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= 005593
(689 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AQL|A Chain A, Structure Of Bacterial Protein (Apo Form Ii)
pdb|3AQL|B Chain B, Structure Of Bacterial Protein (Apo Form Ii)
pdb|3AQN|A Chain A, Complex Structure Of Bacterial Protein (Apo Form Ii)
pdb|3AQN|B Chain B, Complex Structure Of Bacterial Protein (Apo Form Ii)
Length = 415
Score = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/177 (35%), Positives = 90/177 (50%), Gaps = 20/177 (11%)
Query: 62 GITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFH 121
I+R I + + V+ L G++A+LVGG VRDLLL + PKDFDV T A +Q+R+ F
Sbjct: 11 AISRKDISENALKVMYRLNKAGYEAWLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFR 70
Query: 122 RSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGE-----------GKETVLLSQIPYGCD 170
++GRRF + V +IEV++F H E G+ +LL +G
Sbjct: 71 NCRLVGRRFRLAHVMFGPEIIEVATFR---GHHEGNVSDRTTSQRGQNGMLLRDNIFGSI 127
Query: 171 EIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTED 227
E D R RDFTINSL++ + DY G+ DL+ +R + + ED
Sbjct: 128 EEDAQR------RDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRYRED 178
>pdb|3AQK|A Chain A, Structure Of Bacterial Protein (Apo Form I)
Length = 414
Score = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/177 (35%), Positives = 90/177 (50%), Gaps = 20/177 (11%)
Query: 62 GITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFH 121
I+R I + + V+ L G++A+LVGG VRDLLL + PKDFDV T A +Q+R+ F
Sbjct: 10 AISRKDISENALKVMYRLNKAGYEAWLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFR 69
Query: 122 RSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGE-----------GKETVLLSQIPYGCD 170
++GRRF + V +IEV++F H E G+ +LL +G
Sbjct: 70 NCRLVGRRFRLAHVMFGPEIIEVATFR---GHHEGNVSDRTTSQRGQNGMLLRDNIFGSI 126
Query: 171 EIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTED 227
E D R RDFTINSL++ + DY G+ DL+ +R + + ED
Sbjct: 127 EEDAQR------RDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRYRED 177
>pdb|3AQM|A Chain A, Structure Of Bacterial Protein (Form Ii)
pdb|3AQM|B Chain B, Structure Of Bacterial Protein (Form Ii)
Length = 415
Score = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/177 (35%), Positives = 90/177 (50%), Gaps = 20/177 (11%)
Query: 62 GITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFH 121
I+R I + + V+ L G++A+LVGG VRDLLL + PKDFDV T A +Q+R+ F
Sbjct: 11 AISRKDISENALKVMYRLNKAGYEAWLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFR 70
Query: 122 RSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGE-----------GKETVLLSQIPYGCD 170
++GRRF + V +IEV++F H E G+ +LL +G
Sbjct: 71 NCRLVGRRFRLAHVMFGPEIIEVATFRG---HHEGNVSDRTTSQRGQNGMLLRDNIFGSI 127
Query: 171 EIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTED 227
E D R RDFTINSL++ + DY G+ DL+ +R + + ED
Sbjct: 128 EEDAQR------RDFTINSLYYSVADFTVRDYVGGMKDLKDGVIRLIGNPETRYRED 178
>pdb|1MIY|A Chain A, Crystal Structure Of Bacillus Stearothermophilus
Cca-adding Enzyme In Complex With Ctp
pdb|1MIY|B Chain B, Crystal Structure Of Bacillus Stearothermophilus
Cca-adding Enzyme In Complex With Ctp
Length = 404
