D G + PH W +P
Sbjct: 96 HSHGEEEGHDDHSHDGHDHGSESEKEKAKGALMVADPHIWLSPT 139
>2vhh_A CG3027-PA; hydrolase; 2.8A {Drosophila melanogaster} PDB: 2vhi_A
Length = 405
Score = 27.9 bits (62), Expect = 6.9
Identities = 9/24 (37%), Positives = 9/24 (37%)
Query: 30 PSPRSVPDSGELKYQHHHHHHHHH 53
P HHHHHHHH
Sbjct: 380 PQIIKETQFPGDDDDKHHHHHHHH 403
>3e46_A Ubiquitin-conjugating enzyme E2-25 kDa; huntington interacting,
ligase, alternative splicing, cytoplasm, UBL
conjugation, UBL conjugation pathway; 1.86A {Homo
sapiens} SCOP: a.5.2.1 d.20.1.1 PDB: 3f92_A*
Length = 253
Score = 27.6 bits (61), Expect = 7.0
Identities = 14/49 (28%), Positives = 19/49 (38%)
Query: 48 HHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHN 96
HHHHHH P +G + +A P G D +M I +
Sbjct: 2 HHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGS 50
>1yx4_A 26S proteasome non-ATPase regulatory subunit 4; polyubiquitin,
UIM, hydrolase; NMR {Homo sapiens} PDB: 1yx5_A 1yx6_A
2kde_A 2kdf_A
Length = 132
Score = 26.9 bits (58), Expect = 7.1
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVSLSAAH 72
HHHHHHHH S H + L A+
Sbjct: 3 HHHHHHHHHHSSGHIEGRHMLGLGASD 29
>2xig_A Ferric uptake regulation protein; hpfur, transcription,
homeostasis; HET: CIT; 1.85A {Helicobacter pylori}
Length = 150
Score = 26.9 bits (60), Expect = 7.2
Identities = 4/17 (23%), Positives = 6/17 (35%)
Query: 37 DSGELKYQHHHHHHHHH 53
+Y+ HH H
Sbjct: 83 SKSGRRYEIAAKEHHDH 99
>3hss_A Putative bromoperoxidase; alpha beta hydrolase, oxidoreductase,
hydrolase; 1.90A {Mycobacterium tuberculosis} PDB:
3e3a_A 3hys_A 3hzo_A
Length = 293
Score = 27.7 bits (62), Expect = 7.5
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 HHHHHHHHQVPSSPSPNGHP 65
++HHHHHH + N +
Sbjct: 3 YYHHHHHHDYDIPTTENLYF 22
>3s5s_A Mandelate racemase/muconate lactonizing enzyme FA protein;
PSI-biology, structural genomics, NEW YORK structural
genomi research consortium; 2.40A {Sorangium cellulosum}
Length = 389
Score = 27.7 bits (62), Expect = 7.7
Identities = 12/27 (44%), Positives = 12/27 (44%)
Query: 30 PSPRSVPDSGELKYQHHHHHHHHHQVP 56
P RS E Y HHHHHH P
Sbjct: 359 PQRRSPAAGAENLYFQSHHHHHHWSHP 385
>2c1i_A Peptidoglycan glcnac deacetylase; carbohydrate esterase,
peptidoglycan deacetylase, metalloenzyme, D275N mutant,
hydrolase; HET: MES; 1.35A {Streptococcus pneumoniae}
SCOP: c.6.2.3 d.341.1.1 PDB: 2c1g_A
Length = 431
Score = 27.6 bits (61), Expect = 7.7
Identities = 7/16 (43%), Positives = 9/16 (56%), Gaps = 1/16 (6%)
Query: 370 EG-QLGMHGYHHPDLH 384
EG +G H + HP L
Sbjct: 287 EGHVVGNHSWSHPILS 302
>2oar_A Large-conductance mechanosensitive channel; stretch activated ION
channel mechanosensitive, membrane protein; 3.50A
{Mycobacterium tuberculosis H37RA} SCOP: f.16.1.1
Length = 174
Score = 27.1 bits (59), Expect = 8.0
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 45 HHHHHHHHHQVP 56
HHHHHHHHH
Sbjct: 3 HHHHHHHHHHSS 14
>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, hydrolase; 1.75A {Anaplasma phagocytophilum}
PDB: 3lo0_A
Length = 199
Score = 27.3 bits (61), Expect = 8.0
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 47 HHHHHHHQVPSSPSPNGHPVSLS 69
HHHHHH + + ++L
Sbjct: 3 HHHHHHMGTLEAQTQGPGSMNLD 25
>3p2m_A Possible hydrolase; alpha/beta hydrolase superfamily; 2.80A
{Mycobacterium tuberculosis}
Length = 330
Score = 27.4 bits (61), Expect = 8.4
Identities = 19/109 (17%), Positives = 25/109 (22%), Gaps = 33/109 (30%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQ 104
HHHHHH VP + S+ G S +
Sbjct: 5 HHHHHHSSGLVPR--------------GSHMASMTGGQQMGRVLSDDELTGLDEFALLAE 50
Query: 105 QSPVDIKPPPDMHRTSHQ-------------------HGGMGSPHSWHT 134
+ P Q HGG + H+W T
Sbjct: 51 NAEQAGVNGPLPEVERVQAGAISALRWGGSAPRVIFLHGGGQNAHTWDT 99
>1wue_A Mandelate racemase/muconate lactonizing enzyme FA protein;
structural genomics, unknown function, nysgxrc target
