RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780288|ref|YP_003064701.1| exodeoxyribonuclease III
protein [Candidatus Liberibacter asiaticus str. psy62]
(281 letters)
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5'
exonuclease, AP endonuclease; HET: PG4; 1.23A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A*
3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A
Length = 265
Score = 228 bits (581), Expect = 1e-60
Identities = 66/268 (24%), Positives = 112/268 (41%), Gaps = 12/268 (4%)
Query: 1 MSVVTVATWNVNSIRA-RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYH--I 57
M+V+ + +WNVN +RA W E PDI+CLQE K + P + Y
Sbjct: 1 MAVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFF 60
Query: 58 ETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGN 117
+K Y+GVA+ +K P + + D + R A F + N+Y P+G
Sbjct: 61 TPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADF----DDFLLYNIYFPNGA 116
Query: 118 PITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTL 177
+ K+ + FL ++ + +I GD+N + D P N + F
Sbjct: 117 MSE-ERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLP 175
Query: 178 EVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237
R K G+ D R + Y++W Y + +N G R+D+ ++ E +
Sbjct: 176 VERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVK 235
Query: 238 SARIDTKPRGWTKPSDHTPVIVSLDIPE 265
+ I + G SDH P+ + +++ E
Sbjct: 236 RSWILSDVMG----SDHCPIGLEIELLE 259
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 194 bits (492), Expect = 3e-50
Identities = 87/259 (33%), Positives = 137/259 (52%), Gaps = 6/259 (2%)
Query: 6 VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65
+AT+NVNSIR+R+H + W+KEN PDI+C+QETK E++ FP + YH+ G K
Sbjct: 4 IATFNVNSIRSRLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFSGSKGR 63
Query: 66 NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125
NGVAI S +P ++ L + D I + N Y+P G I S KY
Sbjct: 64 NGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGI-----DVINTYVPQGFKIDSEKYQ 118
Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185
K+ W++R + + ++ ++ GD N+ P+P D ++P +N CF + R++++K
Sbjct: 119 YKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVCFHEDARRAYKK 178
Query: 186 LQNMGFTDAIRATHDTHHLYSFWDYYA-DSWSKNKGIRIDHIMLSPEATSLLHSARIDTK 244
+ +GF D +R H +Y+F+DY + + G R D I+ +P D K
Sbjct: 179 ILELGFVDVLRKIHPNERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDCYADIK 238
Query: 245 PRGWTKPSDHTPVIVSLDI 263
PR KPSDH P++ D+
Sbjct: 239 PRLAEKPSDHLPLVAVFDV 257
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair,
endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens}
SCOP: d.151.1.1 PDB: 1e9n_A 2isi_A
Length = 318
Score = 189 bits (481), Expect = 6e-49
Identities = 73/265 (27%), Positives = 122/265 (46%), Gaps = 17/265 (6%)
Query: 6 VATWNVNSIRARIHN-LAAWIKENNPDIICLQETKTEDKNFPFETLQSL----NYHIETC 60
+ +WNV+ +RA I W+KE PDI+CLQETK + P E + Y
Sbjct: 64 ICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPS 123
Query: 61 GQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT 120
++ Y+GV +LS+ P+++ + ++ D + R I A F + + Y+P+
Sbjct: 124 DKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEF----DSFVLVTAYVPNAGRGL 179
Query: 121 STKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVR 180
+ + L +PL+ GD N+ + D NP + +A FT + R
Sbjct: 180 VRLEYRQRWDEAFRKFL--KGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQER 237
Query: 181 QSFQKLQNM-GFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHS 238
Q F +L D+ R + +T + Y+FW Y ++ SKN G R+D+ +LS L
Sbjct: 238 QGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCD 297
Query: 239 ARIDTKPRGWTKPSDHTPVIVSLDI 263
++I R SDH P+ + L +
Sbjct: 298 SKI----RSKALGSDHCPITLYLAL 318
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 183 bits (465), Expect = 4e-47
Identities = 56/320 (17%), Positives = 100/320 (31%), Gaps = 65/320 (20%)
Query: 6 VATWNVNSIRARIHN----LAAWIKENNPDIICLQETKTEDKNFPFETLQSL-----NYH 56
TWNV +R + L A+++ PD++CLQETK +
Sbjct: 152 FITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSFVD 211
Query: 57 IETCGQKSYNGVAILSKYQPIEIVTH-----------------------LPGDDLDVQAR 93
++ Y+G K H L D + R
Sbjct: 212 HPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAGDEEGR 271
