RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 003602
(808 letters)
>3hnc_A Ribonucleoside-diphosphate reductase large subuni; oxidoreductase,
ribonucleotide reductase, allosteric enzyme, binding,
DNA replication; HET: TTP; 2.41A {Homo sapiens} PDB:
3hnd_A* 3hne_A* 3hnf_A*
Length = 792
Score = 1266 bits (3277), Expect = 0.0
Identities = 540/811 (66%), Positives = 655/811 (80%), Gaps = 22/811 (2%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
M+V+KRDG+QE V FDKIT+R++KL YGL+++ DP ++ KV G+Y GVTT +LD LA
Sbjct: 1 MHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLA 60
Query: 61 AETAAAMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDV 120
AETAA +TT HPDYA LAARI VSNLHK TKK FS+ ++D+YN+ N +G +P++A
Sbjct: 61 AETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKST 120
Query: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHK 180
DI++ N RL+S IIYDRDF Y+YFGFKTLERSYLLK+ GKV ERPQHMLMRV+VGIHK
Sbjct: 121 LDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHK 180
Query: 181 DDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAI 240
+DID+AI+TY+++S+RWFTHASPTLFNAGT R QLSSCFL+ MKDDSIEGIYDTLK+CA+
Sbjct: 181 EDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCAL 240
Query: 241 ISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY 300
ISKSAGGIGV+V IRATGSYI GTNG SNG+VPMLRV+N+TARYVDQGG KR GAFA+Y
Sbjct: 241 ISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIY 300
Query: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLA 360
LEPWH DIFEFLDL+KN GKEE RARDLF+ALW+PDLFM+RV++N WSL CPNE PGL
Sbjct: 301 LEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLD 360
Query: 361 DCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNL 420
+ WG EFE+LY YEK+G+ +KVV+AQ LW+ I++SQ ETGTPYML+KD+CN+KSNQQNL
Sbjct: 361 EVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNL 420
Query: 421 GTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYF 480
GTIK SNLCTE+++YTS E AVCNLAS+AL YV + +
Sbjct: 421 GTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYV-------------------TSEHTY 461
Query: 481 DFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDS 540
DF+KLAEVT +V NLNKIID+NYYPV A SN RHRPIGIGVQGLAD FIL+ PF+S
Sbjct: 462 DFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFES 521
Query: 541 TEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDW 600
EAQ LNK IFETIYY AL S ++A +GPYETY GSPVSKGILQ DMW V P+D WDW
Sbjct: 522 AEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDW 581
Query: 601 GGLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
L++ I+K G+RNSLL+APMPTAST+QILGNNE EPYTSNIY+RRVLSGEF +VN HL
Sbjct: 582 KVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHL 641
Query: 661 LHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCY 720
L DLTE GLW +KN+II +GS+Q IP+IP++LK +YKTVWEI QKT++ MA +RG +
Sbjct: 642 LKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAF 701
Query: 721 IDHSQSLNIHMDQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDTSVLKENP 780
ID SQSLNIH+ +PN+GKLTS+HF+ W +GLKTGMYYLR+R AA+ I+FT++ LK+
Sbjct: 702 IDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTRPAANPIQFTLNKEKLKDKE 761
Query: 781 KVTDDDDAK---MAQMVCSLTNREECMACGS 808
KV+ +++ K A MVCSL NR+EC+ CGS
Sbjct: 762 KVSKEEEEKERNTAAMVCSLENRDECLMCGS 792
>3k8t_A Ribonucleoside-diphosphate reductase large chain; eukaryotic
ribonucleotide reductase, nucleotide analogs, all enzyme
ATP-binding; HET: DGT 2A5; 2.10A {Saccharomyces
cerevisiae} PDB: 1zyz_A 2cvs_A 2cvt_A* 2cvu_A* 2cvv_A*
1zzd_A* 2cvw_A* 2cvy_A* 2eud_A* 2zlf_A 2zlg_A* 2cvx_A*
3paw_A 3s87_A* 3s8b_A* 3s8c_A* 3s8a_A* 3tb9_A* 3tba_A*
Length = 888
Score = 1240 bits (3210), Expect = 0.0
Identities = 494/805 (61%), Positives = 631/805 (78%), Gaps = 19/805 (2%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
MYV KRDG++E V FDKITAR+ +L YGL +H D V V+Q++ +GVY+GVTT +LD LA
Sbjct: 1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLA 60
Query: 61 AETAAAMTTNHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDV 120
AET A MTT HPDYA+LAARI +SNLHK T K FS+ ++D+Y + N +G AP+I+DDV
Sbjct: 61 AETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDV 120
Query: 121 YDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHK 180
Y+I+M+N +L+S I+YDRDF Y YFGFKTLERSYLL++ G+V ERPQH++MRVA+GIH
Sbjct: 121 YNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHG 180
Query: 181 DDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAI 240
DI++A++TY++MS ++FTHASPTLFNAGTP+ Q+SSCFLV MK+DSIEGIYDTLKECA+
Sbjct: 181 RDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECAL 240
Query: 241 ISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVY 300
ISK+AGGIG+ +HNIR+TGSYI GTNGTSNG++PM+RVFN+TARYVDQGG KR GAFA+Y
Sbjct: 241 ISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALY 300
