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= psy14489
(284 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 146 bits (369), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 84/207 (40%), Positives = 120/207 (57%), Gaps = 3/207 (1%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ +LLVDG YR F+AL + PV A+YG K L K K + +FDAK
Sbjct: 11 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKE-DGDAVIVVFDAK 69
Query: 62 GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
+FR+ Y YKA R P + Q+ LI ++V +G L + G EADDV+ +LAK+A
Sbjct: 70 APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGD 180
K +V I T DKD+ QL+S++I +++ + + ++G+ P++ DY +L GD
Sbjct: 130 -EKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGD 188
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLE 207
SDNLPGVK IG KTA KLL ++ SLE
Sbjct: 189 ESDNLPGVKGIGEKTARKLLEEWGSLE 215
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 146 bits (369), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 84/207 (40%), Positives = 120/207 (57%), Gaps = 3/207 (1%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ +LLVDG YR F+AL + PV A+YG K L K K + +FDAK
Sbjct: 11 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKE-DGDAVIVVFDAK 69
Query: 62 GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
+FR+ Y YKA R P + Q+ LI ++V +G L + G EADDV+ +LAK+A
Sbjct: 70 APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGD 180
K +V I T DKD+ QL+S++I +++ + + ++G+ P++ DY +L GD
Sbjct: 130 -EKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGD 188
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLE 207
SDNLPGVK IG KTA KLL ++ SLE
Sbjct: 189 ESDNLPGVKGIGEKTARKLLEEWGSLE 215
>pdb|1UT5|A Chain A, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT5|B Chain B, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT8|A Chain A, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
pdb|1UT8|B Chain B, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
Length = 291
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 52/220 (23%), Positives = 97/220 (44%), Gaps = 26/220 (11%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ L++VDG++ +R + N P + Y + ++ L K+Y A + D K
Sbjct: 19 RRNLMIVDGTNLGFRFKH------NNSKKPFASSY--VSTIQSLAKSYSARTTIVLGD-K 69
Query: 62 GKN-FRNILYPSYKATR-----------KKMPYNLILQINLIHQMVKAIGWPILIIKGVE 109
GK+ FR P YK R K + + ++ K +P I+GVE
Sbjct: 70 GKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTT-FPTFTIRGVE 128
Query: 110 ADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA---LINNNKIHDRTTIISRFGV 166
ADD+ + K ++ +IST D D L+++K++ + H R
Sbjct: 129 ADDMAAYIVKLIGHLYDHVWLIST-DGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVD 187
Query: 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSL 206
E+ + +++GD+ DN+ GV+ IG K ++ ++ ++
Sbjct: 188 DVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNV 227
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a
pdb|1XO1|B Chain B, T5 5'-Exonuclease Mutant K83a
Length = 291
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 51/220 (23%), Positives = 96/220 (43%), Gaps = 26/220 (11%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ L++VDG++ +R + N P + Y + ++ L K+Y A + D K
Sbjct: 19 RRNLMIVDGTNLGFRFKH------NNSKKPFASSY--VSTIQSLAKSYSARTTIVLGD-K 69
Query: 62 GKN-FRNILYPSYKATR-----------KKMPYNLILQINLIHQMVKAIGWPILIIKGVE 109
GK+ FR P Y R K + + ++ K +P I+GVE
Sbjct: 70 GKSVFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTT-FPTFTIRGVE 128
Query: 110 ADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA---LINNNKIHDRTTIISRFGV 166
ADD+ + K ++ +IST D D L+++K++ + H R
Sbjct: 129 ADDMAAYIVKLIGHLYDHVWLIST-DGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVD 187
Query: 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSL 206
E+ + +++GD+ DN+ GV+ IG K ++ ++ ++
Sbjct: 188 DVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNV 227
>pdb|1EXN|A Chain A, T5 5'-Exonuclease
pdb|1EXN|B Chain B, T5 5'-Exonuclease
Length = 290
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 52/220 (23%), Positives = 94/220 (42%), Gaps = 26/220 (11%)
Query: 2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
+ L +VDG++ +R + N P + Y + ++ L K+Y A + D K
Sbjct: 18 RRNLXIVDGTNLGFRFKH------NNSKKPFASSY--VSTIQSLAKSYSARTTIVLGD-K 68
Query: 62 GKN-FRNILYPSYKATR-----------KKMPYNLILQINLIHQMVKAIGWPILIIKGVE 109
GK+ FR P YK R K + + ++ K +P I+GVE
Sbjct: 69 GKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTT-FPTFTIRGVE 127
Query: 110 ADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA---LINNNKIHDRTTIISRFGV 166