Query: 94 FIEATFTINTQT------LRIGNLYLPHGNPITSTKYDDKISWIKRFLRF---------- 137
+ + + + + + N Y+ + + S+ +
Sbjct: 272 VLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWATE 331
Query: 138 --------ASQRLELEEPLIFAGDYNIIPQPHDCYNPIIW---ENDACFTLEVRQSFQK- 185
A I+AGD N+ + +D Y + + + F E R SF++
Sbjct: 332 NAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAPEERMSFRET 391
Query: 186 LQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTK 244
+Q D R + +YSFW + +N G R+D+ ++S S +
Sbjct: 392 MQRTNSVDIFRQLYPQAGPVYSFWSQRINGRPRNLGWRLDYFVVSSRLASYVVDCFP--- 448
Query: 245 PRGWTKPSDHTPVIVSLDIP 264
SDH P + + P
Sbjct: 449 -MPTVMGSDHCPFQMWMRHP 467
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 166 bits (421), Expect = 4e-42
Identities = 91/257 (35%), Positives = 133/257 (51%), Gaps = 4/257 (1%)
Query: 6 VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65
+ TWNVNS+ R+ + + +N PDI+ LQE K + FP LQ + +H GQK+Y
Sbjct: 3 ITTWNVNSLNVRLPQVQNLLADNPPDILVLQELKLDQDKFPAAALQMMGWHCVWSGQKTY 62
Query: 66 NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125
NGVAI+S+ P ++ LP D Q R I AT +R+ N+Y +G + S K+
Sbjct: 63 NGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATV----SGVRVINVYCVNGEALDSPKFK 118
Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185
K W F + L+ GD+NI P DCY+P W + RQ FQ
Sbjct: 119 YKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWFQN 178
Query: 186 LQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKP 245
L ++G TD++R H Y+++DY + + G+RIDHI++SP + L R+D +
Sbjct: 179 LLDLGLTDSLRQVHPEGAFYTWFDYRGAMFQRKLGLRIDHILVSPAMAAALKDVRVDLET 238
Query: 246 RGWTKPSDHTPVIVSLD 262
R +PSDH PV D
Sbjct: 239 RALERPSDHAPVTAEFD 255
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 166 bits (420), Expect = 5e-42
Identities = 77/264 (29%), Positives = 118/264 (44%), Gaps = 8/264 (3%)
Query: 6 VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65
++N+N +RAR H L A ++++ PD+I LQETK D FP E + L Y++ GQK +
Sbjct: 3 FVSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYHGQKGH 62
Query: 66 NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125
GVA+L+K PI + PGDD + Q R I A + + N Y P G
Sbjct: 63 YGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKF 122
Query: 126 DK-ISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYN------PIIWENDACFTLE 178
+ + + L+ + P++ GD NI P D + F E
Sbjct: 123 PAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPE 182
Query: 179 VRQSFQKLQNMGFTDAIRATHDTHHLYS-FWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237
R+ +L + G D R + ++DY + + N+G+RID ++ S
Sbjct: 183 EREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCV 242
Query: 238 SARIDTKPRGWTKPSDHTPVIVSL 261
ID + R KPSDH PV +
Sbjct: 243 ETGIDYEIRSMEKPSDHAPVWATF 266
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A
{Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A*
2o3c_A
Length = 285
Score = 148 bits (374), Expect = 1e-36
Identities = 75/265 (28%), Positives = 127/265 (47%), Gaps = 17/265 (6%)
Query: 6 VATWNVNSIRARIHN-LAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCG--- 61
+A+WNV+ +RA I W+KE PDI+CLQETK + P E + +
Sbjct: 31 IASWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPS 90
Query: 62 -QKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT 120
++ Y+GV +LS+ P+++ + ++ D + R I A F Y+P+
Sbjct: 91 DKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLV----TAYVPNAGRGL 146
Query: 121 STKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVR 180
+ + + W + F +F +PL+ GD N+ + D NP + +A FT + R
Sbjct: 147 -VRLEYRQRWDEAFRKFLKGL-ASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQER 204
Query: 181 Q-SFQKLQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHS 238
Q + LQ + D+ R + +T + Y+FW Y ++ SKN G R+D+ +LS L
Sbjct: 205 QGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCD 264
Query: 239 ARIDTKPRGWTKPSDHTPVIVSLDI 263
++I R SDH P+ + L +
Sbjct: 265 SKI----RSKALGSDHCPITLYLAL 285
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens}
Length = 313
Score = 145 bits (367), Expect = 1e-35
Identities = 44/301 (14%), Positives = 83/301 (27%), Gaps = 48/301 (15%)