Query: 301 LEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLA 360
LEPWHADIF+F+D+RKNHGKEE RARDLF ALW+PDLFM+RV+ NG W+LF P APGL+
Sbjct: 301 LEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLS 360
Query: 361 DCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNL 420
DC+G EFE LYT+YEKEG+ K ++AQ LW+ IL++Q ETGTP++++KD CN+KSNQ+NL
Sbjct: 361 DCYGDEFEALYTRYEKEGRGKT-IKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNL 419
Query: 421 GTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYF 480
G IKSSNLC E+++Y++P ETAVCNLAS+ALP ++ S K +
Sbjct: 420 GVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIET--------------SEDGKTSTY 465
Query: 481 DFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDS 540
+F+KL E+ +VT NLN++ID NYYPVE AR+SN+RHRPI +GVQGLADTF+LL +PFDS
Sbjct: 466 NFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDS 525
Query: 541 TEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDW 600
EA+ LN IFETIY+ ++ S E+A ++GPYET+ GSP S+GILQ DMW P WDW
Sbjct: 526 EEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDW 585
Query: 601 GGLRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHL 660
LR I K+GVRNSL +APMPTASTSQILG NECFEP TSN+YSRRVLSGEF VVN +L
Sbjct: 586 DTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYL 645
Query: 661 LHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCY 720
L DL ++G+W +K +I +GS+Q +P +P+ELK +YKTVWEI QKT+++MA DR Y
Sbjct: 646 LRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVY 705
Query: 721 IDHSQSLNIHMDQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDTSVLKENP 780
ID S SLN+ + P GKLTS+HF+ W +GLKTGMYYLR++AA+ AI+FT+D + +
Sbjct: 706 IDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQAASAAIQFTIDQKIADQAT 765
Query: 781 KVTDD----DDAKMAQMVCSLTNRE 801
+ D S +
Sbjct: 766 ENVADISNLKRPSYMPSSASYAASD 790
>2wgh_A Ribonucleoside-diphosphate reductase large subunit; DNA
replication, allosteric enzyme, nucleotide-binding,
cytoplasm, ATP-binding, polymorphism; HET: DTP; 2.30A
{Homo sapiens}
Length = 676
Score = 1133 bits (2933), Expect = 0.0
Identities = 473/691 (68%), Positives = 562/691 (81%), Gaps = 19/691 (2%)
Query: 74 YASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDVYDIIMKNAARLDS 133
A LAARI VSNLHK TKK FS+ ++D+YN+ N +G +P++A DI++ N RL+S
Sbjct: 1 MAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNS 60
Query: 134 EIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHKDDIDSAIKTYHMM 193
IIYDRDF Y+YFGFKTLERSYLLK+ GKV ERPQHMLMRV+VGIHK+DID+AI+TY+++
Sbjct: 61 AIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLL 120
Query: 194 SQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVH 253
S+RWFTHASPTLFNAGT R QLSSCFL+ MKDDSIEGIYDTLK+CA+ISKSAGGIGV+V
Sbjct: 121 SERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVS 180
Query: 254 NIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLD 313
IRATGSYI GTNG SNG+VPMLRV+N+TARYVDQGG KR GAFA+YLEPWH DIFEFLD
Sbjct: 181 CIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEPWHLDIFEFLD 240
Query: 314 LRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTK 373
L+KN GKEE RARDLF+ALW+PDLFM+RV++N WSL CPNE PGL + WG EFE+LY
Sbjct: 241 LKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYAS 300
Query: 374 YEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVI 433
YEK+G+ +KVV+AQ LW+ I++SQ ETGTPYML+KD+CN+KSNQQNLGTIK SNLCTE++
Sbjct: 301 YEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIV 360
Query: 434 QYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVT 493
+YTS E AVCNLAS+AL YV +DF+KLAEVT +V
Sbjct: 361 EYTSKDEVAVCNLASLALNMYVTS-------------------EHTYDFKKLAEVTKVVV 401
Query: 494 ENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFET 553
NLNKIID+NYYPV A SN RHRPIGIGVQGLAD FIL+ PF+S EAQ LNK IFET
Sbjct: 402 RNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFET 461
Query: 554 IYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVR 613
IYY AL S ++A +GPYETY GSPVSKGILQ DMW V P+D WDW L++ I+K G+R
Sbjct: 462 IYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIR 521
Query: 614 NSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPI 673
NSLL+APMPTAST+QILGNNE EPYTSNIY+RRVLSGEF +VN HLL DLTE GLW
Sbjct: 522 NSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEE 581
Query: 674 IKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQ 733
+KN+II +GS+Q IP+IP++LK +YKTVWEI QKT++ MA +RG +ID SQSLNIH+ +
Sbjct: 582 MKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAE 641
Query: 734 PNFGKLTSLHFHAWLRGLKTGMYYLRSRAAA 764
PN+GKLTS+HF+ W +GLKTGMYYLR+RA
Sbjct: 642 PNYGKLTSMHFYGWKQGLKTGMYYLRTRAHH 672
>2xap_A Ribonucleoside-diphosphate reductase 1 subunit alpha;
oxidoreductase, DNA replication, allosteric enzyme,
nucleotide-binding; HET: NIY; 2.10A {Escherichia coli}
PDB: 2xo5_A* 2x0x_A 2r1r_A 3r1r_A* 3uus_A* 1r1r_A
