RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12708
(695 letters)
>1nfk_A Protein (nuclear factor kappa-B (NF-KB)); NF-KB P50, complex
(transcription factor/DNA), transcription/DNA complex;
HET: DNA; 2.30A {Mus musculus} SCOP: b.1.18.1 b.2.5.3
PDB: 2v2t_B 1ooa_A 1lei_B* 1le9_B 1le5_B* 2i9t_B 1vkx_B*
3gut_B 2o61_B
Length = 325
Score = 257 bits (658), Expect = 3e-80
Identities = 120/324 (37%), Positives = 158/324 (48%), Gaps = 31/324 (9%)
Query: 39 PYIEILEQPKSK-VRFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
PY++ILEQPK + RFRY CEG S G + GA+S KSYP++ I NYVG A ++V V+
Sbjct: 2 PYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVT 61
Query: 98 KDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDIQA--FRLYLQF 155
H H LV K C +G+ T DM F NLGI + KK + +
Sbjct: 62 NGKNIHLHAHSLVGKH-CEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEA 120
Query: 156 CQRPFNSEKNSAWTLLGVMGFNNRD--------------------NLDLNAVRLCFQAYL 195
C R +N L + D +DL+ VRL F A+L
Sbjct: 121 CIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFL 180
Query: 196 P-KDKDNVIKLEPVVSDIIYD--AKTYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDI 252
P +LEPVVSD IYD A S+L I + + V G ++ +LCDKV KDDI
Sbjct: 181 PDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDI 240
Query: 253 EVRFYEEQDGVVVWDERVKTLE--VHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD-- 308
++RFYEE++ VW+ VH+Q+AIV KTP YK I P V +QL K D
Sbjct: 241 QIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLE 300
Query: 309 ISEPYNFMLTPLDSGRPIFWRYRK 332
SEP F+ P + R R+
Sbjct: 301 TSEPKPFLYYPEIKDKEEVQRKRQ 324
>1ikn_A P65, protein (NF-kappa-B P65 subunit); transcription factor,
IKB/NFKB complex; 2.30A {Mus musculus} SCOP: b.1.18.1
b.2.5.3 PDB: 1nfi_A 2ram_A* 1ram_A* 2i9t_A 1lei_A*
1le9_A 1le5_A* 1vkx_A* 3gut_A
Length = 286
Score = 255 bits (652), Expect = 6e-80
Identities = 120/302 (39%), Positives = 161/302 (53%), Gaps = 25/302 (8%)
Query: 39 PYIEILEQPKSKV-RFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
PY+EI+EQPK + RFRY+CEGRSAGSI G ST K++P I I Y G + +S V+
Sbjct: 1 PYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT 60
Query: 98 KDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDI-QAFRLYLQFC 156
KD P+R HPH+LV KD C +G + A L +SF NLGIQC+KK+D+ QA +Q
Sbjct: 61 KDPPHRPHPHELVGKD-CRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTN 119
Query: 157 QRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDNVIKLEPVVSDIIYDA 216
PF+ R + DLNAVRLCFQ + + L PV+S I+D
Sbjct: 120 NNPFHVPIE-----------EQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDN 168
Query: 217 K--TYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT-- 272
+ ++L I ++ S +G ++ +LCDKV K+DIEV F W+ R
Sbjct: 169 RAPNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPG-----WEARGSFSQ 223
Query: 273 LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWRY 330
+VH+Q AIV +TP Y + PV V +QL D +SEP F P R
Sbjct: 224 ADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEK 283
Query: 331 RK 332
RK
Sbjct: 284 RK 285
>2v2t_A RELB, transcription factor RELB;
4-diphosphocytidyl-2C-methyl-D-erythritol, aquifex
aeolicus, nucleotide-binding, isoprene biosynthesis;
3.05A {Mus musculus} PDB: 3do7_A
Length = 288
Score = 251 bits (643), Expect = 1e-78
Identities = 116/296 (39%), Positives = 162/296 (54%), Gaps = 28/296 (9%)
Query: 35 ASRRPYIEILEQPKSKV-RFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVV 93
RPY+ I EQPK + RFRYECEGRSAGSI+G +ST K+ P I +R+ G + V
Sbjct: 9 PCPRPYLVITEQPKQRGMRFRYECEGRSAGSILGESSTEASKTQPAIELRDCGGLREVEV 68
Query: 94 SC--VSKDSPYRSHPHKLVSKDNCTNGIFCATL-LEGDMTYSFTNLGIQCMKKKDI-QAF 149
+ V KD P+R HPH LV KD CT+G+ L +SF NLGIQC++KK+I A
Sbjct: 69 TACLVWKDWPHRVHPHSLVGKD-CTDGVCRVRLRPHVSPRHSFNNLGIQCVRKKEIEAAI 127
Query: 150 RLYLQFCQRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDNVIKLEPVV 209
+Q P+N+ N +D+N VR+CFQA + ++ +++P++
Sbjct: 128 ERKIQLGIDPYNAGS-----------LKNHQEVDMNVVRICFQASYRDQQGHLHRMDPIL 176
Query: 210 SDIIYDAK--TYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWD 267
S+ +YD K S+L I ++ S P G ++ +LCDKV K+DI V F W+
Sbjct: 177 SEPVYDKKSTNTSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTA-----SWE 231
Query: 268 ERVKT--LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTP 319
R +VH+Q AIV KTP Y+ EI++PV V + L D SEP F P
Sbjct: 232 GRADFSQADVHRQIAIVFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLP 287
>1gji_A C-REL protein, C-REL proto-oncogene protein; NF-KB/DNA complex,
transcription factor, C-REL homodimer, transcription/DNA
complex; 2.85A {Gallus gallus} SCOP: b.1.18.1 b.2.5.3
Length = 275
Score = 251 bits (642), Expect = 1e-78
Identities = 120/290 (41%), Positives = 167/290 (57%), Gaps = 25/290 (8%)
Query: 39 PYIEILEQPKSKV-RFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
PYIEI EQP+ + RFRY+CEGRSAGSI G +ST K++P I I NY G + + V+
Sbjct: 1 PYIEIFEQPRQRGMRFRYKCEGRSAGSIPGEHSTDNNKTFPSIQILNYFGKVKIRTTLVT 60
Query: 98 KDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDI-QAFRLYLQFC 156
K+ PY+ HPH LV KD C +G + A SF NLGIQC+KKKD+ ++ L +
Sbjct: 61 KNEPYKPHPHDLVGKD-CRDGYYEAEFGPERRVLSFQNLGIQCVKKKDLKESISLRISKK 119
Query: 157 QRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLP-KDKDNVIKLEPVVSDIIYD 215
PFN + +N D DLN VRLCFQA+LP + + + L P++S+ IYD
Sbjct: 120 INPFNVPEEQL---------HNIDEYDLNVVRLCFQAFLPDEHGNYTLALPPLISNPIYD 170
Query: 216 AK--TYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT- 272
+ ++L I ++ V G ++ ILCDKV KDDIEVRF + W+ +
Sbjct: 171 NRAPNTAELRICRVNKNCGSVKGGDEIFILCDKVQKDDIEVRFVLDN-----WEAKGSFS 225
