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= 008067
(579 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 68/219 (31%), Positives = 103/219 (47%), Gaps = 23/219 (10%)
Query: 98 VAGGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPDQSK 157
V GG+VRD LLG DIDI ++ A + AEY +P +
Sbjct: 39 VVGGFVRDLLLGIKNLDIDIVVEGN-----ALEFAEYAKR----------FLPGKLVKHD 83
Query: 158 HLETATMKLYD-LWIDFVNLRCEDYSENSRIPTMRFGTAEEDAYRRDLTINSLFYNINTS 216
TA++ L L ID R E Y +++P + T ++D YRRD TIN++ +N
Sbjct: 84 KFMTASLFLKGGLRIDIATARLEYYESPAKLPDVEMSTIKKDLYRRDFTINAMAIKLNPK 143
Query: 217 SVE---DLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARFDFILDEELKKAA 273
D G G DLK G V + +F+DDP R+LRAIRF RFDF + EE +
Sbjct: 144 DFGLLIDFFG-GYRDLKEG--VIRVLHTLSFVDDPTRILRAIRFEQRFDFRI-EETTERL 199
Query: 274 ASDEVKAALAAKISRERVGTEIDLMVSGNQPVKAMTHIC 312
V+ + + R+ E++ ++ P+K++ +
Sbjct: 200 LKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMA 238
>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 = 85.5 bits (210), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 68/215 (31%), Positives = 101/215 (46%), Gaps = 23/215 (10%)
Query: 98 VAGGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPDQSK 157
V GG+VRD LLG DIDI ++ A + AEY +P +
Sbjct: 39 VVGGFVRDLLLGIKNLDIDIVVEGN-----ALEFAEYAKR----------FLPGKLVKHD 83
Query: 158 HLETATMKLYD-LWIDFVNLRCEDYSENSRIPTMRFGTAEEDAYRRDLTINSLFYNINTS 216
TA++ L L ID R E Y +++P + T ++D YRRD TIN+ +N
Sbjct: 84 KFXTASLFLKGGLRIDIATARLEYYESPAKLPDVEXSTIKKDLYRRDFTINAXAIKLNPK 143
Query: 217 SVE---DLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARFDFILDEELKKAA 273
D G G DLK G V + +F+DDP R+LRAIRF RFDF + EE +
Sbjct: 144 DFGLLIDFFG-GYRDLKEG--VIRVLHTLSFVDDPTRILRAIRFEQRFDFRI-EETTERL 199
Query: 274 ASDEVKAALAAKISRERVGTEIDLMVSGNQPVKAM 308
V+ + + R+ E++ ++ P+K++
Sbjct: 200 LKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSI 234
>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 = 82.4 bits (202), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 67/206 (32%), Positives = 103/206 (50%), Gaps = 28/206 (13%)
Query: 98 VAGGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPDQSK 157
+ GG VRD LLGK+ +D+D ++ A ++A+ L+ G V P +
Sbjct: 15 IVGGVVRDILLGKEVWDVDFVVEGN-----AIELAKELARR-----HGVNVHPFPEFGTA 64
Query: 158 HLETATMKLYDLWIDFVNLRCEDYSENSRIPTMRFGTAEEDAYRRDLTINSLFYNIN--- 214
HL+ +KL +F R E Y P + + +ED RRD TIN++ ++N
Sbjct: 65 HLKIGKLKL-----EFATARRETYPRPGAYPKVEPASLKEDLIRRDFTINAMAISVNLED 119
Query: 215 TSSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARFDFILD---EELKK 271
++ D G G+ DLK K++ L P +F++DP+R+LRA+RF R +F L E+L K
Sbjct: 120 YGTLIDYFG-GLRDLKD-KVIRVLHP-VSFIEDPVRILRALRFAGRLNFKLSRSTEKLLK 176
Query: 272 AAASDEVKAALAAKISRERVGTEIDL 297
A V L + R R+ EI L
Sbjct: 177 QA----VNLGLLKEAPRGRLINEIKL 198
>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 = 70.1 bits (170), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 35/77 (45%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 192 FGTAEEDAYRRDLTINSLFYNINTSSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRV 251
FG+ EEDA RRD TINSL+Y++ +V D G G+ DLK G I P+ + +DP+R+
Sbjct: 124 FGSIEEDAQRRDFTINSLYYSVADFTVRDYVG-GMKDLKDGVIRLIGNPETRYREDPVRM 182
