RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14294
(314 letters)
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA
replication, RTH, RAD27, DNA repair; 2.00A
{Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2
PDB: 1a77_A
Length = 326
Score = 163 bits (413), Expect = 4e-48
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 18/177 (10%)
Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D L+Q G + + G++++ LL I P++VFDG P+L
Sbjct: 27 DGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKL 86
Query: 206 KKQTIS------------TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
K++T E + + E K + S +T +M + LL L G+P+
Sbjct: 87 KEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPY 146
Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
+ AP E EAQ + + V++ D D L+GA V +N K ++
Sbjct: 147 VEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEV 203
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair,
DNA-binding, endonuclease, metal-BIND excision repair,
DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus
solfataricus}
Length = 346
Score = 159 bits (404), Expect = 1e-46
Identities = 41/170 (24%), Positives = 73/170 (42%), Gaps = 18/170 (10%)
Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D L+Q G + +HL GL++R +L + P++VFDG P+
Sbjct: 24 DGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFDGKPPEQ 83
Query: 206 KKQTISTLEKDRDQ------------LLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
K + + K +++ + E K ++ ++ M E+++LL+ G+P
Sbjct: 84 KSEELERRRKAKEEAERKLERAKSEGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPI 143
Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVL 303
+ AP E EA+ A L + + D D LFGA+ + +N L
Sbjct: 144 VQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKL 193
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3
turn-helix, hydrophobic wedge, 3' FLA site,
hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus}
SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Length = 336
Score = 159 bits (403), Expect = 1e-46
Identities = 44/166 (26%), Positives = 69/166 (41%), Gaps = 17/166 (10%)
Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D L+Q G + +HL G+ +R+ ++ I+PVFVFDG P+
Sbjct: 27 DAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEF 86
Query: 206 KKQTISTLEKDRDQLLL-----------ERGKQTRLASTITEQMSREAQELLQLFGVPFI 254
KK I +K R + + K + A + E + A+ LL G+PF+
Sbjct: 87 KKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFV 146
Query: 255 VAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS 300
AP E EAQ A + + + D D LFG+ + +N
Sbjct: 147 DAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGK 192
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap
binding site, hydrolase-DNA complex, DNA repair,
replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A*
3q8m_A*
Length = 341
Score = 159 bits (404), Expect = 1e-46
Identities = 49/179 (27%), Positives = 81/179 (45%), Gaps = 20/179 (11%)
Query: 152 DVSIWLHQLTK-----GTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLK 206
D S+ ++Q G +HL+G+++R +++ IKPV+VFDG PQLK
Sbjct: 33 DASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLK 92
Query: 207 KQTISTLEKDRDQ------------LLLERGKQTRLASTITEQMSREAQELLQLFGVPFI 254
++ + R + E K T+ +T+Q + E + LL L G+P++
Sbjct: 93 SGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYL 152
Query: 255 VAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFD---KKSHVLRYTAPDI 310
AP EAEA CA+L T+D D FG+ + ++ KK + + I
Sbjct: 153 DAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRI 211