Query: 273 -LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTP 319
+VH+Q AIV +TP + +I +P+ VK+QL D +SEP +F P
Sbjct: 226 QADVHRQVAIVFRTPPFLR-DITEPITVKMQLRRPSDQEVSEPMDFRYLP 274
>1svc_P Protein (nuclear factor kappa-B (NF-KB)); DNA-binding,
transcription regulation, activator, nuclear protein,
phosphorylation, repeat, DNA; HET: DNA; 2.60A {Homo
sapiens} SCOP: b.1.18.1 b.2.5.3
Length = 365
Score = 254 bits (649), Expect = 1e-78
Identities = 122/348 (35%), Positives = 164/348 (47%), Gaps = 31/348 (8%)
Query: 15 QNTLQSQVDQSMDSVQSRLDASRRPYIEILEQPKSK-VRFRYECEGRSAGSIMGANSTLE 73
+ + + + Q L + PY++ILEQPK + RFRY EG S G + GA+S
Sbjct: 18 PSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVAEGPSHGGLPGASSEKN 77
Query: 74 CKSYPKIMIRNYVGDAHLVVSCVSKDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSF 133
KSYP++ I NYVG A ++V V+ H H LV K C +GI T DM F
Sbjct: 78 KKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKH-CEDGICTVTAGPKDMVVGF 136
Query: 134 TNLGIQCMKKKDIQA--FRLYLQFCQRPFNSEKNSAWTLLGVMGFNNRD----------- 180
NLGI + KK + + C R +N L + D
Sbjct: 137 ANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELI 196
Query: 181 ---------NLDLNAVRLCFQAYLP-KDKDNVIKLEPVVSDIIYD--AKTYSDLTIHTLS 228
+DL+ VRL F A+LP +LEPVVSD IYD A S+L I +
Sbjct: 197 RQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMD 256
Query: 229 HVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLE--VHKQYAIVLKTP 286
+ V G ++ +LCDKV KDDI++RFYEE++ VW+ VH+Q+AIV KTP
Sbjct: 257 RTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTP 316
Query: 287 AYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWRYRK 332
YK I P V +QL K D SEP F+ P + R R+
Sbjct: 317 KYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQ 364
>2o61_A Transcription factor P65/interferon regulatory FA 7/interferon
regulatory factor...; protein-DNA complex,
transcription-DNA complex; 2.80A {Homo sapiens}
Length = 540
Score = 251 bits (642), Expect = 2e-75
Identities = 118/299 (39%), Positives = 158/299 (52%), Gaps = 25/299 (8%)
Query: 39 PYIEILEQPKSKV-RFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
Y+EI+EQPK + RFRY+CEGRSAGSI G ST K++P I I Y G + +S V+
Sbjct: 2 GYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT 61
Query: 98 KDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDI-QAFRLYLQFC 156
KD P+R HPH+LV KD C +G + A L +SF NLGIQC+KK+D+ QA +Q
Sbjct: 62 KDPPHRPHPHELVGKD-CRDGFYEAELCPDRCIHSFQNLGIQCVKKRDLEQAISQRIQTN 120
Query: 157 QRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDNVIKLEPVVSDIIYD- 215
PF R + DLNAVRLCFQ + ++L PV+S I+D
Sbjct: 121 NNPFQVPIE-----------EQRGDYDLNAVRLCFQVTVRDPSGRPLRLPPVLSHPIFDN 169
Query: 216 -AKTYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT-- 272
A ++L I ++ S +G ++ +LCDKV K+DIEV F W+ R
Sbjct: 170 RAPNTAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPG-----WEARGSFSQ 224
Query: 273 LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWR 329
+VH+Q AIV +TP Y + PV V +QL D +SEP F P S
Sbjct: 225 ADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDGSLSSGSSL 283
>1a3q_A Protein (nuclear factor kappa-B P52); transcription factor, immune
response, DNA-protein complex, transcription/DNA
complex; HET: DNA; 2.10A {Homo sapiens} SCOP: b.1.18.1
b.2.5.3 PDB: 3do7_B 3jv6_B 3jv5_A
Length = 285
Score = 241 bits (615), Expect = 2e-74
Identities = 107/292 (36%), Positives = 148/292 (50%), Gaps = 19/292 (6%)
Query: 39 PYIEILEQPKSK-VRFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
PY+ I+EQPK + RFRY CEG S G + GA+S K+YP + I NY G A + V V+
Sbjct: 2 PYLVIVEQPKQRGFRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVT 61
Query: 98 KDSPYRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDIQAF----RLYL 153
P R+H H LV K GI ++ DMT F NLG+ + KK++
Sbjct: 62 HSDPPRAHAHSLVGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQ 121
Query: 154 QFCQRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDNVIKLEPVVSDII 213
+ RP + L + +DL+ VRL F A+L + L+PV+S I
Sbjct: 122 RLRSRPQGLTEAEQRELEQEAK-ELKKVMDLSIVRLRFSAFLRS-----LPLKPVISQPI 175
Query: 214 YDAK--TYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVK 271
+D+K S+L I + + V G ++ +LCDKV KDDIEVRFYE+ + W
Sbjct: 176 HDSKSPGASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDEN--GWQAFGD 233
Query: 272 TLE--VHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTP 319
VHKQYAIV +TP Y +I PV V +QL K+ +S+ F P
Sbjct: 234 FSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYP 285
>1imh_C NF-AT5, tonebp, nuclear factor of activated T cells 5; beta barrel,
protein-DNA complex, double helix, DNA encirclement,
transcription/DNA complex; 2.86A {Homo sapiens} SCOP:
b.1.18.1 b.2.5.3
Length = 281
Score = 200 bits (510), Expect = 2e-59
Identities = 52/300 (17%), Positives = 95/300 (31%), Gaps = 49/300 (16%)
Query: 36 SRRPYIEILEQPKSKVRFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSC 95
S ++I+ QP+++ R RY EG G+ + +P + + + L V
Sbjct: 14 SEGKELKIVVQPETQHRARYLTEGSR-----GSVKDRTQQGFPTVKLEGHNEPVVLQVFV 68
Query: 96 VSKDSPYRSHPHKLVSKDNCTNGIFCATLL-------------EGDMTYSFTNLGIQCMK 142
+ + H + N C + +MT + +GI ++
Sbjct: 69 GNDSGRVKPHGFYQACRVTGRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLR 128
Query: 143 KKDI-QAFRLYLQFCQRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDN 201
D+ + RL F+ + + +
Sbjct: 129 NADVEARIGI--------------------------AGSKKKSTRARLVFRVNIMRKDGS 162
Query: 202 VIKLEPVVSDIIYDAKTYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQD 261