T2185; 2.10A {Enterococcus faecalis} SCOP: c.1.11.2
d.54.1.1
Length = 386
Score = 27.6 bits (62), Expect = 8.4
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 46 HHHHHHHHQVPSSPS 60
HHHHHHHH P
Sbjct: 2 HHHHHHHHHHGLVPR 16
>3rlk_A A1 protein; beta-barrel, polyproline helix, structural protein;
HET: PG4; 1.76A {Enterobacteria phage qbeta} PDB:
3rlc_A*
Length = 192
Score = 27.0 bits (59), Expect = 8.5
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 46 HHHHHHHHQVPSSPSPNGHP 65
HHHHHH P P P P
Sbjct: 2 HHHHHHSKPDPVIPDPPIDP 21
>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH,
niaid, borellia burgdorferi, plasmid partition protein,
iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A
Length = 267
Score = 27.2 bits (61), Expect = 8.7
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 47 HHHHHHHQVPSSPSPNGHP 65
HHHHHH + +
Sbjct: 3 HHHHHHMGTLEAQTQGPGS 21
>2r9r_B Paddle chimera voltage gated potassium channel KV; voltage
sensor, voltage dependent, ION CH shaker, membrane
protein, eukaryotic; HET: NAP PGW; 2.40A {Rattus
norvegicus} PDB: 3lnm_B* 3lut_B* 2a79_B*
Length = 514
Score = 27.7 bits (61), Expect = 8.9
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 46 HHHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGIHNHH 98
HHHHHHHH P + V+ + +L PG D + +
Sbjct: 3 HHHHHHHHHHGLVPRGSM-TVATGDPVDEAAAL-PGHPQDTYDPEADHESSER 53
>1xpn_A Hypothetical protein PA1324; B-barrel, structural genomics,
northeast structural genomics consortium, NESG, protein
structure initiative; NMR {Pseudomonas aeruginosa}
SCOP: b.3.7.1
Length = 170
Score = 26.8 bits (58), Expect = 9.5
Identities = 10/26 (38%), Positives = 11/26 (42%)
Query: 45 HHHHHHHHHQVPSSPSPNGHPVSLSA 70
HHHHHH VP +P L
Sbjct: 4 HHHHHHSSGLVPRGSHMASNPNDLPD 29
>2i32_A Anti-silencing factor 1 paralog A; histone deposition, chromatin
regulation, histone chaperones, ASF1, HIRA, CAF-1,
replication chaperone; 2.70A {Homo sapiens} SCOP:
b.1.22.1 PDB: 1tey_A 2iij_A 3aad_B
Length = 182
Score = 26.9 bits (59), Expect = 9.5
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 46 HHHHHHHHQVPSS 58
HHHHHH + +P++
Sbjct: 5 HHHHHHDYDIPTT 17
>2w3z_A Putative deacetylase; PGDA, glcnac DE-N-acetylase, hydrolase,
divale metal cation dependent, carbohydrate esterase
family 4; 1.45A {Streptococcus mutans UA159}
Length = 311
Score = 27.2 bits (60), Expect = 9.6
Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 370 EG-QLGMHGYHHPDLHGSPMGPHS 392
EG LG+H + H P +
Sbjct: 159 EGHALGIHSFSHVYSLLYPNRVGN 182
>1t7l_A 5-methyltetrahydropteroyltriglutamate-- homocysteine
methyltransferase; TIM barrel, methyltetrahydrofolate,
zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A
1xdj_A 1xr2_A* 1xpg_A*
Length = 766
Score = 27.5 bits (61), Expect = 9.6
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 4/34 (11%)
Query: 47 HHHHHHHQVPSSPSPNGHPVSLSAAHNPWVSLQP 80
HHHHHH P PN S + + + P
Sbjct: 2 HHHHHH----GKPIPNPLLGLDSTENLYFQQIDP 31
>3ix9_A Dihydrofolate reductase; central beta sheet surrounded by 4 alpha
helices, oxidoreductase; HET: NDP MTX; 1.95A
{Streptococcus pneumoniae}
Length = 190
Score = 26.8 bits (60), Expect = 9.9
Identities = 8/9 (88%), Positives = 9/9 (100%)
Query: 44 QHHHHHHHH 52
+HHHHHHHH
Sbjct: 2 KHHHHHHHH 10
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
0.314 0.128 0.401
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,033,776
Number of extensions: 462640
Number of successful extensions: 11057
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10512
Number of HSP's successfully gapped: 420
Length of query: 417
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 321
Effective length of database: 4,021,377
Effective search space: 1290862017
Effective search space used: 1290862017
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 (22.0 bits)
S2: 58 (26.4 bits)