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 159 bits (404), Expect = 2e-46
Identities = 46/180 (25%), Positives = 74/180 (41%), Gaps = 18/180 (10%)
Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D L+Q G + +HL GL++R ++ IKPV+VFDG P+L
Sbjct: 41 DGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPEL 100
Query: 206 KKQTIS------------TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
K + I E + L + +++ +TE+M R+A+ LL G+P+
Sbjct: 101 KAREIERRKAVKEEAAKKYEEAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPW 160
Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 313
+ AP E EAQ A + + D D LFG+ + +N L +
Sbjct: 161 VQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVK 220
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 158 bits (402), Expect = 5e-46
Identities = 49/179 (27%), Positives = 81/179 (45%), Gaps = 20/179 (11%)
Query: 152 DVSIWLHQLTK-----GTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLK 206
D S+ ++Q G +HL+G+++R +++ IKPV+VFDG PQLK
Sbjct: 33 DASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLK 92
Query: 207 KQTISTLEKDRDQ------------LLLERGKQTRLASTITEQMSREAQELLQLFGVPFI 254
++ + R + E K T+ +T+Q + E + LL L G+P++
Sbjct: 93 SGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYL 152
Query: 255 VAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFD---KKSHVLRYTAPDI 310
AP EAEA CA+L T+D D FG+ + ++ KK + + I
Sbjct: 153 DAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRI 211
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication,
transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1
c.120.1.2 PDB: 1mc8_A
Length = 340
Score = 154 bits (391), Expect = 1e-44
Identities = 46/180 (25%), Positives = 76/180 (42%), Gaps = 18/180 (10%)
Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
D ++Q G + +HL GL++R L+ IKPV+VFDG P+
Sbjct: 27 DALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDGEPPEF 86
Query: 206 KKQTISTLEKDRDQ------------LLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
KK+ + + R++ + E K + A+ + E + +A++LL+L G+P
Sbjct: 87 KKKELEKRREAREEAEEKWREALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPI 146
Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 313
+ AP E EAQ A + + D D LFGA + +N L +
Sbjct: 147 VQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIK 206
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 132 bits (333), Expect = 3e-36
Identities = 41/164 (25%), Positives = 65/164 (39%), Gaps = 13/164 (7%)
Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIG-LYHRICKLLFFKIKPVFVFDGGVPQLKKQTI 210
D WLH+ + P +G + LL IKP+ VFDG KK+
Sbjct: 30 DTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVE 89
Query: 211 ST------------LEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPG 258
+ + R+ + E + + IT M+ + + + GV +VAP
Sbjct: 90 RSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPY 149
Query: 259 EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHV 302
EA+AQ A L Q +IT+DS + FG + V + +
Sbjct: 150 EADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGL 193
>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 = 46.8 bits (110), Expect = 6e-06
Identities = 54/371 (14%), Positives = 104/371 (28%), Gaps = 109/371 (29%)
Query: 19 SDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFE-LPPAPAQTVQDEEEDSDSDD-- 75
D+ K++L ++ ++ ++ +VS + +F L + VQ E+ +
Sbjct: 39 QDMPKSILSKEEIDHIIMS------KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYK 92
Query: 76 -------TEAK------FRYADLHSVDINSEQ-FSALP---PDMRHEILTELLEQRKLSS 118
TE + Y + N Q F+ ++ LLE R +
Sbjct: 93 FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP-AK 151