+ L S I + I S S V G+ ++ ++ K +V F E
Sbjct: 163 TLTL-QTPSSPILCTQPAGVPEILKKSLHSCSVKGEEEVFLIGKNFLK-GTKVIFQENVS 220
Query: 262 GVVVWDERVK-TLEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD-ISEPYNFMLTP 319
W + +E+ Q +++K P Y I PV V I +VT + F TP
Sbjct: 221 DENSWKSEAEIDMELFHQNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTP 280
>1p7h_L Nuclear factor of activated T-cells, cytoplasmic 2; DNA binding
protein, transcription regulation, activator,
transcription/DNA complex; 2.60A {Homo sapiens} SCOP:
b.1.18.1 b.2.5.3 PDB: 2o93_L 1a02_N* 1pzu_B 1owr_M
2as5_N 1s9k_C 3qrf_N 1nfa_A 1a66_A*
Length = 286
Score = 187 bits (475), Expect = 2e-54
Identities = 50/307 (16%), Positives = 101/307 (32%), Gaps = 53/307 (17%)
Query: 35 ASRRPYIEILEQPKSKVRFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVS 94
S + I QPK R YE EG S G++ +P + + Y+ + L +
Sbjct: 12 QSGSYELRIEVQPKPHHRAHYETEG-SRGAVKAPTGG-----HPVVQLHGYMENKPLGLQ 65
Query: 95 CV---SKDSPYRSHPHKLVSKDNCTNGIFCATLL--------------EGDMTYSFTNLG 137
+ + + H V + + + +M + G
Sbjct: 66 IFIGTADERILKPHAFYQVHRITGKTVTTTSYEKIVGNTKVLEIPLEPKNNMRATIDCAG 125
Query: 138 IQCMKKKDIQAFRLYLQFCQRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPK 197
I ++ DI+ + VRL F+ ++P+
Sbjct: 126 ILKLRNADIELRKG-------------------------ETDIGRKNTRVRLVFRVHIPE 160
Query: 198 DKDNVIKLEPVVSDIIYDAKTYSD--LTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVR 255
++ L S+ I ++ + + S V G +MI+ + V
Sbjct: 161 SSGRIVSL-QTASNPIECSQRSAHELPMVERQDTDSCLVYGGQQMILTGQNFTSESKVVF 219
Query: 256 FYEEQDGVVVWDERVKT-LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLV-TKKDISEPY 313
+ DG +W+ + + + ++ P Y++ I PV V ++ K+ S+P
Sbjct: 220 TEKTTDGQQIWEMEATVDKDKSQPNMLFVEIPEYRNKHIRTPVKVNFYVINGKRKRSQPQ 279
Query: 314 NFMLTPL 320
+F P+
Sbjct: 280 HFTYHPV 286
>1bvo_A Transcription factor gambif1; REL protein, morphogen, immunity,
development, insects, complex (transcription
factor/DNA); HET: DNA; 2.70A {Anopheles gambiae} SCOP:
b.2.5.3
Length = 175
Score = 180 bits (457), Expect = 3e-53
Identities = 88/184 (47%), Positives = 113/184 (61%), Gaps = 14/184 (7%)
Query: 39 PYIEILEQPKSK-VRFRYECEGRSAGSIMGANSTLECKSYPKIMIRNYVGDAHLVVSCVS 97
PY+EI EQP K +RFRYECEGRSAGSI G N+T E K++P I + Y G A +VVSCV+
Sbjct: 1 PYVEITEQPHPKALRFRYECEGRSAGSIPGVNTTAEQKTFPSIQVHGYRGRAVVVVSCVT 60
Query: 98 KDSP-YRSHPHKLVSKDNCTNGIFCATLLEGDMTYSFTNLGIQCMKKKDI-QAFRLYLQF 155
K+ P ++ HPH LV K+ C G+ + M+Y+F NLGIQC+KKKD+ +A RL +
Sbjct: 61 KEGPEHKPHPHNLVGKEGCKKGVCTVEINSTTMSYTFNNLGIQCVKKKDVEEALRLRQEI 120
Query: 156 CQRPFNSEKNSAWTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDKDNVIK--LEPVVSDII 213
PF + A ++DLNAVRLCFQ +L + L PVVSDII
Sbjct: 121 RVDPFRTGFGHAK---------EPGSIDLNAVRLCFQVFLEGQQRGRFTEPLTPVVSDII 171
Query: 214 YDAK 217
YD K
Sbjct: 172 YDKK 175
>1ikn_C P50D, protein (NF-kappa-B P50D subunit); transcription factor,
IKB/NFKB complex; 2.30A {Mus musculus} SCOP: b.1.18.1
Length = 119
Score = 118 bits (296), Expect = 2e-31
Identities = 46/117 (39%), Positives = 64/117 (54%), Gaps = 4/117 (3%)
Query: 220 SDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT--LEVHK 277
S+L I + + V G ++ +LCDKV KDDI++RFYEE++ VW+ +VH+
Sbjct: 2 SNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHR 61
Query: 278 QYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWRYRK 332
Q+AIV KTP YK I P V +QL K D SEP F+ P + R R+
Sbjct: 62 QFAIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQ 118
>1u36_A DNA-binding, nuclear factor NF-kappa-B P105 subunit; transcription
factor, NF-KB, dimerization domain, intertwined folding;
1.89A {Mus musculus} SCOP: b.1.18.1 PDB: 1u3z_A 1u3y_A
3jv4_B 1bfs_A 1u3j_A 1u42_A 1u41_A 1nfi_B
Length = 106
Score = 114 bits (287), Expect = 2e-30
Identities = 43/104 (41%), Positives = 59/104 (56%), Gaps = 4/104 (3%)
Query: 220 SDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT--LEVHK 277
S+L I + + V G ++ +LCDKV KDDI++RFYEE++ VW+ +VH+
Sbjct: 2 SNLKIVRMDRTAGCVTGGEEIWLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHR 61
Query: 278 QYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTP 319
Q+AI KTP YK I P V +QL K D SEP F+ P
Sbjct: 62 QFAICFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYP 105
>1my7_A NF-kappab P65 (RELA) subunit; immunoglobulin, IG, beta-sandwich,
beta-sheet, homodimerdna- binding, transcription
regulation, activator; 1.49A {Mus musculus} SCOP:
b.1.18.1 PDB: 1my5_A 1bft_A
Length = 114
Score = 109 bits (275), Expect = 1e-28
Identities = 40/117 (34%), Positives = 56/117 (47%), Gaps = 9/117 (7%)
Query: 220 SDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLE--VHK 277
++L I ++ S +G ++ +LCDKV K+DIEV F W+ R + VH+
Sbjct: 2 AELKICRVNRRSGSCLGGDEIFLLCDKVQKEDIEVYFTGPG-----WEARGSFSQADVHR 56
Query: 278 QYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWRYRK 332
Q AIV +TP Y + PV V +QL D +SEP F P R RK
Sbjct: 57 QVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRK 113
>1oy3_C Transcription factor P65; protein-protein complex, transcription
factors, nuclear localization, DNA binding protein;
2.05A {Mus musculus} SCOP: b.1.18.1 PDB: 1k3z_A
Length = 136
Score = 109 bits (273), Expect = 3e-28
Identities = 40/117 (34%), Positives = 56/117 (47%), Gaps = 9/117 (7%)
Query: 220 SDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLE--VHK 277
++L I ++ S +G ++ +LCDKV K+DIEV F W+ R + VH+
Sbjct: 2 AELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPG-----WEARGSFSQADVHR 56
Query: 278 QYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTPLDSGRPIFWRYRK 332
Q AIV +TP Y + PV V +QL D +SEP F P R RK
Sbjct: 57 QVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRK 113
>1zk9_A Transcription factor RELB; NF-KB, transcription factors,
intertwined dimer; 2.18A {Mus musculus} PDB: 1zka_A
3jv6_A 3jv4_A 3jss_A 3juz_A 3jv0_A
Length = 110
Score = 107 bits (270), Expect = 4e-28
Identities = 40/111 (36%), Positives = 54/111 (48%), Gaps = 9/111 (8%)
Query: 213 IYDAKTYSDLTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKT 272
S+L I ++ S P G ++ +LCDKV K+DI V F W+ R
Sbjct: 4 RGSHMNTSELRICRINKESGPCTGGEELYLLCDKVQKEDISVVFSTA-----SWEGRADF 58
Query: 273 --LEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKD--ISEPYNFMLTP 319
+VH+Q AIV KTP Y+ EI++PV V + L D SEP F P
Sbjct: 59 SQADVHRQIAIVFKTPPYEDLEISEPVTVNVFLQRLTDGVCSEPLPFTYLP 109
>2yrp_A Nuclear factor of activated T-cells, cytoplasmic 4; beta-sandwich,
immunoglobulin-like fold, TIG domain, IPT domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 83.5 bits (206), Expect = 1e-19
Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 4/102 (3%)
Query: 222 LTIHTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEE-QDGVVVWDERVKT-LEVHKQY 279
+ S + V G ++++ D +V F E DG + W+E +
Sbjct: 9 PQVEAYSPSACSVRGGEELVLTGSNFLP-DSKVVFIERGPDGKLQWEEEATVNRLQSNEV 67
Query: 280 AIVLKTPAYKSFEINDPVHVKIQLVT-KKDISEPYNFMLTPL 320
+ L P Y + ++ PV V + ++ S +F P+
Sbjct: 68 TLTLTVPEYSNKRVSRPVQVYFYVSNGRRKRSPTQSFRFLPV 109
>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 = 73.0 bits (178), Expect = 2e-13
Identities = 81/566 (14%), Positives = 158/566 (27%), Gaps = 150/566 (26%)
Query: 181 NLDLNAVRLCFQAYLPKDKDNVIKLEPVVSDIIYDAKTYSDLTIHTLSHVSAPVVGDMKM 240
+ + + ++ L + + V + +D K D+ LS ++
Sbjct: 8 DFETGEHQYQYKDILS------VFEDAFVDN--FDCKDVQDMPKSILSK------EEIDH 53
Query: 241 IILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLEVHKQYAIVLKTPAYKSFEINDPVHVK 300
I + D + W K E+ +++ + YK F + P+ +
Sbjct: 54 I-----IMSKDAVSGTL-----RLFWTLLSKQEEMVQKFVEEVLRINYK-F-LMSPIKTE 101
Query: 301 IQLVTKKDISEPYNFMLTPLDSGRPIFWRYRKNKAQPL-----ALVNLFQNTMTQFV--- 352
+ ++ Y L + +F +Y ++ QP AL+ L + V
Sbjct: 102 QR--QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA---KNVLID 156
Query: 353 --PGEEKKISQDEQIVSAEPIKEKENDYARVDKSVNINMKPHV---TFSQHDTDMETNQV 407
G K V+ + V M + ++ V
Sbjct: 157 GVLGSGK------TWVALDVCL---------SYKVQCKMDFKIFWLNLKNCNSP---ETV 198
Query: 408 PDVLFDTKEKIDERFEELLNEVSNLKDTLEE----KNDFLLIEDSNNAVITLDELDDL-- 461
++L +ID + + SN+K + L + N ++ L + +
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258
Query: 462 ---------------NNNVNESSVTIEEVHEFPKEHLGQRTEGYGSYSSLQLAMKNQYFI 506
V + H H T L +K ++
Sbjct: 259 WNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE----VKSLLLK---YL 311
Query: 507 DRNSGGECYEDVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTK 566
D PQD+ P EV T P LS +I A + +
Sbjct: 312 D-----------CRPQDL---PREVLT--TNPRRLS----II--AESIRDGLATWDNWKH 349
Query: 567 PN-----------LATLQRKSTSDKFDSVSTHDDNIPPLPPKR----------------- 598
N L L+ FD +S + +P
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA-HIPTILLSLIWFDVIKSDVMVVV 408
Query: 599 ---SRKSGLDKNLPPVPKYKSFFHKLFFKSKSKSKPATPRERSLSIDSRKVGGGGSINDD 655
+ S ++K ++ + K K + RS+ +D + +DD
Sbjct: 409 NKLHKYSLVEKQPKE---STISIPSIYLELKVKLENEYALHRSI-VDHYNIPKTFD-SDD 463
Query: 656 VMLTEAEHYALYTSVAPHATQSEFDE 681
++ + Y Y+ + H E E
Sbjct: 464 LIPPYLDQY-FYSHIGHHLKNIEHPE 488
Score = 69.9 bits (170), Expect = 2e-12
Identities = 75/596 (12%), Positives = 180/596 (30%), Gaps = 162/596 (27%)
Query: 5 ECASDGQEECQNTLQS-QVDQSMDSVQSRLDASRRPYIEILEQPKSKV-RFRYECEGRSA 62
+C D Q+ ++ L ++D + S + + + R + +L + + V +F E +
Sbjct: 34 DC-KDVQDMPKSILSKEEIDHIIMS-KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY 91
Query: 63 GSIMGANSTLECKSYPKIMIRNYV---GDAHLVVSCVSKDSPYRSHPH----KLVSKDNC 115
+M T E + P +M R Y+ + +K + R P+ + + +
Sbjct: 92 KFLMSPIKT-EQRQ-PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP 149
Query: 116 TNGIFCATLLEGDMTYSFTNLGI--QCMKKKDIQAFRLYLQFCQRPFNSEKNSAWTLLGV 173
+ ++G + LG + ++++ + + F W L
Sbjct: 150 AKNVL----IDG-V------LGSGKTWVALDVCLSYKVQCKMDFKIF-------W--LN- 188
Query: 174 MGFNNRDNLDLNAV-RLCFQAYLPKDKDNVIKLEPVVSDI--IYDAKTYSDLTIHTLSHV 230
+ N L + +L +Q D + + + + I+ + + + +
Sbjct: 189 LKNCNSPETVLEMLQKLLYQI----DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244
Query: 231 SAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERV-KTLEVHKQYAIVLKTPAYK 289
+ +++L + V + + + + +L T +K
Sbjct: 245 NC-------LLVL------LN-------------VQNAKAWNAFNLSCK---ILLTTRFK 275
Query: 290 SFEINDPVHVKIQLVTKKDISEPYNFMLTPLDSGRPIFWRYRKNKAQ----------PLA 339
+ D + T + ++ LTP D + + +Y + Q P
Sbjct: 276 Q--VTDFLSAA---TTTHISLDHHSMTLTP-DEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 340 L----------VNLFQNTMTQFVPGEEKKISQDEQIVSAEPIKEKEN--DYARVDKSVNI 387
L + + N + V ++ + + EP + ++ + S +I
Sbjct: 330 LSIIAESIRDGLATWDNW--KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 388 ----------NMKPHVTFS-----------QHDTDMETNQVPDVLFDTKEKIDERFEELL 426
++ + T +P + + K K++ +
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA--- 444
Query: 427 NEVSNLKDTLEEKNDFLLIEDSNNAVITLDELDD---------LNNNVNESSVTIEEVHE 477
L ++ + + DS++ + LD L N + E +
Sbjct: 445 -----LHRSIVDHYNIPKTFDSDD--LIPPYLDQYFYSHIGHHLKNIEHP-----ERMTL 492
Query: 478 FPK------------EHLGQRTEGYGSYSSL--QLAMKNQYFIDRNSGGECYEDVL 519
F H GS + QL Y D + E + +
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI 548
Score = 56.8 bits (136), Expect = 2e-08
Identities = 82/513 (15%), Positives = 158/513 (30%), Gaps = 156/513 (30%)