2xav_A* 7r1r_A 2xax_A* 6r1r_A 2xaw_A* 5r1r_A 2xo4_A*
2xak_A* 4r1r_A* 2xaz_A* 2xay_A* 1rlr_A 1qfn_B
Length = 761
Score = 1114 bits (2883), Expect = 0.0
Identities = 209/813 (25%), Positives = 335/813 (41%), Gaps = 100/813 (12%)
Query: 1 MYVVKRDGKQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELA 60
+ V KRDG E ++ DKI L + GL + V + Y G+ TS + E
Sbjct: 5 LLVTKRDGSTERINLDKIHRVLDWAAEGL--HNVSISQVELRSHIQFYDGIKTSDIHETI 62
Query: 61 AETAAAMTT-NHPDYASLAARIVVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADD 119
+ AA + + + PDY LAAR+ + +L K F + G + +D
Sbjct: 63 IKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLED 122
Query: 120 VYDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLL--KVQGKVVERPQHMLMRVAVG 177
+ + ++D+ I +DRD + Y K LE YL+ +V G++ E Q + + VA
Sbjct: 123 YTE---EEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAAC 179
Query: 178 IH-----KDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCMKDDSIEGIY 232
+ + + + Y +S + +P + TP Q SSC L+ DS++ I
Sbjct: 180 LFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIEC-GDSLDSIN 238
Query: 233 DTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGK 292
T GIG++ IRA GS IRG G +P + F + QGG
Sbjct: 239 ATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGG-V 297
Query: 293 RKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFC 352
R GA ++ WH ++ L L+ N G E +R R + Y + + L R+ +LF
Sbjct: 298 RGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFS 357
Query: 353 PNEAPGLADCWGT---EFERLYTKYEKEGK-AKKVVQAQNLWFEILKSQIETGTPYMLFK 408
P++ PGL D + EFERLYTKYEK+ K+ V+A L+ +++ + TG Y+
Sbjct: 358 PSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNV 417
Query: 409 DTCNKKSN-QQNLGTIKSSNLCTEVIQYTSPT--------ETAVCNLASIALPRYVREMG 459
D CN S + ++ SNLC E+ T P E A+C L++ L
Sbjct: 418 DHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAIN---- 473
Query: 460 VPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRP 519
+ ++L E+ + L+ ++D YP+ A+R + R
Sbjct: 474 ---------------------NLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRT 512
Query: 520 IGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSP 579
+GIGV A G + A L FE I Y+ L+ S+E+A +G ++ +
Sbjct: 513 LGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETT 572
Query: 580 VSKGILQPDMWG------VNPSDRWDWGGLRDMISKNGVRNSLLVAPMPTASTSQILGNN 633
+KGIL D + N +DW LR+ I +G+RNS L A MP+ ++SQI
Sbjct: 573 YAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNAT 632
Query: 634 ECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPE 693
EP + + G V E
Sbjct: 633 NGIEPPRGYVSIKASKDGILRQVVPDY--------------------------------E 660
Query: 694 ELKAIYKTVWEIK-QKTLVDMAVDRGCYIDHSQSLNIHMDQPNF-------GKLTSLHFH 745
L Y+ +WE+ + + +ID S S N + D F +L
Sbjct: 661 HLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLT 720
Query: 746 AWLRGLKTGMYYLRSRAAADAIKFTVDTSVLKE 778
A+ G+KT +Y +R A+ + + S+ +
Sbjct: 721 AYKFGVKT-LYXQNTRDGAEDAQDDLVPSIQDD 752
>1peq_A Ribonucleoside-diphosphate reductase 2 alpha chain; stranded
alpha/beta barrel, protein-specificity-effector complex,
DTTP; HET: TTP; 2.80A {Salmonella typhimurium} SCOP:
a.98.1.1 c.7.1.2 PDB: 1peo_A* 1pem_A* 1peu_A* 2bq1_E*
Length = 714
Score = 955 bits (2472), Expect = 0.0
Identities = 168/766 (21%), Positives = 283/766 (36%), Gaps = 122/766 (15%)
Query: 59 LAAETAAAMTTNHPDYASLAARIVVSNL--HKNTKKSFSETIKDMYNHYNERSGLKAP-- 114
+A T + DY +L A + + + H K H S A
Sbjct: 1 MATTTPERVMQETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQH 60
Query: 115 -----LIADDVYDIIM------KNAARLDSEIIYDRDFDYDYFGFKTLERSYLLK--VQG 161
L+ + YD + RL + G SY LK
Sbjct: 61 ERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGK 120
Query: 162 KVVERPQHMLMRVAVGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTP-RAQLSSCFL 220
+ +E + + VA+ + + D A + M F A+PT N G R +L SCFL
Sbjct: 121 RYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFL 180
Query: 221 VCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFN 280
+ + +D++E I + +SK GG+ + N+R G+ I+ S+G++P++++
Sbjct: 181 LRI-EDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLE 239
Query: 281 DTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFME 340
D Y +Q G R+GA AVYL H DI FLD ++ + E+ R + L + +PD+
Sbjct: 240 DAFSYANQLG-ARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFR 298
Query: 341 RVQSNGLWSLFCPNEAPGLADCWGTEFE-----RLYTKYEKEGK-AKKVVQAQNLWFEIL 394
+ N +LF P + +G F Y + + K + A++ + +
Sbjct: 299 LAKENAQMALFSPYDIQ---RRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLA 355
Query: 395 KSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPT------------ETA 442
+ Q E+G PY++F+DT N+ + G I SNLC+E++Q S +
Sbjct: 356 EIQFESGYPYIMFEDTVNRANPIA--GRINMSNLCSEILQVNSASRYDDNLDYTHIGHDI 413
Query: 443 VCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDV 502