Query: 252 LRAIRFGARFDFILDEE 268
LRA+RF A+ + E
Sbjct: 183 LRAVRFAAKLGMRISPE 199
>pdb|3AQK|A Chain A, Structure Of Bacterial Protein (Apo Form I)
Length = 414
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 35/77 (45%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 192 FGTAEEDAYRRDLTINSLFYNINTSSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRV 251
FG+ EEDA RRD TINSL+Y++ +V D G G+ DLK G I P+ + +DP+R+
Sbjct: 123 FGSIEEDAQRRDFTINSLYYSVADFTVRDYVG-GMKDLKDGVIRLIGNPETRYREDPVRM 181
Query: 252 LRAIRFGARFDFILDEE 268
LRA+RF A+ + E
Sbjct: 182 LRAVRFAAKLGMRISPE 198
>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 = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 35/77 (45%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 192 FGTAEEDAYRRDLTINSLFYNINTSSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRV 251
FG+ EEDA RRD TINSL+Y++ +V D G G+ DLK G I P+ + +DP+R+
Sbjct: 124 FGSIEEDAQRRDFTINSLYYSVADFTVRDYVG-GMKDLKDGVIRLIGNPETRYREDPVRM 182
Query: 252 LRAIRFGARFDFILDEE 268
LRA+RF A+ + E
Sbjct: 183 LRAVRFAAKLGMRISPE 199
>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 = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 69/219 (31%), Positives = 100/219 (45%), Gaps = 21/219 (9%)
Query: 96 LRVAGGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPDQ 155
LR+AGG VRD L G DID A + T++ E + G + N
Sbjct: 73 LRIAGGAVRDLLNGVKPQDIDFAT-----TATPTQMKEMFQSAG--------IRMINNRG 119
Query: 156 SKHLETATMKLYDLWIDFVNLRCEDYSENSRIPTMRFGTA-EEDAYRRDLTINSLFYNIN 214
KH T T +L++ + LR D + + R + F T ++DA RRDLTINS+F +
Sbjct: 120 EKH-GTITARLHEENFEITTLRI-DVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFD 177
Query: 215 TSSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARF-DFILDEELKKAA 273
+ + G DLK+ K+ K +D LR+LR RF R D D + +
Sbjct: 178 GTLFDYFN--GYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLE 235
Query: 274 ASDEVKAALAAKISRERVGTEIDLMVSGNQPVKAMTHIC 312
A E LA IS ER+ E+ ++ GN V + H+
Sbjct: 236 AIAENAKGLAG-ISGERIWVELKKILVGNH-VNHLIHLI 272
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 56/213 (26%), Positives = 93/213 (43%), Gaps = 30/213 (14%)
Query: 100 GGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPD-QSKH 158
GG VRD LLG+ D+DIA + A + P D SKH
Sbjct: 26 GGAVRDLLLGRPIGDVDIATSALPEDVMA-------------------IFPKTIDVGSKH 66
Query: 159 LETATM---KLYDLWIDFVNLRCEDYSENSRIPTMRFGTAEEDAYRRDLTINSLFYNINT 215
+ K Y++ + EDY + +R + EED RRD T+N++ +
Sbjct: 67 GTVVVVHKGKAYEVTTFKTDGDYEDYRRPESVTFVR--SLEEDLKRRDFTMNAIAMDEYG 124
Query: 216 SSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARFDFILDEELKKAAAS 275
+ ++ GR + + V + F +D LR++RA+RF + F L + ++A
Sbjct: 125 TIIDPFGGREAIRRRIIRTVGEA--EKRFREDALRMMRAVRFVSELGFALAPDTEQAIVQ 182
Query: 276 DEVKAALAAKISRERVGTEIDLMVSGNQPVKAM 308
+ A L A IS ER+ E++ ++ G +A+
Sbjct: 183 N---APLLAHISVERMTMEMEKLLGGPFAARAL 212
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 57/213 (26%), Positives = 91/213 (42%), Gaps = 30/213 (14%)
Query: 100 GGWVRDKLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGFGVIPSNPD-QSKH 158
GG VRD LLG+ D+DIA + + E + A + P D SKH
Sbjct: 26 GGAVRDLLLGRPIGDVDIA---------TSALPEDVXA----------IFPKTIDVGSKH 66
