BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 005987
(666 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 54/246 (21%), Positives = 103/246 (41%), Gaps = 47/246 (19%)
Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
++W EKY+PR+L+E+ Q + ++ ++ + E + + L+ +G G GKTAT
Sbjct: 5 EIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK--------NIPHLLFSGPPGTGKTATAI 56
Query: 197 QIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDE--FENFVERIRRYGSTSPSI 254
+A L + N + + DE + +I+ + T+P I
Sbjct: 57 ALARDL-----------------FGENWRDNFIEMNASDERGIDVVRHKIKEFARTAP-I 98
Query: 255 PGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQ 314
G L D + + A LR+ + + +S C S + ++
Sbjct: 99 GGAPFKIIFLDEADALTADAQAA---LRRTMEMYSKS-----------CRFILSCNYVSR 144
Query: 315 SFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQ 374
E +QS P+ ++K+ L +IC +E ++ + ++ + SGGD R+
Sbjct: 145 IIEPIQS-----RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRK 199
Query: 375 AITSLQ 380
AI +LQ
Sbjct: 200 AINALQ 205
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 55/248 (22%), Positives = 104/248 (41%), Gaps = 51/248 (20%)
Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGKTAT 194
++W EKY+PR+L+E+ Q + ++ ++ + E + N+ L+ +G G GKTAT
Sbjct: 5 EIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGKTAT 54
Query: 195 VRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDE--FENFVERIRRYGSTSP 252
+A L + N + + DE + +I+ + T+P
Sbjct: 55 AIALARDL-----------------FGENWRDNFIEMNASDERGIDVVRHKIKEFARTAP 97
Query: 253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST 312
I G L D + + A LR+ + + +S C S +
Sbjct: 98 -IGGAPFKIIFLDEADALTADAQAA---LRRTMEMYSKS-----------CRFILSCNYV 142
Query: 313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI 372
++ E +QS P+ ++K+ L +IC +E ++ + ++ + SGGD
Sbjct: 143 SRIIEPIQS-----RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDF 197
Query: 373 RQAITSLQ 380
R+AI +LQ
Sbjct: 198 RKAINALQ 205
>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 516
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 55/260 (21%), Positives = 100/260 (38%), Gaps = 45/260 (17%)
Query: 134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFST---------NVLVIT 184
++ +LW KY P +L+++ + V +++ W K+ F ++
Sbjct: 24 ASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLY 83
Query: 185 GQAGVGKTATVRQIASHLGARLYEW---DTPTPTIWQEYMHNCKTGLEYTSKLDEFENFV 241
G G+GKT +A LG + E D + T+ K L+ S + F
Sbjct: 84 GPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNA---GVKNALDNMSVVGYF---- 136
Query: 242 ERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG--RTAFERLRQCLLLLVRSTHIPTAVV 299
++ + ++ G+ ++++D++ +G R +L Q R T P ++
Sbjct: 137 ----KHNEEAQNLNGK---HFVIIMDEVDGMSGGDRGGVGQLAQ----FCRKTSTPLILI 185
Query: 300 LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTE 359
E + +D R+ N SIK L I +E++ L
Sbjct: 186 CNE--------RNLPKMRPFDRVCLDIQFRRPDAN-----SIKSRLMTIAIREKFKLDPN 232
Query: 360 QIDLVAQASGGDIRQAITSL 379
ID + Q + GDIRQ I L
Sbjct: 233 VIDRLIQTTRGDIRQVINLL 252
>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 323
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 55/252 (21%), Positives = 108/252 (42%), Gaps = 44/252 (17%)
Query: 130 SASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGV 189
S + S Q W EKY+P+ L ++ ++ ++ ++ +KD + ++I+G G+
Sbjct: 2 SKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQI-------AKDGNMPH-MIISGMPGI 53
Query: 190 GKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVE-RIRRYG 248
GKT +V +A L R Y LE + D + V +I+ +
Sbjct: 54 GKTTSVHCLAHELLGRSYADGV----------------LELNASDDRGIDVVRNQIKHFA 97
Query: 249 STSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADS 308
+P K ++L + +T G A + LR+ + L ST A C +++
Sbjct: 98 QKKLHLP-PGKHKIVILDEADSMTAG--AQQALRRTMELYSNSTRFAFA-----CNQSNK 149
Query: 309 VDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS 368
+ E LQS + + +++ + + L +I + E + + ++ + +
Sbjct: 150 I------IEPLQS-----QCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTA 198
Query: 369 GGDIRQAITSLQ 380
GD+RQAI +LQ
Sbjct: 199 EGDMRQAINNLQ 210
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 55/253 (21%), Positives = 97/253 (38%), Gaps = 65/253 (25%)
Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
W EKY+P +L+E+ Q + + VR + +E K L+ G G GKT+T+ +
Sbjct: 15 WVEKYRPETLDEVYGQNEVITTVRKFVDE------GKLPH--LLFYGPPGTGKTSTIVAL 66
Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVE-RIRRYGSTSPSIPGE 257