CNL S+ + + D + L + D+
Sbjct: 414 SCNLGSLNIAHVM-------------------------DSPDIGRTVETAIRGLTAVSDM 448
Query: 503 NYY-PVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRT 561
++ V + N IG+G L G+ + S EA F TI +HA+ T
Sbjct: 449 SHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHT 508
Query: 562 SSEIAAREGP-YETYHGSPVSKGIL----QPDMW--------------GVNPSDRWDWGG 602
S +A G + + S + G D W G+ R W
Sbjct: 509 SMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLK 568
Query: 603 LRDMISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRV-LSGEFVVVNKHLL 661
LRD + + G+ N L A PT S S I P + I R+ +G +
Sbjct: 569 LRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFM- 627
Query: 662 HDLTEMGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYI 721
E +Y+ ++I + ++D + ++
Sbjct: 628 ------------------------------TNENLDMYQDAYDIGPEKIIDTYAEATRHV 657
Query: 722 DHSQSLNIHM-DQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADA 766
D SL + D + +AW +G+K+ +YY+R R A
Sbjct: 658 DQGLSLTLFFPDTATTRDINKAQIYAWRKGIKS-LYYIRLRQLALE 702
>3o0q_A Ribonucleoside-diphosphate reductase; alpha/beta barrel,
adenosylcobalamin dependent, ribonucle reductase; HET:
TTP GDP ADN; 1.80A {Thermotoga maritima} PDB: 1xjf_A*
1xjg_A* 1xje_A* 1xjk_A* 1xjm_A* 1xjn_A* 3o0n_A* 3o0o_A*
1xjj_A*
Length = 644
Score = 867 bits (2243), Expect = 0.0
Identities = 159/693 (22%), Positives = 273/693 (39%), Gaps = 99/693 (14%)
Query: 130 RLDSEIIYDRDFDYDYFGFKTLERSYLLK-VQGKVVERP-QHMLMRVAVGI--------- 178
+L I D + L Y +K + G +E + + RVA +
Sbjct: 2 KLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPS 61
Query: 179 --HKDDIDS----AIKTYHMMSQRWFTHASPTLFNAG----------------------- 209
+ +D + ++ R F SPTLFNAG
Sbjct: 62 YKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEI 121
Query: 210 ----TPRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGT 265
LS+CF+V + DSIE I++ +KE A+I+K GG+G + +R GS++ GT
Sbjct: 122 YRSRNHLHMLSACFVVPV-GDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGT 180
Query: 266 NGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEH-R 324
+G ++G V + VFN V Q G +R+GA L H DI EF+D +K + E
Sbjct: 181 HGKASGPVSFMHVFNSAISVVKQ-GSRRRGALMGILNINHPDIEEFIDAKKENTGEAVLN 239
Query: 325 ARDLFYALWV-PDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKV 383
+L + ++ + +G L P +K
Sbjct: 240 FFNLSVGFPMDKKEILKLYEEDGELELSHP-----------------------RSTIRKK 276
Query: 384 VQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAV 443
V+ + L+ +I + ++G P + F NK I S+N C E+ ++
Sbjct: 277 VKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEI----GLSDYEA 332
Query: 444 CNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDVN 503
CNL SI + ++ N + D E L E+ I L+ +IDVN
Sbjct: 333 CNLGSIDVAKFY--------------------NNGFVDLEALQELVQIAVRFLDNVIDVN 372
Query: 504 YYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSS 563
+P++ ++ R +G+G+ G AD L +P++S EA+ ++ I HA RTS
Sbjct: 373 VFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSY 432
Query: 564 EIAAREGPYETYHGSPVSKGILQPDMWGVNPSDRWDWGGLRDMISKNGVRNSLLVAPMPT 623
E+ +G + S + + S+ D ++K RN L+ PT
Sbjct: 433 ELGKEKGNFPLLEISRYRTE-DNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPT 491
Query: 624 ASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTEMGLWSPIIK--NKIIYD 681
S S I + EP Y+R V + ++ + L I+K K + +
Sbjct: 492 GSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIE 551
Query: 682 DGSVQKIPQIPEELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLNIHMDQ-PNFGKLT 740
GS++ IP +PE++K ++ +I + M Y+D++ S I+M Q +
Sbjct: 552 KGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVL 611
Query: 741 SLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDT 773
+++ A ++ Y + + T
Sbjct: 612 NVYLEALRTNVRGITVYRDGSLQTQVLTKALKT 644
>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 = 77.0 bits (189), Expect = 2e-14
Identities = 118/682 (17%), Positives = 205/682 (30%), Gaps = 241/682 (35%)
Query: 16 DKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDE-----LAAETAAAMTTN 70
D + R LS+G S+EH +LV T + SQL E L T +
Sbjct: 2 DAYSTRPLTLSHG-SLEH--VLLVP----TASF--FIASQLQEQFNKILPEPTEGFAADD 52
Query: 71 HP-DYASLAARI---VVSNLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDVYDIIMK 126
P A L + V S + + F + + + E L+ +D++ +
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEF-ENCYLEG----NDIHAL--- 104
Query: 127 NAARLDSEIIYDRDFDYDYFGFKTLERSYL--LKVQGKVVERP-QHMLMR-VAVGIHK-- 180
AA+L E D K L ++Y+ + + ++ L R V G +
Sbjct: 105 -AAKLLQEN------DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 181 -------------DDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCF------LV 221
+++ +TYH++ ++ TL F L
Sbjct: 158 AIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE 217
Query: 222 CMKDDSIEGIYDTLKECAIISKSAGGIGVS--VHNI---RATG-------SYIRGTNGTS 269