Query: 4 VTVATWNVNSIRARIHNLAAWIK--ENNPDI--ICLQETKTEDKNFPFETLQSLNYHIET 59
T+NVN + L W+ PD+ + QE + F F +
Sbjct: 10 FFAGTYNVNGQSPK-ECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKA 68
Query: 60 -------------CGQKSYNGVAIL-----------SKYQPIEIVTHLPGDDLDVQARFI 95
G+ +L S+ + + T + G + I
Sbjct: 69 VSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAI 128
Query: 96 EATFTINTQTLRIGNLYLPHGNPITS------TKYDDKISWIKRFLRFASQRLELEEPLI 149
F + ++ + N +L ++ + + + + ++
Sbjct: 129 --RFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVIL 186
Query: 150 FAGDYNIIPQPHDCYNPIIW--ENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSF 207
+ GD N + D E D Q ++ + T
Sbjct: 187 WLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYK 246
Query: 208 WDYYADSWSKNKGIRI----DHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDI 263
+D +D W ++ R D I+ + + L K SDH PV DI
Sbjct: 247 YDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQS-----HMALKTSDHKPVSSVFDI 301
Query: 264 P 264
Sbjct: 302 G 302
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 142 bits (357), Expect = 1e-34
Identities = 63/263 (23%), Positives = 115/263 (43%), Gaps = 13/263 (4%)
Query: 6 VATWNVNSIRARI-HNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETC--GQ 62
+ + NVN IR+ +I + DI+C+QE K ++ + + H +
Sbjct: 4 IISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEK 63
Query: 63 KSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITST 122
+ Y+GVA+ SK +P + + ++ D + RF+ F L + +LYLP G+
Sbjct: 64 RGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDF----GRLSVISLYLPSGSSAE-E 118
Query: 123 KYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQS 182
+ K ++ F ++ GD+NI Q D N + ++ F E R+
Sbjct: 119 RQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREW 178
Query: 183 FQKLQNMGFTDAI-RATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARI 241
K+ + + R + Y++W +++K+ G RID+ M++PE + SA +
Sbjct: 179 IGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHV 238
Query: 242 DTKPRGWTKPSDHTPVIVSLDIP 264
K SDH P++V D
Sbjct: 239 YK----DEKFSDHAPLVVEYDYA 257
>3nr8_B Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; structural
genomics consortium, SGC, trisphosphate 5-phosphatase 2,
SHIP2, INPPL1, SHIP-2; 2.80A {Homo sapiens}
Length = 316
Score = 133 bits (334), Expect = 5e-32
Identities = 47/309 (15%), Positives = 89/309 (28%), Gaps = 56/309 (18%)
Query: 4 VTVATWNVNSIRARI------------HNLAAWIKENNPDI--ICLQETKTEDKNFPFET 49
V + TWN+ S+ L DI QE D+ +
Sbjct: 10 VFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLL 69
Query: 50 LQSLN------YHIETCGQKSYNGVAILSKYQPIEIVTH---------LPGDDLDVQARF 94
L Y VA+L K + ++H + + A
Sbjct: 70 RGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVG 129
Query: 95 IEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEE------PL 148
+ +F N + N +L GN T+ + + + ++ L ++L + L
Sbjct: 130 V--SFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRL-LSLGDRQLNAFDISLRFTHL 186
Query: 149 IFAGDYNIIPQPHDCY-----NPIIWENDACFTLEVRQSFQKLQNMGFTDA-------IR 196
+ GD N + +E + + + F++ R
Sbjct: 187 FWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPPTYR 246
Query: 197 ATHDTHHLYSFWDYYADSWSKNKGIRIDHIM--LSPEATSLLHSARIDTKPRGWTKPSDH 254
+ Y++ N D I+ PE + +S SDH
Sbjct: 247 YERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGC----TDDIVTSDH 302
Query: 255 TPVIVSLDI 263
+PV + ++
Sbjct: 303 SPVFGTFEV 311
>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport
protein; HET: HEM; 1.30A {Cimex lectularius} SCOP:
d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X*
Length = 282
Score = 129 bits (325), Expect = 6e-31
Identities = 27/283 (9%), Positives = 62/283 (21%), Gaps = 34/283 (12%)
Query: 4 VTVATWNVNSIRAR--IHNLAAWIKENNPDI--ICLQETKTEDKNFPFETLQSLNYHIET 59
V +WN RA + L PD+ + +Q + +
Sbjct: 9 VHTVSWNSGHERAPTNLEELLGLNSGETPDVIAVAVQGFGFQTDKPQQG-PACVKNFQSL 67
Query: 60 CGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPI 119
K Y + V L + T + + G +
Sbjct: 68 LTSKGYTKLKNTITETMGLTVYCLE----KHLDQNTLKNET----IIVTVDDQKKSGGIV 119
Query: 120 TSTKYDDKISWI-----------KRFLRFASQRLELEEPLIFAGDYNIIPQPHDCY---- 164
TS +K ++A D+ +
Sbjct: 120 TSFTIYNKRFSFTTSRMSDEDVTSTNTKYAYDTRLDYSKKDDPSDFLFWIGDLNVRVETN 179