Query: 119 WHKMHEMP-------------QNDQHSMLEF--------RCNI--VINKLLVDLISDVSI 155
+ + ++F CN + ++L L
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL------ 205
Query: 156 WLHQLTKGTHDLAGGSVPNAHLIG-LYHRICKLLFFKIKP--------------VFVFDG 200
L+Q+ + S I + + +LL K F+
Sbjct: 206 -LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL 264
Query: 201 GVPQLKKQTISTLEKDR---DQLLLERGKQTRL---ASTITEQMSREAQELLQLF-GVPF 253
L ++T + + D L L + T+T E + LL +
Sbjct: 265 SCKIL----LTT--RFKQVTDFLSAATTTHISLDHHSMTLTP---DEVKSLLLKYLDCRP 315
Query: 254 IVAPGEAEAQCASLELGNHTQGVI----TDDSDIWLFGARTVYKN-FFDKKSHVLRY--- 305
P E L +I D W +K+ DK + ++
Sbjct: 316 QDLPREV-LTTNPRRL-----SIIAESIRDGLATWDN-----WKHVNCDKLTTIIESSLN 364
Query: 306 --TAPDIRYYF 314
+ R F
Sbjct: 365 VLEPAEYRKMF 375
Score = 34.8 bits (79), Expect = 0.037
Identities = 39/303 (12%), Positives = 85/303 (28%), Gaps = 84/303 (27%)
Query: 12 SNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDM-------FELPPAP---- 60
+ S + + +EQ+ D L + +VSR EL PA
Sbjct: 99 KTEQRQPSMMTRMYIEQR---DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 61 ------------AQTVQDEEEDS--------------DSDDTEAKFRYADLHSVDINSEQ 94
+ +S +T + L+ +D N
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215
Query: 95 FSALPPDMRHEI------LTELLEQRKLSS--------WHKMHEMPQNDQHSMLEFRCNI 140
S +++ I L LL+ + + + + C I
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW-------NAFNLSCKI 268
Query: 141 VI---NKLLVDLISDVS---IWLHQLTKG-THD-----LAGGSVPNAHLIGLYHRICKLL 188
++ K + D +S + I L + T D L + L +
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPREVL--- 323
Query: 189 FFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQL 248
P + + + + ++T + + + ++ T + S++ E +++
Sbjct: 324 --TTNPRRL--SIIAESIRDGLATWDNWK-HVNCDK-LTTIIESSLNVLEPAEYRKMFDR 377
Query: 249 FGV 251
V
Sbjct: 378 LSV 380
Score = 28.7 bits (63), Expect = 3.0
Identities = 37/303 (12%), Positives = 78/303 (25%), Gaps = 112/303 (36%)
Query: 72 DSDDTEAKFRYADLHSVDINSEQFSA-----LPPDMRHEILTE----------------- 109
D + E +++Y D+ + + + F DM IL++
Sbjct: 8 DFETGEHQYQYKDI--LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 110 -----LLEQRK------------------LSSWHKMHEMPQ------NDQHSMLEFRCNI 140
LL +++ +S P +Q L + N
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL-YNDNQ 124
Query: 141 VINKLLV---DLISDVSIWLHQLTKGT----HDLAG-G-SVPNAHLIGLYHRICKLLFFK 191
V K V + L +L + G G + + +C +K
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-------VALDVCL--SYK 175
Query: 192 IKPVFVFDGGV----------PQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSRE 241
++ D + P+ + + L D R + + E
Sbjct: 176 VQC--KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 242 AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDD-SDIWLFGARTVYKNFFDKKS 300
+ LL+ + L ++ + + + A F+
Sbjct: 234 LRRLLKS------------KPYENCL--------LVLLNVQNAKAWNA-------FNLSC 266
Query: 301 HVL 303
+L
Sbjct: 267 KIL 269
>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 = 38.1 bits (88), Expect = 0.004
Identities = 41/248 (16%), Positives = 74/248 (29%), Gaps = 70/248 (28%)
Query: 40 MALPPPSVSREVDMFELPPAPAQTVQD---EEEDSDSDDTEAKF-RYADLH-SVDINS-E 93
+LPP + ++ E P+P ++ + E+ + T + + S+ +N +
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL-VNGAK 375
Query: 94 QF--SALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQ---------------HSMLEF 136
S P + L L + K S +P +++ HS L
Sbjct: 376 NLVVSGPPQSLYG--LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHL-- 431
Query: 137 RCNIVINKLLVDLIS-DVSIWLHQL------TKGTHDL--AGGSVPNAHLIGLYHRICKL 187
+ + DL+ +VS + T DL GS+ RI