Query: 3 FKECASDGQE-ECQNTLQSQVDQSMDSVQSRLDASRRPYIEILEQPKSKVRFRYECEGRS 61
K C S E L Q+D + SR D S + I ++++R R
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNW---TSRSDHSSNIKLRI-HSIQAELR-RL------ 237
Query: 62 AGSIMGANSTLECKSYPK--IMIRNYVGDAHLV----VSC----VSKDSPYRSHPHKLVS 111
L+ K Y +++ N V +A +SC ++ K V+
Sbjct: 238 ----------LKSKPYENCLLVLLN-VQNAKAWNAFNLSCKILLTTRF--------KQVT 278
Query: 112 KDNCTNGIFCATLLEGDMTYSFT---NLGIQCMKKKDIQAFRLYLQFCQR-PFNSEKNSA 167
D + L+ + + T + +K D + L + P
Sbjct: 279 -DFLSAATTTHISLD-HHSMTLTPDEVKSL-LLKYLDCRPQDLPREVLTTNPR------- 328
Query: 168 WTLLGVMGFNNRDNLDLNAVRLCFQAYLPKDK-DNVIK-----LEPVVSDIIYDAKT-YS 220
L ++ + RD L ++ DK +I+ LEP + + +
Sbjct: 329 --RLSIIAESIRDGLA----TWDNWKHVNCDKLTTIIESSLNVLEP------AEYRKMFD 376
Query: 221 DLTI---------HTLSHVSAPVVGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVK 271
L++ LS + V+ M+++ +E + E
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES------------ 424
Query: 272 TLEVHKQYAIVLKTPAYKSFEINDPVHVKIQLVTKKDISEPY---NFMLTPLDSGRPIFW 328
T+ + Y + LK + + H I V +I + + + + LD +
Sbjct: 425 TISIPSIY-LELKVKLENEYAL----HRSI--VDHYNIPKTFDSDDLIPPYLDQ--YFYS 475
Query: 329 R--YRKNKAQPLALVNLFQNTMT--QFVPGEEKKISQDEQIVSAEPIKEKENDYARVDKS 384
+ + + LF+ +F+ E+KI D +A N ++
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFL---EQKIRHDSTAWNASG--SILNTLQQLKF- 529
Query: 385 VNINMKPHVTFSQHDTDMETNQVPDVLFDTKEKIDERFEELLNEVSNLKDTLEEKNDFLL 444
KP++ D ++E L+N + D L + + L+
Sbjct: 530 ----YKPYIC----------------------DNDPKYERLVNA---ILDFLPKIEENLI 560
Query: 445 IEDSNNAV-ITLDELDDLNNNVNESSVTIEEVH 476
+ + I L + E EE H
Sbjct: 561 CSKYTDLLRIAL---------MAEDEAIFEEAH 584
>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 = 54.3 bits (130), Expect = 1e-07
Identities = 89/525 (16%), Positives = 158/525 (30%), Gaps = 190/525 (36%)
Query: 120 FCATLLEGDMTYSFTNL--------GIQCMKKKDIQAF-------------------RLY 152
+ ++L+E F + ++ DI A + Y
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNY 126
Query: 153 LQ---FCQRPFNSEKNSAW------------TLLGVMGFNNRDNLD-LNAVRLCFQAYLP 196
+ +RPF+ + NSA + G G N D + L R +Q Y
Sbjct: 127 ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQG-NTDDYFEEL---RDLYQTYHV 182
Query: 197 KDKDNVIK-----LEPVVSDIIYDAKTYSD-LTIHT-LSH--------------VSAPVV 235
D +IK L ++ + K ++ L I L + +S P++
Sbjct: 183 LVGD-LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
Query: 236 GDMKM---IILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLEVHKQYAIVL-----KTPA 287
G +++ ++ + E+R +K H Q +V +T +
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGELR------------SYLKGATGHSQ-GLVTAVAIAETDS 288
Query: 288 YKSFEINDPVHVKIQLVTKKDISEPYNFMLTPLDSGRPIFWR-YRKNKAQPLALVNLFQN 346
++SF V K +T L F+ R +A P +L +
Sbjct: 289 WESFF---------VSVRK---------AITVL------FFIGVRCYEAYP--NTSLPPS 322
Query: 347 TMTQFVPGEEKKIS--------QDEQIVSAEPIKEKENDYARVDKSVNI---NMKPH--V 393
+ + E S EQ+ + K N + K V I N + V
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQV---QDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 394 T--------FSQH------DTDMETNQVPDVLFDT-KEKIDERF--------EELLNE-V 429
+ + + ++ +++P F K K RF LL
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIP---FSERKLKFSNRFLPVASPFHSHLLVPAS 436
Query: 430 SNLKDTLEEKNDFLLIEDSNNAVI-TLDELD--DLNNNVNESSV---TIEEVH-----EF 478
+ L + N +D V T D D L+ +++E V V +F
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQF 496
Query: 479 PKEH-----------LGQRT----EGYG----SYSSLQLAMKNQY 504
H LG T +G G +L + + Y
Sbjct: 497 KATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDY 541
Score = 46.6 bits (110), Expect = 3e-05
Identities = 86/517 (16%), Positives = 149/517 (28%), Gaps = 223/517 (43%)
Query: 181 NLDLNAVRL--CFQAYLPKDKDNVIKLEPVVSDIIYDAKTYSDLTIHTLSHVSAPV---- 234
A +L F LP+ + + + +L L +VS+ V
Sbjct: 25 ASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA--------ELVGKFLGYVSSLVEPSK 76
Query: 235 VGDMKMIILCDKVNKDDIEVRFYEEQDGVVVWDERVKTLEVHKQYAIVLKTPAYKSFEIN 294
VG ++ + + E + E D +H A+ K + N
Sbjct: 77 VGQFDQVL---NLCLTEFENCYLEGND-------------IH---ALAAKLL-----QEN 112
Query: 295 DPVHVKIQLVTKKDISEPYNFMLTPLDSGRPIFWRYRKNKAQPLALVNLFQ-------NT 347
D VK + + K N++ + + RP +K A LF+
Sbjct: 113 DTTLVKTKELIK-------NYITARIMAKRPF------DKKSNSA---LFRAVGEGNAQL 156
Query: 348 MTQFVPGEEKKISQDEQIVSAEPIKE-KE--NDYARVDKSVNINMKPHVTFSQHDTDMET 404
+ F G Q + + +E ++ Y V
Sbjct: 157 VAIF-GG---------QGNTDDYFEELRDLYQTY-----------HVLVG---------- 185
Query: 405 NQVPDVLFDTKEKIDERFEELLNEVS----------NLKDTLEEKN-----DFL------ 443
D + E EL+ N+ + LE + D+L
Sbjct: 186 --------DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 444 --LIE--DSNNAVITLDELD----DLNNNVNESSVTIEEV------------HEFPKEHL 483
LI + V+T L +L + + ++ + + F
Sbjct: 238 CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESF----- 292
Query: 484 GQRTEGYGSYSSLQLAMKNQYFIDRNSGGECYEDV----LPP---QD-------IPTP-- 527
+ S++ A+ +FI G CYE LPP +D +P+P
Sbjct: 293 ---------FVSVRKAITVLFFI----GVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 528 ------PPEVAT---------PPVKPVALSNV----KVVI--PPAS---------KVTTP 557
+V P K V +S V +V+ PP S K P
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399
Query: 558 PP----RPPSHTKPNLATLQRKST-SDKFDSVST--H 587
R P + +RK S++F V++ H
Sbjct: 400 SGLDQSRIP-FS-------ERKLKFSNRFLPVASPFH 428
Score = 34.3 bits (78), Expect = 0.16
Identities = 36/239 (15%), Positives = 75/239 (31%), Gaps = 81/239 (33%)
Query: 407 VPDVLFDTKEKIDERFEELLNEVSNLKDTLEEKND----------FL-----LIEDSN-- 449
VP F ++ E+F ++L E + + ++ FL L+E S