Query: 165 NPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRI- 223
++ +F +L+ + + + + +
Sbjct: 180 ATHAKSLVDQNNIDGLMAFDQLKKAKEQKLFDGWTEPQVTFKPTYKFKPNTDEYDLSATP 239
Query: 224 ---DHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDI 263
D + + ++ K ++H PV+ +
Sbjct: 240 SWTDRALYKSGTGKTIQPLSYNS--LTNYKQTEHRPVLAKFRV 280
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling,
SGC stockholm, structural genomics CONS hydrolase; 1.90A
{Homo sapiens}
Length = 357
Score = 125 bits (314), Expect = 1e-29
Identities = 36/298 (12%), Positives = 87/298 (29%), Gaps = 41/298 (13%)
Query: 4 VTVATWNVNSIRARIHNLAAWI----KENNPDI--ICLQETKTEDKNFPFETLQSLNYHI 57
+ VATWN+ + +L ++ + D+ I +QE ++ + + ++L H
Sbjct: 28 LFVATWNMQGQKELPPSLDEFLLPAEADYAQDLYVIGVQEGCSDRREWETRLQETLGPHY 87
Query: 58 ETCGQKSYNGVAIL-----------SKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTL 106
++ + + S+ + + T + A I FT +
Sbjct: 88 VLLSSAAHGVLYMSLFIRRDLIWFCSEVECSTVTTRIVSQIKTKGALGIS--FTFFGTSF 145
Query: 107 RIGNLYLPHG------------NPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDY 154
+ G + + + + A+ + + + GD+
Sbjct: 146 LFITSHFTSGDGKVAERLLDYTRTVQALVLPRNVPDTNPYRSSAADVTTRFDEVFWFGDF 205
Query: 155 NI-IPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATH---DTHHLYSFWDY 210
N + + ++ + + Q Q ++ M + +D
Sbjct: 206 NFRLSGGRTVVDALLCQGLVVDVPALLQHDQLIREMRKGSIFKGFQEPDIHFLPSYKFDI 265
Query: 211 YADSWSKNKGIRI----DHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIP 264
D++ R D ++ + + K SDH PV +
Sbjct: 266 GKDTYDSTSKQRTPSYTDRVLYRSRHKGDIC--PVSYSSCPGIKTSDHRPVYGLFRVK 321
>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I,
microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1
Length = 262
Score = 109 bits (273), Expect = 5e-25
Identities = 36/292 (12%), Positives = 65/292 (22%), Gaps = 74/292 (25%)
Query: 1 MSVVTVATWNVNSIRARIHN------LAAWIKENNPDIICLQETKTEDKNFPFE------ 48
++ VATWN+ A + EN DI+ +QE +
Sbjct: 13 LTDFRVATWNLQGASATTESKWNINVRQLISGENAVDILAVQEAGSPPSTAVDTGRVIPS 72
Query: 49 -----------------TLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQ 91
Q Y +A++S + E+ P
Sbjct: 73 PGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVFVLSPVRQGGRP 132
Query: 92 ARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFA 151
I + + +++ F R + + +
Sbjct: 133 LLGIR------IGNDAFFTAHAIAMRNNDAPALVEEVYN---FFRDSRDPVHQALNWMIL 183
Query: 152 GDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYY 211
GD+N P + +
Sbjct: 184 GDFNREPADLEMN----------------------------------LTVPVRRASEIIS 209
Query: 212 ADSWSKNKGIRIDHIMLSPEATSLLH--SARIDTKPRGWTKPSDHTPVIVSL 261
+ ++ +D+ + A I R SDH PV VS
Sbjct: 210 PAAATQTSQRTLDYAVAGNSVAFRPSPLQAGIVYGARRTQISSDHFPVGVSR 261
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 108 bits (270), Expect = 1e-24
Identities = 37/273 (13%), Positives = 79/273 (28%), Gaps = 29/273 (10%)
Query: 4 VTVATWNV---------NSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLN 54
V AT+N+ N+ + R + +IK++ DI+ +QE L +
Sbjct: 4 VRWATFNIRYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGMQEVLHNQFQDLRAGLPEYD 63
Query: 55 YHI--ETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLY 112
G+ + + + E++ + + + +
Sbjct: 64 GIGVGRDDGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCVRIATWAKF 123
Query: 113 LPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWEND 172
+ + R S L + + + P + D
Sbjct: 124 KDKATGKIFMAVNTHFDHVGEEARRQSALLIIRK-----------IKEIVGERPAVVTGD 172
Query: 173 ACFTLE--VRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSP 230
T ++ + + A T Y+F D+ +ID I ++P
Sbjct: 173 FNVTDASDAYETITTNEFVMKDAYKTAARVTGVDYTFHDF--ARIPAEDCEKIDFIFVTP 230
Query: 231 EATSLLHSARIDTKPRGWTKPSDHTPVIVSLDI 263
+ + S I + SDH P + L++
Sbjct: 231 QVL--VKSCEIPAEVPEA-LLSDHNPQLADLEL 260
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 107 bits (267), Expect = 3e-24
Identities = 31/263 (11%), Positives = 65/263 (24%), Gaps = 40/263 (15%)
Query: 4 VTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQK 63
V N+ + LA I +QE + T
Sbjct: 20 YRVLQANLQRKKLATAELAIEAATRKAAIALIQEPYVGGAKSMKGFRGVRVFQS-TAQGD 78
Query: 64 SYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTK 123
AI ++++ + ++ I + + + Y