Sbjct: 432 -LVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS--------ERIVDC 482
Query: 188 LFFKIKPVF-------------VFD-GGVPQLKKQTISTLEKDRDQLLLERGKQTRLAST 233
+ PV F GG L T + G + +A T
Sbjct: 483 II--RLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDG--------TGVRVIVAGT 532
Query: 234 ITEQMSRE 241
+ +
Sbjct: 533 LDINPDDD 540
Score = 36.2 bits (83), Expect = 0.013
Identities = 56/346 (16%), Positives = 96/346 (27%), Gaps = 133/346 (38%)
Query: 36 GKNEMALPPPS-----VSREVDMFELP-PAPAQTVQDEEEDSDSDDTEAKFRYADLHSVD 89
G E L P+ S+ + F P P + ++E + + KF L V
Sbjct: 14 GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF----LGYV- 68
Query: 90 INSEQFSALPPDMRHEILTELL---EQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLL 146
S ++L L E L ND H+ L
Sbjct: 69 --SSLVEPSKVGQFDQVLNLCLTEFENCYLEG---------NDIHA------------LA 105
Query: 147 VDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKL------------LF----- 189
L+ + L + LI Y + LF
Sbjct: 106 AKLLQENDTTLVK--------------TKELIKNYITARIMAKRPFDKKSNSALFRAVGE 151
Query: 190 --FKIKPVFVFDGG-------VPQLKK--QT----ISTLEKDRDQLLLERGKQTRLAST- 233
++ +F GG +L+ QT + L K + L E + T A
Sbjct: 152 GNAQLVAIF---GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKV 208
Query: 234 ----------ITEQMSREAQE-------------LLQLFGVPFIVA-------PGEAEAQ 263
+ + ++ ++QL ++V PGE +
Sbjct: 209 FTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQL--AHYVVTAKLLGFTPGELRSY 266
Query: 264 CASLELGNHTQGVIT----DDSDIWLFGARTVYKNFFDKKSHVLRY 305
G H+QG++T ++D W ++FF +
Sbjct: 267 LKGA-TG-HSQGLVTAVAIAETDSW--------ESFFVSVRKAITV 302
>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 = 31.1 bits (69), Expect = 0.26
Identities = 12/65 (18%), Positives = 19/65 (29%), Gaps = 37/65 (56%)
Query: 206 KKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQC- 264
+KQ + L+ AS L+L+ A A A
Sbjct: 18 EKQALKKLQ----------------AS-------------LKLY------ADDSAPALAI 42
Query: 265 -ASLE 268
A++E
Sbjct: 43 KATME 47
>2zy9_A Mg2+ transporter MGTE; membrane protien, metal transport; 2.94A
{Thermus thermophilus} PDB: 2yvx_A
Length = 473
Score = 30.3 bits (69), Expect = 0.95
Identities = 13/87 (14%), Positives = 23/87 (26%), Gaps = 16/87 (18%)
Query: 40 MALPPPSVSREVDMFELPPAPAQTVQDEEED-----SDSDDTEAKFRYADLHSVDI---- 90
M + LP P + + D + ++H D+
Sbjct: 1 MGSSHHHHHHSSGLGVLPGGPLHMEEKLAVSLQEALQEGDTRALREVLEEIHPQDLLALW 60
Query: 91 ---NSEQ----FSALPPDMRHEILTEL 110
E + LP E+L+ L
Sbjct: 61 DELKGEHRYVVLTLLPKAKAAEVLSHL 87
>3gty_X Trigger factor, TF; chaperone-client complex, cell cycle, cell
division, chapero isomerase, rotamase,
ribonucleoprotein, binding; 3.40A {Thermotoga maritima}
PDB: 3gu0_A
Length = 433
Score = 29.6 bits (67), Expect = 1.6
Identities = 9/77 (11%), Positives = 24/77 (31%), Gaps = 1/77 (1%)
Query: 6 LKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVD-MFELPPAPAQTV 64
LK ++ +K + +QLL + E+ + ++ V+ +
Sbjct: 251 LKESLKKEGKEIYDVEMKESMREQLLEKLPEIVEIEISDRTLEILVNEAINRLKREGRYE 310
Query: 65 QDEEEDSDSDDTEAKFR 81
Q + + +
Sbjct: 311 QIVSSYESEEKFREELK 327
>1t11_A Trigger factor, TF; helix-turn-helix, four-helix-bundle, ppiase,
chaperone; 2.50A {Vibrio cholerae} SCOP: a.223.1.1
d.241.2.1 d.26.1.1 PDB: 1l1p_A
Length = 392
Score = 28.8 bits (65), Expect = 2.3
Identities = 9/47 (19%), Positives = 27/47 (57%)
Query: 6 LKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVD 52
LK++ N ++ +K +++Q + ++ +NE+ +P + +E++
Sbjct: 269 LKAEVRKNMERELKQAIKARIKEQAIEGLVKENEIQVPSALIDQEIN 315
>1w26_A Trigger factor, TF; chaperone, protein folding, ribosome associated