+++ S D L I S IGV H + + G SY++G G S
Sbjct: 218 WLENPSNTPDKDYLLSIPI---SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHS 274
Query: 270 NGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLF 329
G+V TA + A E + + + + + LF
Sbjct: 275 QGLV--------TAVAI---------AETDSWESFFVSVRKAITV-------------LF 304
Query: 330 YALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKAKKVVQAQNL 389
++ G+ + +L
Sbjct: 305 ---FI-----------------------GVR-------------------CYEAYPNTSL 319
Query: 390 WFEILKSQIET--GTP-YMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQYTSPTETAVCNL 446
IL+ +E G P ML + + + +Q + +N P V
Sbjct: 320 PPSILEDSLENNEGVPSPML---SISNLTQEQVQDYVNKTNS-------HLPAGKQV--- 366
Query: 447 ASIAL---PR-YVREMGVPMESHPSKLVGSRGSKNRYFDFEKLAEVTGIVTENLNKIIDV 502
I+L + V + P L G + K +G+ + ++I
Sbjct: 367 -EISLVNGAKNLV------VSGPPQSLYGLNLT------LRKAKAPSGL---DQSRI--- 407
Query: 503 NYYPVETARRSNLRHR--PIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFETIYYHALR 560
P + R+ +R P+ PF S L + I ++
Sbjct: 408 ---PF-SERKLKFSNRFLPVAS--------------PFHS----HLLVPASDLINKDLVK 445
Query: 561 TSSEIAARE--GP-YETYHGS---PVSKGILQP--DMWGVNPSDRW------------DW 600
+ A++ P Y+T+ GS +S I + D P W D+
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK-WETTTQFKATHILDF 504
Query: 601 G-----GLRDMISKN----GVR 613
G GL + +N GVR
Sbjct: 505 GPGGASGLGVLTHRNKDGTGVR 526
Score = 43.5 bits (102), Expect = 3e-04
Identities = 96/611 (15%), Positives = 174/611 (28%), Gaps = 244/611 (39%)
Query: 282 TARYVDQGGGKRKGAFAVYLEPWHADIFE--FL--------------DLRKNHGKEEHRA 325
+ V+ + G F L + FE +L + K +
Sbjct: 68 VSSLVEPS---KVGQFDQVLNLCLTE-FENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Query: 326 RDLFYALWVPDLFMERVQSNGLWSLFCPNEAP--------GLADCWGTEFERLYTKYEKE 377
++ A + ++ ++ L+ A G D + E LY Y
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 378 GKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSSNLCTEVIQY-- 435
A+ L E++++ ++ +F N ++++
Sbjct: 184 VGDLIKFSAETLS-ELIRTTLDAEK---VFTQGLN-------------------ILEWLE 220
Query: 436 ---TSPTETAVCNLASIALP--------RYV---REMGVPMESHPSKLVGS-RGSKNRYF 480
+P + + + I+ P YV + +G P +L +G+
Sbjct: 221 NPSNTPDKDYLLS-IPISCPLIGVIQLAHYVVTAKLLGF----TPGELRSYLKGA----- 270
Query: 481 DFEKLAEVTGIVT--------------ENLNKIIDVNYYPVETARRSNLRHRPIGIGVQG 526
G+VT ++ K I V ++ IGV+
Sbjct: 271 ----TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF----------------IGVRC 310
Query: 527 LADTFILLGMPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREG-PYETYHGSP------ 579
+ + P S L + EG P SP
Sbjct: 311 Y-EAY-----PNTSLPPSIL---------------EDSLENNEGVP------SPMLSISN 343
Query: 580 VSKGILQPDMWGVN---PSDRWDWGGLRDMIS-KNGVRN--------SL--LV------- 618
+++ +Q + N P+ + + IS NG +N SL L
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGK------QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 619 APMPTASTSQILGNNECFEPYTSNIYSRR--VLSGEFVVV----NKHLLHDLTEMGLWSP 672
AP S+I P +S R S F+ V + HLL +++
Sbjct: 398 AP-SGLDQSRI--------P-----FSERKLKFSNRFLPVASPFHSHLLVPASDL----- 438
Query: 673 IIKNKIIYDDGSVQKIPQIPEELK-AIYKTV---------WEIKQKTLVDMAVDRGCYID 722
I D + ++++ +Y T I ++ +VD + +
Sbjct: 439 ------INKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER-IVDCIIRLPVKWE 491
Query: 723 HSQSLNI-HM-DQPNFG-----KLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVDTSV 775
+ H+ D FG L L H G TG+ R +
Sbjct: 492 TTTQFKATHILD---FGPGGASGLGVL-THRNKDG--TGV---R----------VIVAGT 532
Query: 776 LKENPKVTDDD 786
L NP DDD
Sbjct: 533 LDINP---DDD 540
Score = 43.1 bits (101), Expect = 4e-04
Identities = 49/323 (15%), Positives = 96/323 (29%), Gaps = 92/323 (28%)
Query: 518 RPIGIGVQGLADTFILLGMPFDS-TEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYH 576
RP+ + L ++ P S A QL ++ F I + AA + P
Sbjct: 7 RPLTLSHGSLEHVLLV---PTASFFIASQL-QEQFNKILPEP---TEGFAADDEP----- 54
Query: 577 GSPVSKGILQPDMWG-----VNPSDRWDWGGLRDMISKNGV----RNSL-------LVAP 620
+P ++ G V+ G D + + L L A
Sbjct: 55 TTPA-------ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107
Query: 621 MPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKH---LLHDLTEMGLWSPIIKNK 677
+ + + ++ E + Y + R+++ K L + E N
Sbjct: 108 LLQENDTTLVKTKELIKNY----ITARIMAKR-PFDKKSNSALFRAVGE--------GNA 154
Query: 678 IIYDDGSV---QKIPQIP-EELKAIYKTVWEIKQKTLVDMAVDRGCYIDHSQSLN----I 729
+ ++ Q EEL+ +Y+T LV + +++L+
Sbjct: 155 QLV---AIFGGQGNTDDYFEELRDLYQT-----YHVLVGDLIKF-----SAETLSELIRT 201
Query: 730 HMD-QPNFGKLTSLHFHAWLRGLKT--GMYYLRSRAAA-------DAIKFTVDTSVLKEN 779
+D + F + L+ WL YL S + + V +L
Sbjct: 202 TLDAEKVFTQ--GLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFT 259
Query: 780 PKVTDDDDAKMAQMVCSLTNREE 802
P ++ + T +
Sbjct: 260 P-------GELRSYLKGATGHSQ 275
Score = 42.0 bits (98), Expect = 0.001
Identities = 28/168 (16%), Positives = 50/168 (29%), Gaps = 57/168 (33%)