Sbjct: 22 VPTASFFIASQLQEQFNKILPEPT---EGFAADDEPTTPAELVGKFLGYVSSLVEPSKVG 78
Query: 450 --NAVIT--LDELDD--L-NNNVN--------ESSVTIEEVHE-----FPKEHLGQRTEG 489
+ V+ L E ++ L N+++ E+ T+ + E + +R
Sbjct: 79 QFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD 138
Query: 490 YGSYSSL-QLAMKNQ---Y--FIDRNSGG----ECYEDVLPPQDI-PTPPPEVATPPVKP 538
S S+L + + F GG + Y + L +D+ T V
Sbjct: 139 KKSNSALFRAVGEGNAQLVAIF-----GGQGNTDDYFEEL--RDLYQTYHVLVGD----- 186
Query: 539 VALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSDKFDSVS--THDDNIPPLP 595
+I +++ + R + + + + + N P
Sbjct: 187 --------LIKFSAETLSELIRTTLDAEKVF--------TQGLNILEWLENPSNTPDKD 229
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex,
inter-protein beta sheet, protein-protein, metal
transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A
{Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Length = 229
Score = 37.8 bits (87), Expect = 0.007
Identities = 14/77 (18%), Positives = 25/77 (32%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
PPQ + PP V P +P + P + P P+P + ++
Sbjct: 47 PPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKP 106
Query: 580 KFDSVSTHDDNIPPLPP 596
++ +N P
Sbjct: 107 VESRPASPFENTAPARL 123
Score = 37.8 bits (87), Expect = 0.008
Identities = 20/93 (21%), Positives = 28/93 (30%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
P+ P P P P V K P KV P R + A+ +
Sbjct: 62 EPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPA 121
Query: 580 KFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVP 612
+ S + P+ S L +N P P
Sbjct: 122 RLTSSTATAATSKPVTSVASGPRALSRNQPQYP 154
Score = 36.6 bits (84), Expect = 0.016
Identities = 19/95 (20%), Positives = 27/95 (28%), Gaps = 5/95 (5%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
P+ IP PP E KP P V +P KP + +
Sbjct: 64 EPEPIPEPPKEAPVVIEKPK-----PKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENT 118
Query: 580 KFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVPKY 614
+++ P S SG P+Y
Sbjct: 119 APARLTSSTATAATSKPVTSVASGPRALSRNQPQY 153
Score = 33.9 bits (77), Expect = 0.13
Identities = 18/83 (21%), Positives = 21/83 (25%)
Query: 516 EDVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRK 575
E + P E P KP KV P V RP S +
Sbjct: 66 EPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTS 125
Query: 576 STSDKFDSVSTHDDNIPPLPPKR 598
ST+ S P R
Sbjct: 126 STATAATSKPVTSVASGPRALSR 148
Score = 32.8 bits (74), Expect = 0.31
Identities = 11/50 (22%), Positives = 14/50 (28%)
Query: 518 VLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKP 567
V PP+ PP +PV + P P KP
Sbjct: 37 VTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKP 86
Score = 32.0 bits (72), Expect = 0.43
Identities = 11/77 (14%), Positives = 14/77 (18%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
Q P P E P V+ K P P K
Sbjct: 50 AVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVES 109
Query: 580 KFDSVSTHDDNIPPLPP 596
+ S +
Sbjct: 110 RPASPFENTAPARLTSS 126
Score = 32.0 bits (72), Expect = 0.51
Identities = 19/98 (19%), Positives = 27/98 (27%)
Query: 515 YEDVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQR 574
+ V ++P P ++ V P L + V PP V P P P +P
Sbjct: 19 HMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVV 78
Query: 575 KSTSDKFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVP 612
PKR K + P
Sbjct: 79 IEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFE 116
Score = 30.8 bits (69), Expect = 1.1
Identities = 9/79 (11%), Positives = 14/79 (17%)
Query: 518 VLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKST 577
V P P + PV + PP P + +
Sbjct: 40 VTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQ 99
Query: 578 SDKFDSVSTHDDNIPPLPP 596
+ P
Sbjct: 100 PKRDVKPVESRPASPFENT 118
Score = 29.3 bits (65), Expect = 4.0
Identities = 12/96 (12%), Positives = 23/96 (23%)
Query: 518 VLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKST 577
++ P D+ P P + + P + +P KP +++
Sbjct: 39 MVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQE 98
Query: 578 SDKFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVPK 613
K D P + K
Sbjct: 99 QPKRDVKPVESRPASPFENTAPARLTSSTATAATSK 134
>2wvr_C DNA replication factor CDT1; DNA replication license, DNA
replication inhibitor, phosphoprotein, UBL conjugation,
DNA-binding, polymorphism; HET: DNA; 3.30A {Homo
sapiens} PDB: 2klo_A*
Length = 546
Score = 35.9 bits (81), Expect = 0.043
Identities = 20/126 (15%), Positives = 35/126 (27%), Gaps = 4/126 (3%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
P TP P A S + P + RPP+ + L+ + S S
Sbjct: 23 PKLACRTPSPARPALRAPASATSGSRKRARPPAAPGRDQARPPARRRLRLSVDEVSSPST 82
Query: 580 KFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVPKYKSFFHKLFFKSKSKSKPATPRERSL 639
P P ++ +KS PP + + + R
Sbjct: 83 PEAPDIP----ACPSPGQKIKKSTPAAGQPPHLTSAQDQDTISELASCLQRARELGARVR 138
Query: 640 SIDSRK 645
++ +
Sbjct: 139 ALKASA 144
>2kpy_A Major pollen allergen ART V 1; defensin-like, poly-proline; NMR
{Artemisia vulgaris}
Length = 108
Score = 31.3 bits (70), Expect = 0.32
Identities = 15/46 (32%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 514 CYEDVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPP 559
CY D TP P A PP PPA + PPP
Sbjct: 49 CYFDCSKSPPGATPAPPGAAPPPAAGG-----SPSPPADGGSPPPP 89
>2ck3_G ATP synthase subunit gamma\, mitochondrial; hydrolase; HET: ANP
ADP; 1.9A {Bos taurus} SCOP: c.49.2.1 PDB: 1cow_G*
1bmf_G* 1e1q_G* 1e1r_G* 1efr_G* 1e79_G* 1h8h_G* 1nbm_G*
1ohh_G* 1qo1_G 1w0j_G* 1w0k_G* 1h8e_G* 2jiz_G* 2jj1_G*
2jj2_G* 2v7q_G* 2wss_G* 2xnd_G* 2w6j_G ...