Score = 63.5 bits (153), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 56/205 (27%), Positives = 92/205 (44%), Gaps = 13/205 (6%)
Query: 75 VLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICR 134
+++ LK G+ AY VGG VRDLLL R D D+ T+A + + F ++ +G +
Sbjct: 11 IIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVMAIFPKTIDVGSKHGTVV 70
Query: 135 VHIKGSVIEVSSFETVAKHGEGK--ETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFF 192
V KG EV++F+T + + + E+V + E DL R RDFT+N++
Sbjct: 71 VVHKGKAYEVTTFKTDGDYEDYRRPESVTFVR----SLEEDLKR------RDFTMNAIAM 120
Query: 193 DPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCXXXXXXXXXXXXXXXSFCKDIDTA 252
D + I D G +R +RT+ A F ED + D + A
Sbjct: 121 DEY-GTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRMMRAVRFVSELGFALAPDTEQA 179
Query: 253 MHSLSSSIERLDKSRIMMELNYMLS 277
+ + + + R+ ME+ +L
Sbjct: 180 IVQNAPLLAHISVERMTMEMEKLLG 204
>pdb|1MIV|A Chain A, Crystal Structure Of Bacillus Stearothermophilus
Cca-Adding Enzyme
pdb|1MIV|B Chain B, Crystal Structure Of Bacillus Stearothermophilus
Cca-Adding Enzyme
pdb|1MIW|A Chain A, Crystal Structure Of Bacillus Stearothermophilus
Cca-Adding Enzyme In Complex With Atp
pdb|1MIW|B Chain B, Crystal Structure Of Bacillus Stearothermophilus
Cca-Adding Enzyme In Complex With Atp
Length = 404
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 57/205 (27%), Positives = 90/205 (43%), Gaps = 13/205 (6%)
Query: 75 VLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICR 134
+++ LK G+ AY VGG VRDLLL R D D+ T+A + + F ++ +G +
Sbjct: 11 IIQQLKQHGYDAYFVGGAVRDLLLGRPIGDVDIATSALPEDVXAIFPKTIDVGSKHGTVV 70
Query: 135 VHIKGSVIEVSSFETVAKHGEGK--ETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFF 192
V KG EV++F+T + + + E+V + E DL R RDFT N++
Sbjct: 71 VVHKGKAYEVTTFKTDGDYEDYRRPESVTFVR----SLEEDLKR------RDFTXNAIAX 120
Query: 193 DPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCXXXXXXXXXXXXXXXSFCKDIDTA 252
D + I D G +R +RT+ A F ED + D + A
Sbjct: 121 DEY-GTIIDPFGGREAIRRRIIRTVGEAEKRFREDALRXXRAVRFVSELGFALAPDTEQA 179
Query: 253 MHSLSSSIERLDKSRIMMELNYMLS 277
+ + + + R E +L
Sbjct: 180 IVQNAPLLAHISVERXTXEXEKLLG 204
>pdb|1VFG|A Chain A, Crystal Structure Of Trna Nucleotidyltransferase Complexed
With A Primer Trna And An Incoming Atp Analog
pdb|1VFG|B Chain B, Crystal Structure Of Trna Nucleotidyltransferase Complexed
With A Primer Trna And An Incoming Atp Analog
Length = 390
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 48/159 (30%), Positives = 74/159 (46%), Gaps = 15/159 (9%)
Query: 74 VVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIG-RRFP- 131
+V +I K G +AY+VGG VRD+LL + D D + N ++ ++ R + FP
Sbjct: 1 MVGQIAKEMGLRAYIVGGVVRDILLGKEVWDVDFVVEGNAIELAKELARRHGVNVHPFPE 60
Query: 132 ICRVHIKGSVIEVSSFETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLF 191
H+K +++ F T + + P E DL+R RDFTIN++
Sbjct: 61 FGTAHLKIGKLKL-EFATARRETYPRPGAYPKVEPASLKE-DLIR------RDFTINAMA 112
Query: 192 FDPFL---NKIYDYANGISDLRCLKLRTLIPAYLSFTED 227
L + DY G+ DL+ +R L P +SF ED
Sbjct: 113 ISVNLEDYGTLIDYFGGLRDLKDKVIRVLHP--VSFIED 149
>pdb|1OU5|A Chain A, Crystal Structure Of Human Cca-Adding Enzyme