Query: 364 GTEFERLYTKYEKEGKAKKVV-QA-----QNLWFEIL-----------------KSQ-IE 399
G + Y+ A+ V +A F IL K + I
Sbjct: 1632 GMDL------YKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 400 TGTPYMLFKDTCNKKSNQQNL---GTIKSSNLC----TEVI---QYTSPTETAVCNLASI 449
M+F+ + K + + S++ ++ Q+T P A+ L
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQP---ALT-LMEK 1741
Query: 450 ALPRYVREMG-VPMES----HP----SKLVGSRGSKNRYFDFEKLAEV 488
A ++ G +P ++ H + L E L EV
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSLGEYAALASLADV----MSIESLVEV 1785
Score = 31.9 bits (72), Expect = 1.0
Identities = 44/292 (15%), Positives = 88/292 (30%), Gaps = 115/292 (39%)
Query: 3 VVKRDGKQEAVHFD-----KITARLKKLSYGLSIEHC-DPVLVSQKVCTGVYKGVTT--- 53
+V + +HF +I + + E D L ++K+ + + T+
Sbjct: 1664 IVINNPVNLTIHFGGEKGKRIRENYSAMIF----ETIVDGKLKTEKIFKEINEHSTSYTF 1719
Query: 54 -SQLDELAAETA---AAMTTNHPDYASLAA-RIVVSNLHKNTKKSF---S--ETIKDMYN 103
S+ L+A T A+T AA + S +F S E Y
Sbjct: 1720 RSEKGLLSA-TQFTQPALTL-----MEKAAFEDLKSKGLIPADATFAGHSLGE-----Y- 1767
Query: 104 HYNERSGLKAPLIADDVYDIIMKNAARLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKV 163
+ L + +A DV I ++ + ++ R G
Sbjct: 1768 -----AALAS--LA-DVMSI--ESLVEV----VFYR---------------------GM- 1791
Query: 164 VERPQHMLMRVAVGIHKDDIDSAIKTYHMMSQRWFTHASPTLFNAGTPRAQLSSCFLVCM 223
M+VAV +D++ Y M++ +P A
Sbjct: 1792 -------TMQVAV--PRDEL--GRSNYGMIA------INPGRVAAS-------------F 1821
Query: 224 KDDSIEGIYDTLKECAIISKSAGGIGVSV--HNIRATGS-YIRGTNGTSNGI 272
++++ + + K G + V + +N+ Y+ G +
Sbjct: 1822 SQEALQYV------VERVGKRTGWL-VEIVNYNVE--NQQYVAA--GDLRAL 1862
>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 = 67.2 bits (163), Expect = 2e-11
Identities = 88/683 (12%), Positives = 189/683 (27%), Gaps = 206/683 (30%)
Query: 99 KDMYNHYNERSGLKAPLIAD-DVYDIIMKNAARLDS--EIIYDRDFDYDYFGFKTLERSY 155
KD+ + + + + + D D+ D I+ + D+ + +
Sbjct: 19 KDILSVFED------AFVDNFDCKDV-------QDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 156 -----LLKVQGKVVERPQHMLMR-----VAVGIHKDDIDSAIKTYHMMSQRWFTHASPTL 205
LL Q ++V++ ++R + I + ++ T + QR + +
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 206 FNAGT-PRAQLSSCFLVCMKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRG 264
F R Q Y L++ + + A + + + GS
Sbjct: 126 FAKYNVSRLQP----------------YLKLRQALLELRPAKNVLI--DGV--LGS---- 161
Query: 265 TNGTSNGIVPMLRVFNDTARYVDQGGGKRKGAFAVYLEPW--------HADIFEFL---- 312
G + L V + K F ++ W + E L
Sbjct: 162 --GKT---WVALDVCLSYKV-------QCKMDFKIF---WLNLKNCNSPETVLEMLQKLL 206
Query: 313 -DLRKNHGKEEHRARDLFYAL-----WVPDLFMERVQSNGLWSLFCPNEAPGLADCWGTE 366
+ N + ++ + + L + N L L L +
Sbjct: 207 YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL--LV-------LLNVQ--- 254
Query: 367 FERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGTIKSS 426
K A F + +I L T K L ++
Sbjct: 255 -------------NAKAWNA----FNL-SCKI-------LL--TTRFKQVTDFLSAATTT 287
Query: 427 NLCTEVIQYT-SPTET-----AVCNLASIALPRYVREMGVPMESHPS--KLVGS--RGSK 476
++ + T +P E + LPR E+ + ++P ++ R
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EV---LTTNPRRLSIIAESIRDGL 341
Query: 477 NR-----YFDFEKLAEVTGIVTENLNKIIDVNYY----------PVETARRSNLRHRPIG 521
+ + +KL + L + + T S + I
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIK 401
Query: 522 IGVQGLADTFILLGMPFDSTEAQQLNKDIFE-TIYYHALRTSSEIAAREGP--------- 571
V + + + + K E TI ++ ++
Sbjct: 402 SDVMVVVNKLHKYSL---------VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH 452
Query: 572 YETYHGSPVSKGILQPD-----------MWGVNPSDRWD-----WGGLRDMISKNGVRNS 615
Y I + + +R + R + K +R+
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK--IRHD 510
Query: 616 LLVAPMPTASTSQILGNNECFEPY---TSNIYSRRVLS-GEFVV-VNKHLLH----DLTE 666
A + S L + ++PY Y R V + +F+ + ++L+ DL
Sbjct: 511 ST-AWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
Query: 667 MGLWSPIIKNKIIYDDGS--VQK 687
+ L + ++ I+++ VQ+
Sbjct: 570 IALMAE---DEAIFEEAHKQVQR 589
Score = 49.1 bits (116), Expect = 7e-06
Identities = 71/570 (12%), Positives = 148/570 (25%), Gaps = 202/570 (35%)
Query: 223 MKDDSIEGIYDTLKECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDT 282
+ + + + D K I+SK + +I + + GT LR+F T
Sbjct: 30 VDNFDCKDVQDMPKS--ILSKE------EIDHIIMSKDAVSGT----------LRLF-WT 70
Query: 283 ARYVDQGGGKRKGAFAVYLEPWHADIFEFLDLRKNHGKEEHRARDLFYALWV-------- 334
K++ ++E ++FL + K E R + +++
Sbjct: 71 LL------SKQEEMVQKFVEEVLRINYKFL---MSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 335 -----PDLFMERVQS-----NGLWSLFCPNEAPGLADCWGTEFERLYTKYEKEGKA---K 381
+ R+Q L L A + + G K
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLEL---RPAKNVL---------ID------GVLGSGK 163
Query: 382 KVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKS----NQQNLGTIKSSNLCTEVIQYTS 437
V ++ +++ ++ K CN Q L N + ++