ADD + K ++ +IST D D L+++K++ + H R
Sbjct: 128 ADDXAAYIVKLIGHLYDHVWLIST-DGDWDTLLTDKVSRFSFTTRREYHLRDXYEHHNVD 186
Query: 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSL 206
E+ + ++ GD+ DN+ GV+ IG K ++ ++ ++
Sbjct: 187 DVEQFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNV 226
>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
pdb|3Q8M|B Chain B, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
Length = 341
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLE 207
+ I+ G++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E
Sbjct: 209 SRILQELGLNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIE 256
>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Product 5'-Flap Dna, Sm3+, And K+
pdb|3Q8L|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Substrate 5'-Flap Dna, Sm3+, And K+
Length = 341
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLE 207
+ I+ G++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E
Sbjct: 209 SRILQELGLNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIE 256
>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Y Chain Y, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Z Chain Z, Crystal Structure Of The Human Fen1-Pcna Complex
Length = 379
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLE 207
+ I+ G++ E+ VD L+G SD ++ IGPK AV L+ ++ S+E
Sbjct: 209 SRILQELGLNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIE 256
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 160 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLE 207
++ + G++ E+++D LIG N G++ IGP+ A+K++ +Y +E
Sbjct: 212 LLKKLGITREQLIDIGILIG-TDYNPDGIRGIGPERALKIIKKYGKIE 258
>pdb|2L1C|A Chain A, Shc-Ptb:biphosphorylated Integrin Beta3 Cytoplasmic Tail
Complex (1:1)
Length = 211
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 10/109 (9%)
Query: 75 ATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVI--IS 132
ATR++ P + L L +K G PI + + +++ KQ + H+++ I S
Sbjct: 99 ATRRRKPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFAS 158
Query: 133 TNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIV-DYFSLIGD 180
D D A+ V A + + ++ R I PE + D S IG
Sbjct: 159 GGDPDTAEYV----AYVAKDPVNQRACHILE---CPEGLAQDVISTIGQ 200
>pdb|1SHC|A Chain A, Shc Ptb Domain Complexed With A Trka Receptor
Phosphopeptide, Nmr, Minimized Average Structure
Length = 195
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 10/109 (9%)
Query: 75 ATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVI--IS 132
ATR++ P + L L +K G PI + + +++ KQ + H+++ I S
Sbjct: 83 ATRRRKPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFAS 142
Query: 133 TNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIV-DYFSLIGD 180
D D A+ V A + + ++ R I PE + D S IG
Sbjct: 143 GGDPDTAEYV----AYVAKDPVNQRACHILE---CPEGLAQDVISTIGQ 184
>pdb|1N3H|A Chain A, Coupling Of Folding And Binding In The Ptb Domain Of The
Signaling Protein Shc
pdb|1OY2|A Chain A, Coupling Of Folding And Binding In The Ptb Domain Of The
Signaling Protein Shc
Length = 207
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 10/109 (9%)
Query: 75 ATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVI--IS 132
ATR++ P + L L +K G PI + + +++ KQ + H+++ I S
Sbjct: 95 ATRRRKPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFAS 154
Query: 133 TNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIV-DYFSLIGD 180
D D A+ V A + + ++ R I PE + D S IG
Sbjct: 155 GGDPDTAEYV----AYVAKDPVNQRACHILE---CPEGLAQDVISTIGQ 196
>pdb|2VK9|A Chain A, Crystal Structure Of The Catalytic Domain Of Alpha-Toxin
From Clostridium Novyi
Length = 551
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 25 RNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNL 84
R+I+ V +Y + L +L NY+ Y + + +NFR+ LY + K +
Sbjct: 35 RDIEGTSVKEIYSKLSKLNELVDNYQTKYPSSGRNLALENFRDSLYSELRELIKNSRTST 94
Query: 85 ILQINLIHQMVKAIGWPI 102
I NL IG PI
Sbjct: 95 IASKNL---SFIWIGGPI 109
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
0.323 0.140 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,117,068
Number of Sequences: 62578
Number of extensions: 249532
Number of successful extensions: 632
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 617
Number of HSP's gapped (non-prelim): 15
length of query: 284
length of database: 14,973,337
effective HSP length: 98
effective length of query: 186
effective length of database: 8,840,693
effective search space: 1644368898
effective search space used: 1644368898
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)