Length = 272
Score = 32.1 bits (74), Expect = 0.50
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 8/37 (21%)
Query: 342 NLFQNTMTQFVPGEEKKISQDEQIVSAEPIKEKENDY 378
N F++ ++ ++++ I S + I E+
Sbjct: 163 NRFRSVISY--------KTEEKPIFSLDTISSAESMS 191
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 32.2 bits (74), Expect = 0.51
Identities = 12/50 (24%), Positives = 14/50 (28%), Gaps = 6/50 (12%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNL 569
P D PT P P V P + P PP P +
Sbjct: 7 APDDYPTFPDTSTWPVVFPELPAA------PYGGPCRPPQHTSKAAAPRI 50
>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 190
Score = 30.2 bits (67), Expect = 1.4
Identities = 13/54 (24%), Positives = 21/54 (38%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQ 573
PP P P ++P A + + V P + P+H++P A L
Sbjct: 23 PPPPKPHQPFIASSPSPSNHAAPQFQTLKSRDGSVALNPQQGPNHSEPLSAELA 76
>1mv3_A MYC box dependent interacting protein 1; tumor suppressor,
endocytosis/exocytosis complex; NMR {Homo sapiens} SCOP:
b.34.2.1
Length = 213
Score = 30.0 bits (66), Expect = 1.7
Identities = 23/164 (14%), Positives = 39/164 (23%), Gaps = 5/164 (3%)
Query: 520 PPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSD 579
P P P P + P P PP HT +
Sbjct: 3 SPAATPEIRVNHEPEPAGGATPGATLPKSPSQLRKGPPVPPPPKHTPSKEVK---QEQIL 59
Query: 580 KFDSVSTHDDNIPPLPPKRSRKSGLDKNLPPVPKYKSFFHKLFFKSKSKSKPATPRERSL 639
+ + P + + S + P + ++ S S PA E
Sbjct: 60 SLFEDTFVPEISVTTPSQPAEASEVAGGTQPAAGAQEPGETAASEAASSSLPAVVVETFP 119
Query: 640 SIDSRKVGGGGSINDDVMLTEAEHY--ALYTSVAPHATQSEFDE 681
+ + V GG + A + A + +
Sbjct: 120 ATVNGTVEGGSGAGRLDLPPGFMFKVQAQHDYTATDTDELQLKA 163
>1bw0_A TAT, protein (tyrosine aminotransferase); tyrosine catabolism,
pyridoxal-5'-phosphate, PLP; HET: LLP; 2.50A
{Trypanosoma cruzi} SCOP: c.67.1.1
Length = 416
Score = 30.7 bits (70), Expect = 1.9
Identities = 7/43 (16%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 207 PVVSDIIYDAKTYSDLTIHTLSHVSAPVVGDMKMIILCDKVNK 249
P+ SD IY + + S ++ K
Sbjct: 212 PLFSDEIYAGMVF-KGKDPNATFTSVADFETTVPRVILGGTAK 253
>3ryc_E Stathmin-4; alpha-tubulin, beta-tubulin, GTPase, microtubule,
tubulin, cell cycle; HET: GTP GDP; 2.10A {Rattus
norvegicus} PDB: 3ryf_E* 3ryh_E* 3ryi_E* 1sa0_E* 1sa1_E*
1z2b_E* 3du7_E* 3e22_E* 3hkb_E* 3hkc_E* 3hkd_E* 3hke_E*
3n2g_E* 3n2k_E*
Length = 143
Score = 29.6 bits (66), Expect = 1.9
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 506 IDRNSGGECYEDVLPPQDIPTPPPEVATPPVKP 538
+++ + G+ +E +L P P A+ P +
Sbjct: 9 LNKATSGQSWEVILKPPSFDGVPEFNASLPRRR 41
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 30.3 bits (68), Expect = 2.2
Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 1/56 (1%)
Query: 525 PTPPPEVATPPVKPVALSNVKVVIPPASKV-TTPPPRPPSHTKPNLATLQRKSTSD 579
PT P A PPA T P+P + KP T R + +
Sbjct: 5 PTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDN 60
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 2.3
Identities = 9/50 (18%), Positives = 17/50 (34%), Gaps = 22/50 (44%)
Query: 24 QSMDSVQSRLDASRRPYIEILEQPKSKVRFRYECEGRSAGSIMGANSTLE 73
Q++ +Q+ L + Y S A +I +T+E
Sbjct: 20 QALKKLQASL----KLY-----ADDSA----------PALAI---KATME 47
>2nps_D Syntaxin-6; vesicle fusion, snare complex, early endosomal snare
complex, VTI1A, VAMP4, transport protein; 2.50A {Homo
sapiens}
Length = 82
Score = 28.2 bits (63), Expect = 2.3
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 10 GQE-ECQNTLQSQVDQSMDSVQSRLDASRR 38
G E E Q + ++S QSRLD +
Sbjct: 39 GGELEEQAVMLEDFSHELESTQSRLDNVMK 68
>3h4s_E KCBP interacting Ca2+-binding protein; kinesin, motor protein,
regulation, complex, calcium, EF- hand, calmodulin,
ATP-binding, microtubule; HET: ADP; 2.40A {Arabidopsis
thaliana}
Length = 135
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 413 DTKEKIDERFEELLNEVSNL---KDTLEE-KNDFLLIEDSNNAVITLDELDDLNNNVNES 468
TK + +E++L ++ ++ + E F L+ D +IT + L + +
Sbjct: 15 TTKMETK--YEDMLPVMAEKMDVEEFVSELCKGFSLLADPERHLITAESLRRNSGILGIE 72
Query: 469 SVTIEEVHEFPKE 481
++ E+ +E
Sbjct: 73 GMSKEDAQGMVRE 85
>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface
adhesin WALL, peptidoglycan-anchor, cell adhesion; HET:
PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A
Length = 497
Score = 30.2 bits (66), Expect = 2.8
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 4/49 (8%)
Query: 523 DIPTPPPEVATPPVKPVA----LSNVKVVIPPASKVTTPPPRPPSHTKP 567
++P E TPPVKP A + + PA P T+
Sbjct: 442 NVPKVTKEKPTPPVKPTAPTKPTYETEKPLKPAPVAPNYEKEPTPPTRL 490
>2wd6_A Agglutinin receptor; cell adhesion, secreted, V-region, cell WALL,
AG I/II protei surface adhesin, peptidoglycan-anchor;
2.30A {Streptococcus gordonii}
Length = 349
Score = 29.8 bits (66), Expect = 2.9
Identities = 12/46 (26%), Positives = 15/46 (32%), Gaps = 3/46 (6%)
Query: 517 DVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPP 562
V PT P + KP+ V P TPP + P
Sbjct: 307 GVPTKPVAPTAPTQPMYETEKPLE---PAPVAPSYENEPTPPVKTP 349
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 30.1 bits (67), Expect = 3.0
Identities = 12/60 (20%), Positives = 17/60 (28%), Gaps = 4/60 (6%)
Query: 519 LPPQDIPTPPPEVATPPVKPVALSNVK----VVIPPASKVTTPPPRPPSHTKPNLATLQR 574
L P+ P + L+ + V P P P T + LQR
Sbjct: 14 LVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQR 73
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 29.8 bits (66), Expect = 3.3
Identities = 14/126 (11%), Positives = 32/126 (25%), Gaps = 20/126 (15%)
Query: 505 FIDRNSGGECYEDVLPPQDIPTPPPEVATPPVKPVALSNVKVVIPPASKVTTPPPRPPSH 564
D N + P PPP + + +++ + S
