RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy863
         (216 letters)



>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter.  This
            model describes the photoreceptor protein (rim protein)
            in eukaryotes. It is the member of ABC transporter
            superfamily. Rim protein is a membrane glycoprotein which
            is localized in the photoreceptor outer segment discs.
            Mutation/s in its genetic loci is implicated in the
            recessive Stargardt's disease [Transport and binding
            proteins, Other].
          Length = 2272

 Score = 56.9 bits (137), Expect = 2e-09
 Identities = 33/93 (35%), Positives = 53/93 (56%), Gaps = 2/93 (2%)

Query: 61   DIQVSAITDLIQSHVPDASLHNTQSSQITYTLPTQD--TSPFPALFATLEEKKSALGISS 118
            D  V+ + DL+  HVP+A L      ++ + LP ++     + +LF  LEE  + LG+SS
Sbjct: 1202 DGDVNELMDLVYHHVPEAKLVECIGQELIFLLPNKNFKQRAYASLFRELEETLADLGLSS 1261

Query: 119  IGIACTTIEEVFLKVGDLASKEKIESVDAKSKR 151
             GI+ T +EE+FLKV + A    + +  A+ KR
Sbjct: 1262 FGISDTPLEEIFLKVTEDADSGSLFAGGAQQKR 1294


>gnl|CDD|225146 COG2237, COG2237, Predicted membrane protein [Function unknown].
          Length = 364

 Score = 29.6 bits (67), Expect = 1.3
 Identities = 21/84 (25%), Positives = 31/84 (36%), Gaps = 15/84 (17%)

Query: 138 SKEKIESVDAKSKRSTLEQVPNGESN----------KEPLLHQKVQGVLFLVFLLFATAM 187
           S+ KI+SV    KR  + Q    ES            +P   + V G   LV LL+    
Sbjct: 120 SRVKIDSV----KRVVVRQSRGIESTYYLIKRYLKKTDPEYSRTVLGPPGLVLLLYGILA 175

Query: 188 LLF-TYSYSLIVQGPESLGYYFVL 210
           L    Y    ++     +G Y + 
Sbjct: 176 LANILYPAGAVIGILLIVGLYMLY 199


>gnl|CDD|178591 PLN03017, PLN03017, trehalose-phosphatase.
          Length = 366

 Score = 28.1 bits (62), Expect = 4.1
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 10/79 (12%)

Query: 9  IIVPIHVTSNTRDSIRLLATYFPGYAMICGFKLLGNFEANGAGYQLTFLTSDDIQVSAIT 68
           I+P +V++++  S + L    PG   I   KLL N +    G Q      D ++ S+ T
Sbjct: 15 SIIPNNVSNSSNSSSQKLP---PGLISISKKKLLKNIDIINGGGQRINAWVDSMRASSPT 71

Query: 69 DLIQSHVPDASLHNTQSSQ 87
           L        SL ++ SSQ
Sbjct: 72 HL-------KSLPSSISSQ 83


>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
           transferase subunit alpha; Provisional.
          Length = 762

 Score = 27.9 bits (62), Expect = 4.7
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 13/76 (17%)

Query: 92  LPTQDTSPFPALFATLEE------KKSALGISSIGIACTTIEEVFLKVG------DLASK 139
             T + +P P L   +E       KK    I S  +  + IE + L+V       D+  K
Sbjct: 636 KDTAEQTPPPNLQEKIESLNEEINKKIERVIRSSDLK-SKIELLKLEVAKASKTPDVTEK 694

Query: 140 EKIESVDAKSKRSTLE 155
           EKIE+++ + K+   E
Sbjct: 695 EKIEALEQQIKQKIAE 710


>gnl|CDD|222490 pfam14004, DUF4227, Protein of unknown function (DUF4227).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are approximately 80 amino acids in length.
          Length = 71

 Score = 26.1 bits (58), Expect = 4.8
 Identities = 9/21 (42%), Positives = 11/21 (52%)

Query: 179 VFLLFATAMLLFTYSYSLIVQ 199
           VFLLF    LLF Y+   +  
Sbjct: 9   VFLLFTGCTLLFYYAILWVND 29


>gnl|CDD|179451 PRK02624, psbH, photosystem II reaction center protein H;
           Provisional.
          Length = 64

 Score = 25.8 bits (57), Expect = 5.4
 Identities = 15/29 (51%), Positives = 20/29 (68%), Gaps = 4/29 (13%)

Query: 172 VQGVLFLVFLLFATAMLLFTYSYSLIVQG 200
           V  VLFLVFLL    ++L  Y+ SL++QG
Sbjct: 33  VFMVLFLVFLL----IILQIYNQSLLLQG 57


>gnl|CDD|182964 PRK11102, PRK11102, bicyclomycin/multidrug efflux system;
           Provisional.
          Length = 377

 Score = 27.6 bits (62), Expect = 5.5
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 201 PESLGYYFVLNVVF 214
           P++ GYYF LN+VF
Sbjct: 229 PQNFGYYFALNIVF 242


>gnl|CDD|235030 PRK02315, PRK02315, adaptor protein; Provisional.
          Length = 233