Sbjct: 79 GTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRA----WEITLVSYYFEP-------- 126
Query: 124 YDDKISWIKRFLRFASQRLELEEP--LIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQ 181
I+ +L + P LIF GD N + T
Sbjct: 127 ----DKPIESYLEQIKRVERKMGPKRLIFGGDANAKSTWWGSKEDDARGDQLMGT----- 177
Query: 182 SFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARI 241
+ + + +F ++ R+D + + L+ R+
Sbjct: 178 ---------LGELGLHILNEGDVPTFDTIRGGKRYQS---RVDVTFCTEDMLDLIDGWRV 225
Query: 242 DTKPRGWTKPSDHTPVIVSLDIP 264
D SDH ++ ++ +
Sbjct: 226 DEDLVS----SDHNGMVFNIRLQ 244
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1
type, retrotransposition, retrotransposon, transferase;
1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A
Length = 238
Score = 105 bits (261), Expect = 1e-23
Identities = 56/262 (21%), Positives = 92/262 (35%), Gaps = 32/262 (12%)
Query: 2 SVVTVATWNVNSIRARI--HNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIET 59
S +T+ T N+N + + I H LA+WIK +P + C+QET ++ ++ +
Sbjct: 6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQA 65
Query: 60 CGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPI 119
G++ GVAIL + T D + +I +I + L I N+Y P+
Sbjct: 66 NGKQKKAGVAILVSDKTDFKPT---KIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAP 122
Query: 120 TSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEV 179
K + GD+N D D
Sbjct: 123 RFIKQVLSDLQRDLDSHT-----------LIMGDFNTPLSTLDRSTRQKVNKD------T 165
Query: 180 RQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSA 239
++ L D R H Y+F+ ++S +IDHI+ S S
Sbjct: 166 QELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYS-----KIDHIVGSKALLSKCKRT 220
Query: 240 RIDTKPRGWTKPSDHTPVIVSL 261
I SDH+ + + L
Sbjct: 221 EII-----TNYLSDHSAIKLEL 237
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein;
structural genomics, PSI-2, protein structure
initiative; HET: MSE PEG; 1.90A {Bacteroides
thetaiotaomicron}
Length = 298
Score = 103 bits (257), Expect = 4e-23
Identities = 45/295 (15%), Positives = 79/295 (26%), Gaps = 47/295 (15%)
Query: 4 VTVATWNV-----------NSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQS 52
+TVA++N+ + R +A ++ ++ DI QE E L
Sbjct: 7 LTVASYNLRNANGSDSARGDGWGQRYPVIAQMVQYHDFDIFGTQECFLHQLKDMKEALPG 66
Query: 53 LNYHIETC--GQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGN 110
+Y G+ AI + +IV + + + + G+
Sbjct: 67 YDYIGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAVLPRICSWGH 126
Query: 111 LYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWE 170
++ + I + R S L + P I
Sbjct: 127 FKC-KDTGFEFLFFNLHMDHIGKKARVESAFLV---------QEKMKELGRGKNLPAILT 176
Query: 171 NDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSP 230
D + + D+ + L ++ + + RIDHI +SP
Sbjct: 177 GDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNF--DPNSFTESRIDHIFVSP 234
Query: 231 EATSLLHSARIDTKPRGWTK----------------------PSDHTPVIVSLDI 263
+ DT PSDH PV V L
Sbjct: 235 SFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTPSDHFPVKVELVF 289
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 99.5 bits (246), Expect = 8e-22
Identities = 41/267 (15%), Positives = 73/267 (27%), Gaps = 27/267 (10%)
Query: 4 VTVATWNV---------NSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLN 54
+ +AT+NV R + I ++ + C+QE +
Sbjct: 1 MKIATYNVRVDTEYDQDWQWSFRKEAVCQLINFHDWSLCCIQEVRPNQVRDLKAYTTFTC 60
Query: 55 YHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLP 114
E G G+AIL Q ++ + + + + G
Sbjct: 61 LSAEREGDGQGEGLAILYNEQKVQAIDTGYFWLSETPQQPSIHPEAGCPRIALWGLFKET 120
Query: 115 HGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDAC 174
+ + I R A + LEE Y P + D
Sbjct: 121 -TQNTPFLVINVHLDHISAHARLAGMTVILEELHDKIAQY-----------PTLLMGD-- 166
Query: 175 FTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATS 234
F E + +L F D+ +F ++ + ID+I +
Sbjct: 167 FNAESGEEVHQLVQKKFQDSKNLATHYGPRGTFQNFTYT-KPWAELEEIDYIYVKG---W 222
Query: 235 LLHSARIDTKPRGWTKPSDHTPVIVSL 261
+ T PSDH P+ +
Sbjct: 223 QVQQTASLTDSIDGRFPSDHFPLEAEV 249
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A
Length = 317
Score = 93.9 bits (232), Expect = 3e-20
Identities = 47/303 (15%), Positives = 88/303 (29%), Gaps = 67/303 (22%)