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLK-NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 438 PTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKN----RYFDFE-KLAEVTGIV 492
+ L R ++ + + + L+ +N F+ K+ ++
Sbjct: 223 IKLR--IHSIQAELRRLLKS-----KPYENCLLVLLNVQNAKAWNAFNLSCKI-----LL 270
Query: 493 TENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLADTFILLGMPFDSTEAQQLNKDIFE 552
T ++ D T +L H + E + L
Sbjct: 271 TTRFKQVTDF--LSAATTTHISLDHHSMT----------------LTPDEVKSL------ 306
Query: 553 TIYYHALRTSSEIAAREGPYETYHGSPVSKGIL------QPDMWGVNPSDRWDWGGLRDM 606
L + ++ P E +P I+ W D W +
Sbjct: 307 ------LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-----DNWKHVNCDKL 355
Query: 607 ISKNGVRNSLLVAPMPTASTSQILGNNECFEPYTSNIYSRRVLSGEFVVVNKHLLHDLTE 666
+ +SL EP E+ + + L+
Sbjct: 356 --TTIIESSL-----------------NVLEPA------------EY----RKMFDRLS- 379
Query: 667 MGLWSPIIKNKIIYDDGSVQKIPQIPEELKAIYKTVW-------------EIKQKTLVDM 713
++ + IP L ++ W ++ + +LV+
Sbjct: 380 ------------VFPPSA-----HIPTILLSLI---WFDVIKSDVMVVVNKLHKYSLVEK 419
Query: 714 AVDRGCYIDHSQSLNIHMDQPNFGKLTSLH 743
S L + + N +LH
Sbjct: 420 QPKESTISIPSIYLELKVKLEN---EYALH 446
Score = 48.7 bits (115), Expect = 7e-06
Identities = 60/483 (12%), Positives = 132/483 (27%), Gaps = 118/483 (24%)
Query: 2 YVVKRDGKQEAVHFDKITARLKKLS-------YG--------LSIEHCDPVLVSQKVCTG 46
Y V R + K+ L +L G ++++ C V K+
Sbjct: 129 YNVSR-----LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK 183
Query: 47 VYKGVTTSQLDELAAETAAAMTTNH---PDYASLAARIVVSNLHKNTKKSFSETIKDMYN 103
++ + + + P++ S S+ N K ++
Sbjct: 184 IF-WLNLKNCNSPETVLEMLQKLLYQIDPNWTSR------SDHSSNIKLRIHSIQAELRR 236
Query: 104 HYNERSGLKAPLIADDVYD------------IIM-----KNAARLDSEIIYDRDFDYDYF 146
+ L+ +V + I++ + L + D+
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 147 GFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHK---DDIDSAIKTYHMMSQRW------ 197
+ + K ++ L R + + I +I+ W
Sbjct: 297 TL---TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 198 -FTHASPTLFNAGTPRAQLSSCFLVC--------------------MKDDSIEGIYDTLK 236
T + N P A+ F + + + + L
Sbjct: 354 KLTTIIESSLNVLEP-AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 237 ECAIISKSAGGIGVSVHNIRATGSYIRGTNGTSNGIVPMLRVFNDTARYVDQGGGKRKGA 296
+ +++ K +S+ +I Y+ + R D Y K
Sbjct: 413 KYSLVEKQPKESTISIPSI-----YLE-LKVKLENEYALHRSIVD--HY-----NIPKTF 459
Query: 297 FAVYLEPWHAD--IFEFLDLRKNH--GKEEHRARDLFYALWVPDL-FMER-VQSNGLWSL 350
+ L P + D + + +H E LF +++ D F+E+ ++ +
Sbjct: 460 DSDDLIPPYLDQYFYSHI---GHHLKNIEHPERMTLFRMVFL-DFRFLEQKIRHDSTAWN 515
Query: 351 FCPNEAPGLADCWGTEFERLYTKY--EKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFK 408
+ L + Y Y + + K +++V A IL + + K
Sbjct: 516 ASGSILNTLQQL------KFYKPYICDNDPKYERLVNA------ILDFLPKIEENLICSK 563
Query: 409 DTC 411
T
Sbjct: 564 YTD 566
Score = 42.9 bits (100), Expect = 4e-04
Identities = 62/466 (13%), Positives = 127/466 (27%), Gaps = 142/466 (30%)
Query: 305 HADIFEFLDLRKNHGKEEHRARDLFYALWVPDLFMERVQSNGLWSLFCPNEAPGLADCWG 364
H D FE G+ +++ +D+ + F + N DC
Sbjct: 6 HMD-FET-------GEHQYQYKDI-----LSV-FEDAFVDN--------------FDCKD 37
Query: 365 TE-FER-LYTKYEKEG--KAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNL 420
+ + + +K E + +K V F L S+ E F + + N
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM--VQKFVEE----VLRINY 91
Query: 421 GTIKSSNLCTEVIQYTSPTETAVCNLASIALPRYVREMGVPMESHPSKLVGSRGSKNRYF 480
+ S + TE Q + T Y+ + + + ++ + +R
Sbjct: 92 KFLMSP-IKTEQRQPSMMTR------------MYIEQRD-RLYNDNQVF--AKYNVSRLQ 135
Query: 481 DFEKLAEVTGIVTENLNKIIDVNYYPVETARRSNLRHRPIGIGVQGLA-----DTFILLG 535
+ KL + L ++ + +G G +A +
Sbjct: 136 PYLKL-------RQALLELRPAKNVLI---------DGVLGSGKTWVALDVCLSYKVQCK 179
Query: 536 MPFDSTEAQQLNKDIFETIYYHALRTSSEIAAREGPYETYHGSPVSKGILQPDMWGVNPS 595
M F I++ L+ + + + D N
Sbjct: 180 MDFK--------------IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH-SSNIK 224
Query: 596 DRWDWG--GLRDMISKNGVRNSLLVAPMPTASTSQILGN---NECFEPY---------TS 641
R LR ++ N LL +L N + + + T
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLL-----------VLLNVQNAKAWNAFNLSCKILLTTR 273
Query: 642 NIYSRRVLSG--EFVVVNKHLLHDLTE---MGLWSPIIKNKIIYDD-------GSVQKIP 689
LS + H LT L + + D + +++
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP--QDLPREVLTTNPRRLS 331
Query: 690 QIPEELKAI------YKTVWEIKQKTLVDMAVD-------RGCYID 722
I E ++ +K V K T+++ +++ R +
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Score = 40.6 bits (94), Expect = 0.003
Identities = 31/192 (16%), Positives = 51/192 (26%), Gaps = 53/192 (27%)
Query: 650 SGEFVVVNKHLLHDLTEMGLWSPIIKN----------KIIYDDGSVQKIPQIPEELKAIY 699
+GE K +L + + N K I + I + +
Sbjct: 11 TGEHQYQYKDILSVFED-----AFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 700 KTVW--EIKQKTLVDMAVDRGCYIDHSQSLNIHMDQPNFGKL-TSLHFHAWLRGLKTGMY 756
+ W KQ+ +V V+ + N+ L + + + T MY