 Score = 27.1 bits (61), Expect = 5.8
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 10/99 (10%)

Query: 126 IEEVFLKVGDLASKEKIESVDAKSKRSTLEQVPNGESNKEPL-----LHQKVQGVLFLVF 180
           +   F  + DL S E IE +  +     LEQ    + + +         ++ +  + L +
Sbjct: 82  LPLNFEDLIDLPSDEDIEDLFPEDFFKLLEQSLEDKDDLDATAKQEKEEKEAEDEVQLTY 141

Query: 181 LL-FATAMLLFTYSYSLIVQGPESLGYYF----VLNVVF 214
           +L F     + + + +L V+   S  Y +     L V+F
Sbjct: 142 VLKFDDFEDVISLAKTLKVEDLASELYKYEGRYYLTVLF 180


>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
          Length = 402

 Score = 27.4 bits (61), Expect = 6.3
 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 20  RDSIRLLATYFPGYAMICGFKLLGNFEANGAGYQLTFLTSDDIQ 63
           RDSI   AT++P +  + G ++    E   +G   T L ++D++
Sbjct: 159 RDSID--ATHYPVFHQMEGVRVFSPEEWEASGLDGTDLAAEDLK 200


>gnl|CDD|213276 cd05908, A_NRPS_MycA_like, The adenylation domain of nonribosomal
          peptide synthetases (NRPS) similar to mycosubtilin
          synthase subunit A (MycA).  The adenylation (A) domain
          of NRPS recognizes a specific amino acid or hydroxy
          acid and activates it as (amino)-acyl adenylate by
          hydrolysis of ATP. The activated acyl moiety then forms
          thioester to the enzyme-bound cofactor
          phosphopantetheine of a peptidyl carrier protein
          domain. This family includes NRPS similar to
          mycosubtilin synthase subunit A (MycA). Mycosubtilin,
          which is characterized by a beta-amino fatty acid
          moiety linked to the circular heptapeptide
          Asn-Tyr-Asn-Gln-Pro-Ser-Asn, belongs to the iturin
          family of lipopeptide antibiotics. The mycosubtilin
          synthase subunit A (MycA) combines functional domains
          derived from peptide synthetases, amino transferases,
          and fatty acid synthases. Nonribosomal peptide
          synthetases are large multifunction enzymes that
          synthesize many therapeutically useful peptides. NRPS
          has a distinct modular structure in which each module
          is responsible for the recognition, activation, and, in
          some cases, modification of a single amino acid residue
          of the final peptide product. The modules can be
          subdivided into domains that catalyze specific
          biochemical reactions.
          Length = 499

 Score = 27.2 bits (61), Expect = 6.9
 Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 1  MVLW-CILLIIVPIHVTSNTRDSIRL 25
           V W CIL  I+P+ ++    D  +L
Sbjct: 55 YVFWACILGGIIPVPLSYGNTDEHKL 80


>gnl|CDD|227431 COG5100, NPL4, Nuclear pore protein [Nuclear structure].
          Length = 571

 Score = 27.3 bits (60), Expect = 7.0
 Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 13/115 (11%)

Query: 40  KLLGNFEANGAGYQLTFLTSDDIQVSAITDLIQSHVPDASLHNTQSSQITYTLPTQDTSP 99
           KLL  FE N +  Q++  ++ D Q    + L      D  L + Q   + Y+        
Sbjct: 28  KLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEYSDI------ 81

Query: 100 FPALFATLEEKKSALGISSIGIACTTI--EEVFLKVGDLASKEKIESVDAKSKRS 152
                A+  EKK  +           I  E+  + V      + +E  D   +RS
Sbjct: 82  -----ASNNEKKRDVPGKPKQDCSKGIKREKDSMPVIQDPIDDSLEKEDGLIRRS 131


>gnl|CDD|198420 cd10462, PUB_UBA, PNGase/UBA or UBX (PUB) domain of
          Ubiquitin-associated (UBA) domain containing proteins. 
          The PUB domain functions as a p97 (also known as
          valosin-containing protein or VCP) adaptor by
          interacting with the D1 and/or D2 ATPase domains. The
          type II AAA+ ATPase p97 is involved in a variety of
          cellular processes such as the deglycosylation of ERAD
          substrates, membrane fusion, transcription factor
          activation and cell cycle regulation through
          differential binding to specific adaptor proteins. The
          UBA domain, along with UBL (ubiquitin-like) domain, has
          been implicated in proteasomal degradation by
          associating with substrates destined for degradation as
          well as with subunits of the proteasome, thus
          regulating protein turnover.
          Length = 100

 Score = 25.5 bits (56), Expect = 9.7
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 35 MICGFKLLGNFEANGAGYQLTFLTSDDIQ 63
          + CGF+  G+F         TFL S  I+
Sbjct: 64 LACGFEDTGDFLFIINKIPDTFLCSQAIK 92


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.321    0.136    0.389 

Gapped
Lambda     K      H
   0.267   0.0743    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,575,392
Number of extensions: 955510
Number of successful extensions: 1160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1157
Number of HSP's successfully gapped: 33
Length of query: 216
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 123
Effective length of database: 6,812,680
Effective search space: 837959640
Effective search space used: 837959640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)