Query: 159 LETATM---KLYDLWIDFVNLRCEDYSENSRIPTMRFGTAEEDAYRRDLTINSLFYNINT 215
+ K Y++ + EDY + +R + EED RRD T N++ +
Sbjct: 67 GTVVVVHKGKAYEVTTFKTDGDYEDYRRPESVTFVR--SLEEDLKRRDFTXNAIAXDEYG 124
Query: 216 SSVEDLTGRGIADLKHGKIVTPLPPKATFLDDPLRVLRAIRFGARFDFILDEELKKAAAS 275
+ ++ GR + + V + F +D LR RA+RF + F L + ++A
Sbjct: 125 TIIDPFGGREAIRRRIIRTVGEA--EKRFREDALRXXRAVRFVSELGFALAPDTEQAIVQ 182
Query: 276 DEVKAALAAKISRERVGTEIDLMVSGNQPVKAM 308
+ A L A IS ER E + ++ G +A+
Sbjct: 183 N---APLLAHISVERXTXEXEKLLGGPFAARAL 212
>pdb|3FOA|A Chain A, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|B Chain B, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|C Chain C, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|D Chain D, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOH|A Chain A, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|B Chain B, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|C Chain C, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|D Chain D, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|E Chain E, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|F Chain F, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOI|A Chain A, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|B Chain B, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|C Chain C, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|D Chain D, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|E Chain E, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|F Chain F, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
Length = 510
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 106 KLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGF-GVIPSNPDQSKHLETATM 164
K GKD YD +I +D+ FA +EY+ AT + P GF G++ + S + E
Sbjct: 298 KRGGKDIYDSNIYIDDF----FAKGGSEYIFATAQNWPEGFSGILTLSGGLSSNAEVTAG 353
Query: 165 KLYDLWIDFVNLRCED 180
L + W F + D
Sbjct: 354 DLMEAWDFFADRESVD 369
>pdb|3FO8|D Chain D, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Protease Resistant Fragment Gp18pr
Length = 283
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 106 KLLGKDCYDIDIALDNMMGSEFATKVAEYLSATGETAPSGF-GVIPSNPDQSKHLETATM 164
K GKD YD +I +D+ FA +EY+ AT + P GF G++ + S + E
Sbjct: 216 KRGGKDIYDSNIYIDDF----FAKGGSEYIFATAQNWPEGFSGILTLSGGLSSNAEVTAG 271
Query: 165 KLYDLWIDF 173
L + W DF
Sbjct: 272 DLMEAW-DF 279
>pdb|3SF6|A Chain A, Crystal Structure Of Glutaryl-Coa Dehydrogenase From
Mycobacterium Smegmatis
Length = 403
Score = 32.3 bits (72), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 240 PKATFLDDPLRVLRAIRFGARFDFILDEELKKAAASDEVKAALAAKISRER 290
P AT L PLR L RFG F + AA D ++ ALA SRE+
Sbjct: 246 PGATSLGAPLRCLNEARFGIVFGAL-------GAARDCLETALAYACSREQ 289
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
0.321 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,367,281
Number of Sequences: 62578
Number of extensions: 663240
Number of successful extensions: 1357
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1334
Number of HSP's gapped (non-prelim): 17
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
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: 54 (25.4 bits)