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= 009811
         (525 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|4FU3|A Chain A, Cid Of Human Rprd1b
 pdb|4FU3|B Chain B, Cid Of Human Rprd1b
          Length = 135

 Score =  108 bits (271), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 54/117 (46%), Positives = 74/117 (63%)

Query: 3   SVFSEQILAEKLSKLNCTQQCIETLSHWCIFHRSKAELVVATWDKQFHSSQLVQKVPLLY 62
           S FSE  L +KLS+L+ +QQ ++TLS W I HR  A  +V+ W ++   ++  +K+  LY
Sbjct: 2   SSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61

Query: 63  LANDILQNSKRKGNEFVTEFWKVLPAALKDVVENGDDSGKNVVSRLVNIWDERRVFG 119
           LAND++QNSKRKG EF  EF  VL  A   V    D+  K  + RL+NIW ER V+G
Sbjct: 62  LANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYG 118


>pdb|4HFG|A Chain A, Cid Of Human Rprd1b
 pdb|4HFG|B Chain B, Cid Of Human Rprd1b
          Length = 135

 Score =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/117 (45%), Positives = 73/117 (62%)

Query: 3   SVFSEQILAEKLSKLNCTQQCIETLSHWCIFHRSKAELVVATWDKQFHSSQLVQKVPLLY 62
           S FSE  L +KLS+L+ +Q  ++TLS W I HR  A  +V+ W ++   ++  +K+  LY
Sbjct: 2   SSFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61

Query: 63  LANDILQNSKRKGNEFVTEFWKVLPAALKDVVENGDDSGKNVVSRLVNIWDERRVFG 119
           LAND++QNSKRKG EF  EF  VL  A   V    D+  K  + RL+NIW ER V+G
Sbjct: 62  LANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYG 118


>pdb|4FLB|A Chain A, Cid Of Human Rprd2
          Length = 132

 Score = 62.0 bits (149), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 40/113 (35%), Positives = 54/113 (47%), Gaps = 4/113 (3%)

Query: 7   EQILAEKLSKLNCTQQCIETLSHWCIFHRSKAELVVATWDKQFHSSQLVQKVPLLYLAND 66
           E  L  K   +  T + I+ LS WCI ++     +V  W K    S    ++ L YLAND
Sbjct: 7   ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLAND 66

Query: 67  ILQNSKRKGNEFVTE-FWKVLPAALKDVVENGDDSGKNVVSRLVNIWDERRVF 118
           ++QN KRK      E F  VLP A   V    D S    V R+  IW++R V+
Sbjct: 67  VIQNCKRKNAIIFRESFADVLPEAAALV---KDPSVSKSVERIFKIWEDRNVY 116


>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain
 pdb|2L0I|A Chain A, Solution Structure Of Rtt103 Ctd-Interacting Domain Bound
           To A Ser2 Phosphorylated Ctd Peptide
          Length = 142

 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 60/128 (46%), Gaps = 7/128 (5%)

Query: 5   FSEQILAEKLSKLNCTQQCIETLSHWCIFHRSKAELVVATWDKQFH---SSQLVQKVPLL 61
           FS +    KL+ L  +Q+ I + S W +     A  V   W K++    S    +K+  L
Sbjct: 3   FSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMW-KEYMLRPSVNTRRKLLGL 61

Query: 62  YLANDILQNSK-RKGNEFVTEFWKVLPAALKDVVENGDDSGKNVVSRLVNIWDERRVFGS 120
           YL N ++Q +K +K  +F   F KV    L  + +      K  +SR+VNI  ER +F  
Sbjct: 62  YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSK 121

Query: 121 RARGVKDV 128
           +   V D+
Sbjct: 122 QV--VNDI 127


>pdb|1E0R|B Chain B, Beta-Apical Domain Of Thermosome
          Length = 159

 Score = 30.4 bits (67), Expect = 2.5,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 31/49 (63%), Gaps = 5/49 (10%)

Query: 200 VKKMEKDVDIACTNAKDPKRKTLSKELEEEENMLKQCIEKLKSVEASRV 248
           +KK E D ++     +DP    + K L +EENML++ ++K+KSV A+ V
Sbjct: 33  IKKPEFDTNL---RIEDPS--MIQKFLAQEENMLREMVDKIKSVGANVV 76


>pdb|1A6D|B Chain B, Thermosome From T. Acidophilum
 pdb|1A6E|B Chain B, Thermosome-Mg-Adp-Alf3 Complex
          Length = 543

 Score = 29.6 bits (65), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 24/37 (64%)

Query: 212 TNAKDPKRKTLSKELEEEENMLKQCIEKLKSVEASRV 248
           TN +      + K L +EENML++ ++K+KSV A+ V
Sbjct: 253 TNLRIEDPSMIQKFLAQEENMLREMVDKIKSVGANVV 289


>pdb|2DBB|A Chain A, Crystal Structure Of Ph0061
 pdb|2DBB|B Chain B, Crystal Structure Of Ph0061
          Length = 151

 Score = 29.6 bits (65), Expect = 4.4,   Method: Composition-based stats.
 Identities = 26/109 (23%), Positives = 55/109 (50%), Gaps = 6/109 (5%)

Query: 150 KIVKRDSRSIRTKLTVGGAAEKIVSAYHLVLCEQL--SEEEEMARCKSVVHRVKKMEKDV 207
           +I K     I  K T+    +K+   Y +VL +    S+ +++    S +  VK +EK V
Sbjct: 43  RIDKLKKLGIIRKFTIIPDIDKLGYMYAIVLIKSKVPSDADKVISEISDIEYVKSVEKGV 102

Query: 208 DIACTNAKDPKRKTLSKELEEEENMLKQCIEKLKSVEASRVALVSQLKE 256
                      R  L K++++ EN++ + ++++K+ E   V L+S++++
Sbjct: 103 G----RYNIIVRLLLPKDIKDAENLISEFLQRIKNAENVEVILISEVRK 147


>pdb|3IUK|A Chain A, Crystal Structure Of Putative Bacterial Protein Of Unknown
           Function (Duf885, Pf05960.1, ) From Arthrobacter
           Aurescens Tc1, Reveals Fold Similar To That Of M32
           Carboxypeptidases
 pdb|3IUK|B Chain B, Crystal Structure Of Putative Bacterial Protein Of Unknown
           Function (Duf885, Pf05960.1, ) From Arthrobacter
           Aurescens Tc1, Reveals Fold Similar To That Of M32
           Carboxypeptidases
          Length = 562

 Score = 28.5 bits (62), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 28/66 (42%), Gaps = 7/66 (10%)

Query: 310 AKGAQTPKRTAAAIAAEVADKLTASTSSQMIMHSVLSTF-------AAQEAKNAGLVKAS 362
           AK A       A + AEV DKL A TS+    +S L  F        A E    G  + S
Sbjct: 186 AKXAADASLGDAPLPAEVQDKLDAGTSAARSAYSALGAFLRDELLPVAPEKDAVGRERYS 245

Query: 363 TASNSF 368
            AS SF
Sbjct: 246 LASRSF 251


  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
   0.312    0.126    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,024,476
Number of Sequences: 62578
Number of extensions: 454239
Number of successful extensions: 912
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 903
Number of HSP's gapped (non-prelim): 25
length of query: 525
length of database: 14,973,337
effective HSP length: 103
effective length of query: 422
effective length of database: 8,527,803
effective search space: 3598732866
effective search space used: 3598732866
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)