Sbjct: 9 LSDSNFMANLPNGYMTDLQRPQPPPPPPSAASPGATPGSA----AASAERASTAAPVASP 64
Query: 565 TKP------------NLATLQRKSTSDKFDSVSTHDDNIPPLPPKRSRKSGL----DKNL 608
P +L+ +++T+ + S + + + D+
Sbjct: 65 AAPSPGSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAAARVLLVIDEPH 124
Query: 609 PPVPKY 614
KY
Sbjct: 125 TDWAKY 130
>3g0t_A Putative aminotransferase; NP_905498.1, putative aspartate
aminotransferase, structural genomics, joint center for
structural genomics; HET: MSE LLP PE4; 1.75A
{Porphyromonas gingivalis}
Length = 437
Score = 29.2 bits (66), Expect = 4.5
Identities = 6/32 (18%), Positives = 11/32 (34%)
Query: 208 VVSDIIYDAKTYSDLTIHTLSHVSAPVVGDMK 239
V+ D+ Y + H + P V +
Sbjct: 218 VIEDLAYFGMDFRKDYSHPGEPLYQPSVANYT 249
>3fmu_A VersatIle peroxidase VPL2; class II (fungal) peroxidases,
protoporphyrin IX, electron T lignin peroxidase, lignin
degradation; HET: HEM; 1.04A {Pleurotus eryngii} PDB:
3fjw_A* 2boq_A* 3fm1_A* 3fm4_A* 3fm6_A* 3fkg_A* 2w23_A*
2vka_A*
Length = 331
Score = 29.1 bits (65), Expect = 5.0
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 536 VKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSDKFDSVSTH---DDNIP 592
L + VIP + P + L+ +++ + F +++ ++P
Sbjct: 270 QDKTKLIDCSDVIPTPPALVGAAHLPAGFS---LSDVEQACAATPFPALTADPGPVTSVP 326
Query: 593 PLPP 596
P+P
Sbjct: 327 PVPG 330
>1fio_A SSO1 protein; four helix bundle, alpha helix, membrane protein;
2.10A {Saccharomyces cerevisiae} SCOP: a.47.2.1
Length = 196
Score = 28.5 bits (63), Expect = 5.4
Identities = 14/105 (13%), Positives = 31/105 (29%), Gaps = 5/105 (4%)
Query: 331 RKNKAQPLALVNLFQNTMTQFVPGEEK-KISQDEQIVSAEPIKEKENDYARVDKSVNINM 389
+AQ F + + + K EQ I + E V+ +++
Sbjct: 80 TNKQAQAENSRQRFLKLIQDYRIVDSNYKEENKEQAKRQYMIIQPEATEDEVEAAISDVG 139
Query: 390 KPHVTFSQHDTDMETNQVPDVLFDTKEKIDERFEELLNEVSNLKD 434
+ + L ++ R +ELL ++ +
Sbjct: 140 GQQIFSQALLNANRRGEAKTAL----AEVQARHQELLKLEKSMAE 180
>2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; 3.1A
{Thermomyces lanuginosus} PDB: 2uvb_A*
Length = 1878
Score = 29.5 bits (66), Expect = 5.5
Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 13/88 (14%)
Query: 483 LGQRT-----EGYGSYSSLQLAMKNQYFIDRNSGGECYEDVLPPQDIPTPPPEVATPPVK 537
+ +RT E Y + +S+Q + +++ Y+ + P ++
Sbjct: 56 MARRTLQSKYEAYDAATSVQRQILC---YCKDAKEIYYDVEPIEDEPEPTPAAASSADAA 112
Query: 538 PVALSNVKVVIPPASKVTTPPPRPPSHT 565
P A PA+ P P P S
Sbjct: 113 PAA-----APAAPAAPAAAPAPAPASAG 135
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class
I, activator, RNA polymeras holoenzyme, sigma70, open
complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia
coli k-12}
Length = 613
Score = 28.8 bits (64), Expect = 6.7
Identities = 35/280 (12%), Positives = 80/280 (28%), Gaps = 22/280 (7%)
Query: 243 LCDKVNKDDIEVRFYEEQDGVVVWDERVKTLEVHKQYAIVLKTPAYKSFEINDPVHV--- 299
+ +N I+V ++ E + + A VL + + DPV +
Sbjct: 44 IIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMR 103
Query: 300 ---KIQLVTKKDISEPYNFMLTPLDSGRPIFWRYRKNKAQPLALVNLFQNTMTQFVPGEE 356
++L+T++ + + ++ + Y + L N + + +
Sbjct: 104 EMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEAR-LSDLI 162
Query: 357 KKISQDEQIVSAEPIKEKENDYARVDKSVNINMKPHVTFSQHDTDMETNQVPDVLFDTKE 416
P + + + D + + P E
Sbjct: 163 TGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDP-------E 215
Query: 417 KIDERFEELLNEVSNLKDTLEEKNDFLLIEDSNNAVITLDELDDLNNNVNESSVTIEEVH 476
E+F EL + +DT++ K A + +L ++ + +
Sbjct: 216 LAREKFAELRAQYVVTRDTIKAKG-----RSHATAQEEILKLSEVFKQFRLVPKQFDYLV 270
Query: 477 EFPKEHLGQRTEGYGSYSSL---QLAMKNQYFIDRNSGGE 513
+ + + L Q M + FI +G E
Sbjct: 271 NSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE 310
>1nj1_A PROR, proline-tRNA synthetase, proline--tRNA ligase;
protein-aminoacyladenylate complex class-II tRNA
synthetase,; HET: 5CA; 2.55A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: c.51.1.1
d.68.5.1 d.104.1.1 PDB: 1nj2_A 1nj5_A* 1nj6_A*
Length = 501
Score = 28.9 bits (65), Expect = 7.2
Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 401 DMETNQVPDVLFDTKEKIDERFEELLNEVSNLKDTLEEKNDFLL---IEDSNNAVITLDE 457
D+E DT EK+ + + + L +++ + L E + + +
Sbjct: 380 DLEKGAAVISRRDTGEKVTADLQGIEETLREL---MKDILENLRTRAWERMESEIREAET 436
Query: 458 LDDLNNNVNE 467
L++ + V+E
Sbjct: 437 LEEASRIVDE 446
>2e39_A Peroxidase; heme protein, coordination geometry of heme iron, ARP,
perox oxidoreductase; HET: NAG MAN HEM; 1.30A
{'arthromyces ramosus'} SCOP: a.93.1.1 PDB: 1arp_A*
1arv_A* 1arw_A* 1arx_A* 1ary_A* 1c8i_A* 1ck6_A* 1gza_A*
1gzb_A* 1hsr_A* 1aru_A* 2e3a_A* 2e3b_A* 1lyk_A* 1lyc_A*
1ly9_A* 1h3j_A* 1ly8_A*
Length = 344
Score = 28.3 bits (63), Expect = 9.9
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 536 VKPVALSNVKVVIPPASKVTTPPPRPPSHTKPNLATLQRKSTSDKFDSVSTHDDNIPPLP 595
AL++ VIP A P P T + ++ S+ F ++T +P L
Sbjct: 285 FDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDD---IEVSCPSEPFPEIATASGPLPSLA 341
Query: 596 P 596
P
Sbjct: 342 P 342
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
0.315 0.132 0.384
Gapped
Lambda K H
0.267 0.0489 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,210,839
Number of extensions: 609000
Number of successful extensions: 1313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1149
Number of HSP's successfully gapped: 75
Length of query: 695
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 595
Effective length of database: 3,909,693
Effective search space: 2326267335
Effective search space used: 2326267335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.9 bits)