Query: 4 VTVATWNVNSIRA----------RIHNLAAWIKENNPDIICLQE--TKTEDKNFPFETLQ 51
+ + + NV + R + N D++ E +
Sbjct: 30 LKLVSHNVYMLSTVLYPNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKK 89
Query: 52 SLNYHIETCGQKSY----------------NGVAILSKYQPIEIVTHL----PGDDLDVQ 91
Y G+ GVAI+SKY E + H+ G D D
Sbjct: 90 EYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSGCGFDNDSN 149
Query: 92 ARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISW--IKRFLRF-ASQRLELEEPL 148
F+ N + + + + + +D KI +K F + + +E +
Sbjct: 150 KGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDRKIRAEQMKEISDFVKKKNIPKDETV 209
Query: 149 IFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFW 208
GD N+ + + L+N+ D + A H++
Sbjct: 210 YIGGDLNVNKGTPEFKDM-------------------LKNLNVNDVLYAGHNSTWDPQSN 250
Query: 209 DYYADSWSKNKGIRIDHIMLSPE--ATSLLHSARIDTKPRGW-----------TKPSDHT 255
++ K +D+I + L + + KP+ W SDH
Sbjct: 251 SIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAAAYYYVYNDFSDHY 310
Query: 256 PVI 258
P+
Sbjct: 311 PIK 313
>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence,
DNA damage, genotoxin, cytotoxins, cell cycle,
apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP:
d.151.1.1 PDB: 2f2f_B
Length = 261
Score = 89.4 bits (220), Expect = 9e-19
Identities = 35/297 (11%), Positives = 64/297 (21%), Gaps = 73/297 (24%)
Query: 1 MSVVTVATWNVNSIRA------RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLN 54
+S VATWN+ A I+ E DI+ +QE + + + +
Sbjct: 2 LSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQH 61
Query: 55 YHIETCG-----------------------QKSYNGVAILSKYQPIEIVTHLPGDDLDVQ 91
+ +AI+S+ Q E +
Sbjct: 62 GGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQS 121
Query: 92 ARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFA 151
+ T ++ + I F +S +
Sbjct: 122 RPAVGIRI----GTDVFFTVHALATGGSDAVSLIRNIFT--TFNSSSSPPERRVYSWMVV 175
Query: 152 GDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYY 211
GD+N + + +
Sbjct: 176 GDFN--------------------------------RAPANLEVALRQEPAVSENTIIIA 203
Query: 212 ADSWSKNKGIRIDHIMLSPE------ATSLLHSARIDTKPRGWTKPSDHTPVIVSLD 262
+ G +D+ +L A + SDH PV D
Sbjct: 204 PTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVRD 260
>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich
fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB:
3ngo_A 3ngn_A
Length = 398
Score = 86.6 bits (213), Expect = 6e-18
Identities = 42/360 (11%), Positives = 82/360 (22%), Gaps = 90/360 (25%)
Query: 4 VTVATWNV------------------NSIRARIHNLAAWIKENNPDIICLQE-TKTEDKN 44
TV +NV + R + I + DII LQE +
Sbjct: 32 FTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFT 91
Query: 45 FPFETLQSLNYH-----------IETCGQKSYNGVAILSKYQPIEIVTH----------- 82
L+ Y + +K +G AI K + +V
Sbjct: 92 LFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMA 151
Query: 83 LPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKI-----------SWI 131
+ R + L + G + +
Sbjct: 152 NSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYS 211
Query: 132 KRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGF 191
L + + ++ D + + +L + L N G
Sbjct: 212 DVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGV 271
Query: 192 TDAIR----------------------ATHDTHHLYSFWDYYAD------SWSKNKGIRI 223
D + + H + Y + +++ + I
Sbjct: 272 ADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYTNYTFDFKGVI 331
Query: 224 DHIMLSPEATSLLHSARIDTK----------PRGWTKPSDHTPVIVSLDIPEPRKKQQDS 273
D+I S ++ PSDH ++ L++ P +
Sbjct: 332 DYIFYSKTHMNVEGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQLELHPPLLPLVNG 391
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha
beta sandwich, gene regulation; 2.00A {Bombyx mori}
Length = 240
Score = 81.9 bits (201), Expect = 2e-16
Identities = 27/279 (9%), Positives = 69/279 (24%), Gaps = 53/279 (18%)
Query: 5 TVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKS 64
+ N+ L + ++ DI+ +QE + +
Sbjct: 9 RIGQINLGGAEDATRELPSIARDLGLDIVLVQEQYS--------------MVGFLAQCGA 54
Query: 65 YNGVAILSKY--QPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITST 122
+ + + P ++ HL + V I L + + Y + +PI
Sbjct: 55 HPKAGVYIRNRVLPCAVLHHLSSTHITV--------VHIGGWDLYMVSAYFQYSDPI--- 103