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEV-------------LRINYKFLMSPIKTEQRQPSMMTRMY 112
Query: 757 -YLRSRAAADAIKFTVDTSV---------------LKENPKVTDDDDA---K--MAQMVC 795
R R D F +V L+ V D K +A VC
Sbjct: 113 IEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171
Query: 796 SLTNREECMACG 807
+ M
Sbjct: 172 LSYKVQCKMDFK 183
>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 = 37.6 bits (86), Expect = 0.005
Identities = 7/22 (31%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 339 MERVQSNGLWSLFCPNEAPGLA 360
++++Q++ L L+ + AP LA
Sbjct: 22 LKKLQAS-L-KLYADDSAPALA 41
Score = 30.7 bits (68), Expect = 1.0
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 20/48 (41%)
Query: 725 QSLNIHMDQPNFGKLTSLHFHAWLRGLKTGMYYLRSRAAADAIKFTVD 772
Q+L KL + LK +Y S A A AIK T++
Sbjct: 20 QALK---------KLQA--------SLK--LYADDS-APALAIKATME 47
Score = 29.1 bits (64), Expect = 3.2
Identities = 11/69 (15%), Positives = 18/69 (26%), Gaps = 41/69 (59%)
Query: 9 KQEAVHFDKITARLKKLSYGLSIEHCDPVLVSQKVCTGVYKGVTTSQLDELAAETAAAMT 68
KQ K+ A LK +Y A ++A A+
Sbjct: 19 KQA---LKKLQASLK-----------------------LY-----------ADDSAPALA 41
Query: 69 TNHPDYASL 77
A++
Sbjct: 42 IK----ATM 46
>1m2t_B Mistletoe lectin I B chain; ribosome inactivation, ribosome
inhibitor, hydrolase; HET: NAG FUC ADE; 1.89A {Viscum
album} SCOP: b.42.2.1 b.42.2.1 PDB: 2r9k_B* 3d7w_B*
3cef_B* 1sz6_B* 1pum_B* 1puu_B* 2rg9_B* 3o5w_B* 1onk_B*
1oql_B* 1tfm_B* 1pc8_B* 1yf8_B* 1ce7_B* 2mll_B*
Length = 263
Score = 31.7 bits (71), Expect = 0.91
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 401 GTPYMLFKDTCNKKSNQQ----NLGTIKSSNLCTEVIQYTSPTETAV--CN 445
G L+ N NQ GTI+S+ C YT+ + CN
Sbjct: 32 GNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCN 82
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 31.1 bits (71), Expect = 1.1
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 15/81 (18%)
Query: 130 RLDSEIIYDRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHKDD------I 183
RLD+ + D + F G V+ ++ VG+ KDD
Sbjct: 154 RLDA-ALQDEVAASEGF--LKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAF 210
Query: 184 DSAIK------TYHMMSQRWF 198
D A+ TY M++++F
Sbjct: 211 DKALTELRQDGTYDKMAKKYF 231
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 2.9
Identities = 12/64 (18%), Positives = 21/64 (32%), Gaps = 19/64 (29%)
Query: 363 WGTEF-ERLYTKYEKEGKAKK---VVQAQ---NLWFEILKSQIETGTPYMLFKDTCNKKS 415
W E +RL + K + +A+ W + Q+E NK +
Sbjct: 90 WREEQRKRLQEL-DAASKVMEQEWREKAKKDLEEWNQRQSEQVEK-----------NKIN 137
Query: 416 NQQN 419
N+
Sbjct: 138 NRIA 141
>2k13_X Saratin; collagen binding, mixed alpha/beta structure, fold typical
for PAN domains, toxin; NMR {Haementeria officinalis}
Length = 103
Score = 28.1 bits (62), Expect = 4.1
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 361 DCWGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKK 414
DCW R YT ++K K + E K+ +T Y++F+DT NK+
Sbjct: 5 DCWTFYANRKYTDFDKSFKKSSDLD------ECKKTCFKTEYCYIVFEDTVNKE 52
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 27.5 bits (61), Expect = 6.2
Identities = 10/61 (16%), Positives = 19/61 (31%)
Query: 138 DRDFDYDYFGFKTLERSYLLKVQGKVVERPQHMLMRVAVGIHKDDIDSAIKTYHMMSQRW 197
+D + T +V+ V + V + + A K ++ RW
Sbjct: 33 QEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW 92
Query: 198 F 198
F
Sbjct: 93 F 93
>3rrc_A Duffy receptor; duffy binding like, receptor recognition, duffy
antigen RECE chemokines, cell invasion; HET: EDO; 1.95A
{Plasmodium vivax} PDB: 2c6j_A
Length = 317
Score = 29.1 bits (65), Expect = 6.7
Identities = 9/65 (13%), Positives = 19/65 (29%), Gaps = 12/65 (18%)
Query: 363 WGTEFERLYTKYEKEGKAKKVVQAQNLWFEILKSQIETGTPYMLFKDTCNKKSNQQNLGT 422
+++ L K+ A+K TPY + K ++ +
Sbjct: 238 KKNQWDVLSNKFISVKNAEK------------VQTAGIVTPYDILKQELDEFNEVAFENE 285
Query: 423 IKSSN 427
I +
Sbjct: 286 INKRD 290
>4afl_A P29ING4, inhibitor of growth protein 4; cell cycle, tumour
suppressor, chromatin remodelling; 2.28A {Homo sapiens}
Length = 104
Score = 27.2 bits (60), Expect = 9.4
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 85 NLHKNTKKSFSETIKDMYNHYNERSGLKAPLIADDVYDIIMKNAARLDSEI 135
+L K + + I++ Y E K +A Y+++ K+ RLD+++
Sbjct: 54 SLSSEEKLALLKQIQEAYGKCKEFGDDKV-QLAMQTYEMVDKHIRRLDTDL 103
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
0.319 0.134 0.404
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 12,563,401
Number of extensions: 776648
Number of successful extensions: 1590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1525
Number of HSP's successfully gapped: 33
Length of query: 808
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 707
Effective length of database: 3,881,772
Effective search space: 2744412804
Effective search space used: 2744412804
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: 61 (27.6 bits)