protein, nascent chain, cell division, isomerase; 2.7A
{Escherichia coli} SCOP: a.223.1.1 d.241.2.1 d.26.1.1
PDB: 2vrh_A 1w2b_5
Length = 432
Score = 28.8 bits (65), Expect = 2.8
Identities = 8/47 (17%), Positives = 25/47 (53%)
Query: 6 LKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVD 52
L+++ N ++ ++N ++ Q + ++ N++ +P + E+D
Sbjct: 266 LRAEVRKNMERELKSAIRNRVKSQAIEGLVKANDIDVPAALIDSEID 312
>3izc_t 60S acidic ribosomal protein RPP11 (P1); eukaryotic
ribosome,homology modeling,de novo modeling,ribos
proteins,novel ribosomal proteins; NMR {Saccharomyces
cerevisiae} PDB: 3izs_t
Length = 106
Score = 27.0 bits (59), Expect = 3.1
Identities = 15/72 (20%), Positives = 26/72 (36%)
Query: 4 KTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPAPAQT 63
TL + A + + +D+ L+ Q L D+L P+
Sbjct: 27 LTLTNAANVPDENIWADIFAKALDGQNLKDLLVNFSAGAAAPAGVAGGVAGGEAGEAEAE 86
Query: 64 VQDEEEDSDSDD 75
++EE +SDD
Sbjct: 87 KEEEEAKEESDD 98
>2nsa_A Trigger factor, TF; chaperone; 1.70A {Thermotoga maritima}
Length = 170
Score = 27.3 bits (61), Expect = 4.1
Identities = 8/50 (16%), Positives = 19/50 (38%)
Query: 6 LKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFE 55
LK ++ +K + +QLL + E+ + ++ V+
Sbjct: 9 LKESLKKEGKEIYDVEMKESMREQLLEKLPEIVEIEISDRTLEILVNEAI 58
>2cvz_A Dehydrogenase, 3-hydroxyisobutyrate dehydrogenase; valine
catabolism, NADP+, structural GEN riken structural
genomics/proteomics initiative; HET: NDP; 1.80A {Thermus
thermophilus} SCOP: a.100.1.1 c.2.1.6 PDB: 1wp4_A*
Length = 289
Score = 27.9 bits (63), Expect = 4.2
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 232 STITEQMSREAQELLQLFGVPFIVAP---GEAEAQCASL 267
++ + SR E L+ GV ++ AP G + A+ +L
Sbjct: 90 TSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTL 128
>1jbq_A B, cystathionine beta-synthase, serine sulfhydrase; fold type II of
PLP enzymes, lyase; HET: HEM PLP; 2.60A {Homo sapiens}
SCOP: c.79.1.1 PDB: 1m54_A*
Length = 435
Score = 28.1 bits (63), Expect = 4.7
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 229 RLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQ 263
R + E+MS E ++L+ G + P A
Sbjct: 186 RCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFD 220
>1wr2_A Hypothetical protein PH1789; structural genomics, NPPSFA, national
on protein structural and functional analyses; 2.00A
{Pyrococcus horikoshii}
Length = 238
Score = 27.6 bits (62), Expect = 5.1
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 241 EAQELLQLFGVP---FIVAPGEAEAQCASLELG 270
EA+++L+ +G+P +A EA + E+G
Sbjct: 24 EAKQVLKAYGLPVPEEKLAKTLDEALEYAKEIG 56
>1ex2_A Protein MAF; structural genomics, PSI, protein structure
initiative, midwest center for structural genomics,
MCSG; HET: SUC PO4; 1.85A {Bacillus subtilis} SCOP:
c.51.4.2 PDB: 1exc_A*
Length = 189
Score = 27.0 bits (61), Expect = 6.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 243 QELLQLFGVPFIVAPGEAE 261
+ELL L +P+ + E E
Sbjct: 15 KELLDLLQLPYSIIVSEVE 33
>3qha_A Putative oxidoreductase; seattle structural genomics center for
infectious disease, S mycobacterium avium 104, rossmann
fold; 2.25A {Mycobacterium avium}
Length = 296
Score = 27.3 bits (61), Expect = 6.5
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 232 STITEQMSREAQELLQLFGVPFIVAP---GEAEAQCASL 267
STI++ + E L+ + + AP G A A L
Sbjct: 105 STISDTTAVELARDLKARDIHIVDAPVSGGAAAAARGEL 143
>3iz5_T 60S ribosomal protein L19 (L19E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_T
Length = 209
Score = 26.2 bits (57), Expect = 6.8
Identities = 2/75 (2%), Positives = 13/75 (17%), Gaps = 3/75 (4%)