A + + Y LE + D + V +I+ + ST
Sbjct: 67 AREIYGKNYS----------------NMVLELNASDDRGIDVVRNQIKDFASTRQIF--- 107
Query: 258 SKSSAILLIDDL-PVTNG-----RTAFERL----RQCLLLLVRSTHIPTAVVLTECGKAD 307
SK ++++D+ +TN R ER R C +L H T +L++C
Sbjct: 108 SKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFC--VLANYAHKLTPALLSQCT--- 162
Query: 308 SVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA 367
+ P+ +I+R ++ + E+ LS + +
Sbjct: 163 ----------------------RFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIEL 200
Query: 368 SGGDIRQAITSLQ 380
S GD+R+ + LQ
Sbjct: 201 SNGDMRRVLNVLQ 213
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 129 ASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQ 186
A+ S QQ W EKY+P++L+E+ Q V ++ + S N+ ++ G
Sbjct: 17 AAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLK----------SANLPHMLFYGP 66
Query: 187 AGVGKTATVRQIASHL 202
G GKT+T+ + L
Sbjct: 67 PGTGKTSTILALTKEL 82
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 35.4 bits (80), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 52/246 (21%), Positives = 91/246 (36%), Gaps = 45/246 (18%)
Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
W EKY+P+ L+++ Q V+ ++ + + S L+ G GVGKT +
Sbjct: 15 WVEKYRPQRLDDIVGQEHIVKRLKHYVKTG--------SMPHLLFAGPPGVGKTTAALAL 66
Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFV-ERIRRYGSTSPSIPGE 257
A L + + HN LE + + N + E+++ + T P I G
Sbjct: 67 AREL-------------FGENWRHNF---LELNASDERGINVIREKVKEFARTKP-IGGA 109
Query: 258 SKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFE 317
S L D + + A R + VR + C + + QS
Sbjct: 110 SFKIIFLDEADALTQDAQQALRRTMEMFSSNVR--------FILSCNYSSKIIEPIQSRC 161
Query: 318 ELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT 377
+ P+ + I + L I E L+ E + + + GD+R+AI
Sbjct: 162 AI-----------FRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAIN 210
Query: 378 SLQFSS 383
LQ ++
Sbjct: 211 ILQAAA 216
>pdb|1YE8|A Chain A, Crystal Structure Of Thep1 From The Hyperthermophile
Aquifex Aeolicus
Length = 178
Score = 32.3 bits (72), Expect = 0.96, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 181 LVITGQAGVGKTATVRQIASHLGAR 205
++ITG+ GVGKT V++I LG R
Sbjct: 3 IIITGEPGVGKTTLVKKIVERLGKR 27
>pdb|1VDR|A Chain A, Dihydrofolate Reductase
pdb|1VDR|B Chain B, Dihydrofolate Reductase
Length = 162
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL 285
PSIP + K + DD PV GRT FE +R L
Sbjct: 24 PSIPADKKQYRSRIADD-PVVLGRTTFESMRDDL 56
>pdb|1T9H|A Chain A, The Crystal Structure Of Yloq, A Circularly Permuted
Gtpase
Length = 307
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 132 SSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGK 191
+ T Q +AE Y+ + K ++ L D F V GQ+GVGK
Sbjct: 135 TEDTIQAYAEDYRNIGYDVYLTSSKD--------QDSLADIIPHFQDKTTVFAGQSGVGK 186
Query: 192 TATVRQIASHLGARLYE 208
++ + I+ LG R E
Sbjct: 187 SSLLNAISPELGLRTNE 203
>pdb|2JYB|A Chain A, Binary Hvdhfr1:folate Complex
pdb|2ITH|A Chain A, Nmr Structure Of Haloferax Volcanii Dhfr
Length = 162
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL 285
PSIP + K + DD PV GRT FE +R L
Sbjct: 24 PSIPADKKQYRSRVADD-PVVLGRTTFESMRDDL 56
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 27/66 (40%), Gaps = 16/66 (24%)
Query: 141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIAS 200
EK K R LE LAVQ+ +L + G GVGKT+ + IA
Sbjct: 87 EKVKERILEYLAVQK----------------LTKSLKGPILCLAGPPGVGKTSLAKSIAK 130
Query: 201 HLGARL 206
LG +
Sbjct: 131 SLGRKF 136
>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 354
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 337 TNGSIKRTLSKICRQEQYSLSTEQI-DLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLS 395
++ I LS + E+ L T+ I +AQAS G++R ++ L+ +L + L S
Sbjct: 194 SDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSP 253
Query: 396 ISKPN 400
I KP+
Sbjct: 254 IIKPD 258
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.130 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,046,503
Number of Sequences: 62578
Number of extensions: 770495
Number of successful extensions: 1610
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1590
Number of HSP's gapped (non-prelim): 25
length of query: 666
length of database: 14,973,337
effective HSP length: 105
effective length of query: 561
effective length of database: 8,402,647
effective search space: 4713884967
effective search space used: 4713884967
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)