Query: 123 KYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQS 182
D + + L ++ D N +
Sbjct: 104 --DPYLHRLGNILDRLR-----GARVVICADTNAHSPLWHSLPRHYVGRGQEVADRRAKM 156
Query: 183 FQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARID 242
+ H + N +D + + + R+
Sbjct: 157 EDFIGARRLVVHNADGHLPTF-----------STANGESYVDVTLSTRGV--RVSEWRVT 203
Query: 243 TKPRGWTKPSDHTPVIVSLDIPEPRKK-QQDSTSQNMKP 280
+ SDH ++ + ++ + + +++P
Sbjct: 204 NES-----SSDHRLIVFGVGGGTTGERDEDEEARSDLRP 237
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken
structural genomics/proteomics initiative, RSGI,
structural genomics, hydrolase; 1.40A {Bacillus cereus}
SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X
Length = 306
Score = 80.0 bits (195), Expect = 6e-16
Identities = 42/298 (14%), Positives = 88/298 (29%), Gaps = 40/298 (13%)
Query: 4 VTVATWNVNSIRA----------RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSL 53
+ V T NV + R + A N D++ L E +
Sbjct: 10 LKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKK 69
Query: 54 NYHIETC-------------------GQKSYNGVAILSKYQPIEIVTHL----PGDDLDV 90
Y +T GVAI+SK+ E + ++ G D
Sbjct: 70 EYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLS 129
Query: 91 QARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKI---SWIKRFLRFASQRLELEEP 147
F+ N + + + +L + + + + ++ + E
Sbjct: 130 NKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEY 189
Query: 148 LIFAGDYNIIPQPHDCYNPIIWEN--DACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLY 205
++ GD N+ + N + + + T++I +
Sbjct: 190 VLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPA 249
Query: 206 SFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDI 263
+ DY S I++ +L P++ ++ + SDH PV ++ +
Sbjct: 250 EYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYT--YNDYSDHYPVEATISM 305
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 70.3 bits (170), Expect = 5e-13
Identities = 40/302 (13%), Positives = 78/302 (25%), Gaps = 66/302 (21%)
Query: 5 TVATWNV----------NSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLN 54
+ + NV R +A N D++ L E +
Sbjct: 12 KITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREM 71
Query: 55 YHIETC------------------GQKSYNGVAILSKYQPIEIVTHLPGDDLDVQA---- 92
Y +T GVA++S++ +E H+
Sbjct: 72 YPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGGGADRLSNK 131
Query: 93 RFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIK---RFLRFASQRLELEEPLI 149
F N + I + + + S I + A + + +E +
Sbjct: 132 GFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIAKKNIPKDEIIF 191
Query: 150 FAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWD 209
GD N+ + ++ + N + +
Sbjct: 192 IGGDLNVNYGTDEYHDMLKLLNVSSPAN------------------FNGQMATWDPTTNS 233
Query: 210 YYADSWSKNKGIRIDHIMLSPE--ATSLLHSARIDTKPRGWT-----------KPSDHTP 256
+S+ K +D+I + H+ + TK W+ SDH P
Sbjct: 234 MLKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDFSDHYP 293
Query: 257 VI 258
V+
Sbjct: 294 VV 295
>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3,
structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus}
SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B*
2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D*
Length = 260
Score = 61.5 bits (147), Expect = 2e-10
Identities = 37/284 (13%), Positives = 75/284 (26%), Gaps = 55/284 (19%)
Query: 6 VATWNVNSI---RARIHNLAAWIKE--NNPDIICLQETKTEDKNFPFETLQSLNYHIET- 59
+A +N+ + + LA++I DI+ +QE + + L LN
Sbjct: 3 IAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNT 62
Query: 60 ------------CGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLR 107
++ Y + +K ++ + G + F + +
Sbjct: 63 YHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHS 122
Query: 108 IGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPI 167
++ + Q+ ++ GD+N
Sbjct: 123 TKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADC--------- 173
Query: 168 IWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIM 227
+ T S + + F I + DT + + D I+
Sbjct: 174 -----SYVTSSQWSSIRLRTSSTFQWLIPDSADT-------------TATSTNCAYDRIV 215
Query: 228 LSPE----------ATSLLHSARIDTKPRGWTKPSDHTPVIVSL 261
++ A A SDH PV V+L
Sbjct: 216 VAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTL 259