Query: 4 KTLKSKAASNADKVRSDLLKNLLEQQLLNDVL---GKNEMALPPPSVSREVDMFELPPAP 60
+ + A++ +R + + ++ +
Sbjct: 28 EVNEISMANSRQNIRKLVKDGFIIRKPQKIHSRSRARRAHEAKQKGRHSGYGKRRGTREA 87
Query: 61 AQTVQDEEEDSDSDD 75
+
Sbjct: 88 RLPTKILWMRRMRVL 102
>3cky_A 2-hydroxymethyl glutarate dehydrogenase; rossmann fold, two domain
enzyme, oxidoreductase; 2.30A {Eubacterium barkeri}
Length = 301
Score = 27.2 bits (61), Expect = 7.0
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 232 STITEQMSREAQELLQLFGVPFIVAP---GEAEAQCASL 267
S+++ + + ++ G+ ++ AP G A+ +L
Sbjct: 98 SSVSPSSTLKMAKVAAEKGIDYVDAPVSGGTKGAEAGTL 136
>2h78_A Hibadh, 3-hydroxyisobutyrate dehydrogenase; APC6014, pseudomonas
aeruginosa PA01, PSI-2, structural genomics; HET: PG4;
2.20A {Pseudomonas aeruginosa} PDB: 3cum_A 3obb_A*
3q3c_A*
Length = 302
Score = 27.2 bits (61), Expect = 7.1
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 232 STITEQMSREAQELLQLFGVPFIVAP---GEAEAQCASL 267
STI +R+ + G+ + AP G A A +L
Sbjct: 97 STIAPTSARKIHAAARERGLAMLDAPVSGGTAGAAAGTL 135
>3g0o_A 3-hydroxyisobutyrate dehydrogenase; NAD(P), valine catabolism,
tartaric acid, target 11128H, NYSGXRC, PSI-2, structural
genomics; HET: TLA; 1.80A {Salmonella typhimurium}
Length = 303
Score = 27.2 bits (61), Expect = 7.8
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 232 STITEQMSREAQELLQLFGVPFIVAP---GEAEAQCASL 267
STI+ ++E L + + AP G +A +
Sbjct: 102 STISSADAQEIAAALTALNLNMLDAPVSGGAVKAAQGEM 140
>2r60_A Glycosyl transferase, group 1; rossmann-fold; 1.80A
{Halothermothrix orenii} PDB: 2r66_A* 2r68_A*
Length = 499
Score = 27.4 bits (61), Expect = 7.9
Identities = 11/65 (16%), Positives = 19/65 (29%), Gaps = 4/65 (6%)
Query: 201 GVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVA--PG 258
G+P T +L + + L + + R E L + I+
Sbjct: 143 GLPFT--FTGHSLGAQKMEKLNVNTSNFKEMDERFKFHRRIIAERLTMSYADKIIVSTSQ 200
Query: 259 EAEAQ 263
E Q
Sbjct: 201 ERFGQ 205
>3pc3_A CG1753, isoform A; CBS, synthase, PLP, heme, aminoacrylate, lyase;
HET: HEM P1T; 1.55A {Drosophila melanogaster} PDB:
3pc2_A* 3pc4_A*
Length = 527
Score = 27.3 bits (61), Expect = 8.0
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 229 RLASTITEQMSREAQELLQLFGVPFIVAPGEAEA 262
+ + E+MS E L+ G I P EA
Sbjct: 138 KCIIVMPEKMSNEKVSALRTLGAKIIRTPTEAAY 171
>3bbo_H Ribosomal protein L5; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 220
Score = 26.9 bits (60), Expect = 8.7
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 241 EAQELLQLFGVPFIVAPGEAEAQ 263
EA +LL L G+PF G +
Sbjct: 180 EAYKLLSLMGMPFREGSGPSTLV 202
>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
pleckst homology domain, C1 domain, guanine-nucleotide
releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
2d86_A
Length = 587
Score = 26.9 bits (59), Expect = 9.8
Identities = 10/65 (15%), Positives = 22/65 (33%)
Query: 48 SREVDMFELPPAPAQTVQDEEEDSDSDDTEAKFRYADLHSVDINSEQFSALPPDMRHEIL 107
+ + + +D + ++++ E Y DL + S D R L
Sbjct: 143 DIYSGLSDQIDDTVEEDEDLYDCVENEEAEGDEIYEDLMRSEPVSMPPKMTEYDKRCCCL 202
Query: 108 TELLE 112
E+ +
Sbjct: 203 REIQQ 207
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.134 0.389
Gapped
Lambda K H
0.267 0.0557 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,681,929
Number of extensions: 276510
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 805
Number of HSP's successfully gapped: 53
Length of query: 314
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 221
Effective length of database: 4,105,140
Effective search space: 907235940
Effective search space used: 907235940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.1 bits)