pdb|1OU5|B Chain B, Crystal Structure Of Human Cca-Adding Enzyme
Length = 448
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/146 (32%), Positives = 66/146 (45%), Gaps = 18/146 (12%)
Query: 88 LVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICRVHIKGSVIEVSSF 147
+ GG VRDLL P+D D TTA Q++ F + G R R G++
Sbjct: 75 IAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSA---GIRMINNRGEKHGTI------ 125
Query: 148 ETVAKHGEGKETVLLSQIPYGCD----EIDLVR-W-RNSIHRDFTINSLFFDPFLNKIYD 201
T H E E L +I D E++ W +++ RD TINS+F F ++D
Sbjct: 126 -TARLHEENFEITTL-RIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLG-FDGTLFD 182
Query: 202 YANGISDLRCLKLRTLIPAYLSFTED 227
Y NG DL+ K+R + A ED
Sbjct: 183 YFNGYEDLKNKKVRFVGHAKQRIQED 208
>pdb|3H38|A Chain A, The Structure Of Cca-Adding Enzyme Apo Form Ii
pdb|3H39|A Chain A, The Complex Structure Of Cca-Adding Enzyme With Atp
pdb|3H39|B Chain B, The Complex Structure Of Cca-Adding Enzyme With Atp
pdb|3H3A|A Chain A, The Complex Structure Of Cca-Adding Enzyme With Ctp
pdb|3H3A|B Chain B, The Complex Structure Of Cca-Adding Enzyme With Ctp
Length = 441
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 43/157 (27%), Positives = 71/157 (45%), Gaps = 34/157 (21%)
Query: 86 AYLVGGCVRDLLLRRVPKDFDVITTAN---LKQIRRQFHRSEIIGR-RFPICRVHIKGSV 141
Y+VGG VRDLLL D D++ N + ++F +++ +F + +KG +
Sbjct: 37 VYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGL 96
Query: 142 -IEVSS-----FETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPF 195
I++++ +E+ AK L + + DL R RDFTIN++
Sbjct: 97 RIDIATARLEYYESPAK---------LPDVEMSTIKKDLYR------RDFTINAMAIK-- 139
Query: 196 LNK-----IYDYANGISDLRCLKLRTLIPAYLSFTED 227
LN + D+ G DL+ +R L LSF +D
Sbjct: 140 LNPKDFGLLIDFFGGYRDLKEGVIRVL--HTLSFVDD 174
>pdb|3H37|A Chain A, The Structure Of Cca-Adding Enzyme Apo Form I
pdb|3H37|B Chain B, The Structure Of Cca-Adding Enzyme Apo Form I
Length = 441
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 71/155 (45%), Gaps = 30/155 (19%)
Query: 86 AYLVGGCVRDLLLRRVPKDFDVITTAN---LKQIRRQFHRSEIIGR-RFPICRVHIKGSV 141
Y+VGG VRDLLL D D++ N + ++F +++ +F + +KG +
Sbjct: 37 VYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFXTASLFLKGGL 96
Query: 142 -IEVSS-----FETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTIN--SLFFD 193
I++++ +E+ AK L + + DL R RDFTIN ++ +
Sbjct: 97 RIDIATARLEYYESPAK---------LPDVEXSTIKKDLYR------RDFTINAXAIKLN 141
Query: 194 PF-LNKIYDYANGISDLRCLKLRTLIPAYLSFTED 227
P + D+ G DL+ +R L LSF +D
Sbjct: 142 PKDFGLLIDFFGGYRDLKEGVIRVL--HTLSFVDD 174
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
0.319 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,365,915
Number of Sequences: 62578
Number of extensions: 646987
Number of successful extensions: 1410
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1399
Number of HSP's gapped (non-prelim): 11
length of query: 689
length of database: 14,973,337
effective HSP length: 105
effective length of query: 584
effective length of database: 8,402,647
effective search space: 4907145848
effective search space used: 4907145848
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)