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 44.5 bits (105), Expect = 2e-05
Identities = 45/269 (16%), Positives = 74/269 (27%), Gaps = 139/269 (51%)
Query: 43 KNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEI----------VTHLP----GDDL 88
N E +Q ++ N + L + +EI V+ P G L
Sbjct: 342 SNLTQEQVQD---YVNKT-----N--SHLPAGKQVEISLVNGAKNLVVSGPPQSLYG--L 389
Query: 89 DVQARFIEATFTINTQT--------LRIGNLYLPHGNPITS---TKYDDKISWIKRFLRF 137
++ R +A ++ Q+ L+ N +L P+ S + L
Sbjct: 390 NLTLRKAKAPSGLD-QSRIPFSERKLKFSNRFL----PVASPFHSHL----------LVP 434
Query: 138 ASQRLE---LEEPLIFAGD------Y-------------NIIPQPHD--CYNPIIWENDA 173
AS + ++ + F Y +I + D P+ WE
Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWET-T 493
Query: 174 CFTLEVRQSFQKLQNMGFTDAIRATH--D------------THHLYSFWDYYADSWSKNK 219
F+ ATH D TH NK
Sbjct: 494 T-------QFK------------ATHILDFGPGGASGLGVLTHR--------------NK 520
Query: 220 ---GIRIDHIMLSPEATSLLHSARIDTKP 245
G+R+ I+ A +L D P
Sbjct: 521 DGTGVRV--IV----AGTL------DINP 537
Score = 31.8 bits (72), Expect = 0.17
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 10/78 (12%)
Query: 70 ILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKIS 129
LS + +E V +P A ++ F + L + T+
Sbjct: 10 TLS-HGSLEHVLLVP-TASFFIASQLQEQFN---KILPEPTEGFAADDEPTT-----PAE 59
Query: 130 WIKRFLRFASQRLELEEP 147
+ +FL + S +E +
Sbjct: 60 LVGKFLGYVSSLVEPSKV 77
Score = 30.3 bits (68), Expect = 0.45
Identities = 58/323 (17%), Positives = 99/323 (30%), Gaps = 129/323 (39%)
Query: 18 IHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPI 77
IH LAA + + +T E ++ NY + +P
Sbjct: 101 IHALAA---KLLQEN----DTTLVKTK---ELIK--NY---------ITARIMA--KRPF 137
Query: 78 EIVTHLPGDDL-----DVQARFIEATF----TINT--QTLRIGNLYLPHGNPITSTKYDD 126
L + A+ + A F + + LR +LY T Y
Sbjct: 138 ---DKKSNSALFRAVGEGNAQ-LVAIFGGQGNTDDYFEELR--DLY--------QT-YH- 181
Query: 127 KISWIKRFLRFASQRL-EL-EEPLIFAGDYNIIPQPHDCYNPII-W-EN-----DACFTL 177
+ ++F+++ L EL L + Q + I+ W EN D + L
Sbjct: 182 --VLVGDLIKFSAETLSELIRTTLDAEKVF---TQGLN----ILEWLENPSNTPDKDYLL 232
Query: 178 EVRQSF------QKLQ------NMGFT-----DAIRATHDTHH---------LYSFWDYY 211
+ S Q +GFT ++ T H +
Sbjct: 233 SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA--TGHSQGLVTAVAIAE----- 285
Query: 212 ADSWS---KN--KGIRIDHIML------SPEA---TSLLHSARIDTKPRGWTKPSDHTPV 257
DSW + K I +L EA TSL S D+ PS P+
Sbjct: 286 TDSWESFFVSVRKAIT----VLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS---PM 338
Query: 258 I-VSLDIPEPRKKQQ---DSTSQ 276
+ +S ++ +++ Q + T+
Sbjct: 339 LSIS-NL--TQEQVQDYVNKTNS 358
>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 = 35.7 bits (81), Expect = 0.013
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 8/27 (29%)
Query: 180 RQSFQKLQ-NMG-FTD------AIRAT 198
+Q+ +KLQ ++ + D AI+AT
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKAT 45
>3i1j_A Oxidoreductase, short chain dehydrogenase/reductase family; dimer,
mixed alpha-beta, structural genomics, PSI-2; 1.90A
{Pseudomonas syringae PV}
Length = 247
Score = 27.2 bits (60), Expect = 3.9
Identities = 13/50 (26%), Positives = 17/50 (34%)
Query: 212 ADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSL 261
AD +R + I T + A D P P D PV + L
Sbjct: 182 ADELEGVTAVRANSINPGATRTGMRAQAYPDENPLNNPAPEDIMPVYLYL 231
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae}
Length = 937
Score = 26.0 bits (56), Expect = 9.9
Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 4/70 (5%)
Query: 26 KENNPDIICLQETKTEDKNFPFETLQSL-NYHIETCGQKSYNGVAI--LSKYQPIEIVTH 82
KE PD+ E + K F + + L + + N L+ + +V
Sbjct: 144 KEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGAREDDAIN-RGSVVLASRRTGHLVNE 202
Query: 83 LPGDDLDVQA 92
+ VQA
Sbjct: 203 KASKEAKVQA 212
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.134 0.419
Gapped
Lambda K H
0.267 0.0490 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,522,559
Number of extensions: 113837
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 40
Length of query: 281
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 190
Effective length of database: 3,487,026
Effective search space: 662534940
Effective search space used: 662534940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.9 bits)