RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9802
         (92 letters)



>gnl|CDD|215915 pfam00429, TLV_coat, ENV polyprotein (coat polyprotein). 
          Length = 560

 Score = 30.9 bits (70), Expect = 0.055
 Identities = 14/47 (29%), Positives = 31/47 (65%), Gaps = 3/47 (6%)

Query: 33  FRAVQKTIDREVSYVQSAANELEKTIASSAQVLAKN---LEVLFILQ 76
           F ++Q  +  ++  ++S+ N+LE ++ S A+V+ +N   L++LF+ Q
Sbjct: 425 FTSLQHALISDIQALESSINDLEDSLTSLAEVVLQNRRGLDLLFLEQ 471


>gnl|CDD|214452 MTH00195, ND1, NADH dehydrogenase subunit 1; Provisional.
          Length = 307

 Score = 30.5 bits (69), Expect = 0.085
 Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 15/58 (25%)

Query: 2   FQALYISHDYIFILCLEHSTLKVPYEIL------NKKF------RAVQKTIDREVSYV 47
           F    I+   +F LC+  S+L V Y IL      N K+      RAV +TI  EVS  
Sbjct: 95  FGFSSINLSVLFFLCV--SSLSV-YSILGSGWASNSKYALLGAIRAVAQTISYEVSMG 149


>gnl|CDD|237180 PRK12711, flgJ, flagellar rod assembly protein/muramidase FlgJ;
           Reviewed.
          Length = 392

 Score = 29.2 bits (65), Expect = 0.23
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 39  TIDREVSYVQSAANELEKTIASSAQ 63
           TIDR V+ + +AA +L    AS+A+
Sbjct: 359 TIDRAVAAIGNAAADLSNRYASTAE 383


>gnl|CDD|185262 PRK15364, PRK15364, pathogenicity island 2 effector protein SseB;
          Provisional.
          Length = 196

 Score = 28.1 bits (62), Expect = 0.51
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 22 LKVPYEILNKKFRAVQKTIDREVSYVQSAANELEKTIASSAQVLAKNLE 70
          L V   I N KF  VQK  +R  +  Q  +NE+++ IA +A+  AK  E
Sbjct: 50 LMVIQAIANNKFIEVQKNAERARN-TQEKSNEMDEVIAKAAKGDAKTKE 97


>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
          Length = 956

 Score = 27.5 bits (62), Expect = 1.1
 Identities = 9/50 (18%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 23  KVPYEILNKKFRAVQKTIDREVSYVQSAANELEKTIASSAQVLAKNLEVL 72
           +V +E LN++  AV +    ++  V++   ++ K +  +          L
Sbjct: 845 QVEFESLNRQLSAVNRHTASKL--VKAVQQDIHKLLQKAEAQAEAQAREL 892


>gnl|CDD|234992 PRK01919, tatB, sec-independent translocase; Provisional.
          Length = 169

 Score = 25.7 bits (57), Expect = 3.8
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 47 VQSAANELEKTIASSAQVLAKNLE 70
           +SAA ++E TI  +      +L 
Sbjct: 66 FESAARDVENTIHDNLSEHESDLN 89


>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain.  This is a family of PrkA
          bacterial and archaeal serine kinases approximately 630
          residues long. This is the N-terminal AAA domain.
          Length = 361

 Score = 25.7 bits (57), Expect = 4.1
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 26 YEILNKKFRAVQKTIDREVSYVQSAANELEK 56
          Y   +  F  +++ I+R V+Y +SAA  LE+
Sbjct: 46 YRFFDHDFFGMEEAIERFVNYFKSAAQGLEE 76


>gnl|CDD|177192 MTH00134, ND1, NADH dehydrogenase subunit 1; Provisional.
          Length = 324

 Score = 25.3 bits (56), Expect = 4.5
 Identities = 20/46 (43%), Positives = 24/46 (52%), Gaps = 15/46 (32%)

Query: 12  IFILCLEHSTLKVPYEIL------NKKF------RAVQKTIDREVS 45
           +FIL L  S+L V Y IL      N K+      RAV +TI  EVS
Sbjct: 109 LFILAL--SSLAV-YSILGSGWASNSKYALIGALRAVAQTISYEVS 151


>gnl|CDD|225357 COG2766, PrkA, Putative Ser protein kinase [Signal transduction
           mechanisms].
          Length = 649

 Score = 25.1 bits (55), Expect = 7.6
 Identities = 8/23 (34%), Positives = 15/23 (65%)

Query: 33  FRAVQKTIDREVSYVQSAANELE 55
           F  ++++I++ V Y + AA  LE
Sbjct: 78  FFGMEESIEQIVGYFKHAAQGLE 100


>gnl|CDD|224680 COG1766, fliF, Flagellar basal body M-ring protein [Cell motility
           and secretion].
          Length = 545

 Score = 25.0 bits (55), Expect = 7.9
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 20  STLKVPYEIL--NKKFRAVQKTIDREVSYVQSAANELEKTIASSAQVLA 66
            +  V YE+   N KF        ++V+Y ++   EL +TI +   V A
Sbjct: 106 KSGNVGYELFDDNSKFGLTD--FMQQVNYQRALEGELARTIVAIDGVKA 152


>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
          Length = 230

 Score = 24.7 bits (55), Expect = 8.0
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 29 LNKKFRAVQKTIDREVSYVQSAANELEKTIAS 60
          L+K++RA  + +DR   Y    A  L K  A+
Sbjct: 3  LSKRYRAAAEKVDRTKLYSLEEAIALVKETAT 34


>gnl|CDD|197368 cd09851, HTLV-1-like_HR1-HR2, heptad repeat 1-heptad repeat 2
          region (ectodomain) of the transmembrane subunit of
          human T-cell leukemia virus type 1 (HTLV-1), and
          related domains.  This domain subfamily spans both
          heptad repeats of the glycoprotein
          (gp)/transmembrane(TM) subunit of various endogenous
          retroviruses (ERVs) and infectious retroviruses,
          including HTLV-1, HTLV -2, primate Mason-Pfizer monkey
          virus, Moloney murine leukemia virus, simian T-cell
          lymphotropic virus, feline leukemia virus (FeLV),
          bovine leukemia virus, and various human endogenous
          retroviruses (HERVs), including, HERV-H1_c2q24.3,
          HERV-H2_3q26, HERV-F(c)1_cXq21.33, HERV-T_19q13.11,
          Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), Syncytin-2
          (HERV-FRD_6p24.1), and related domains. This domain
          includes an N-terminal heptad repeat, a CKS17-like
          immunosuppressive region, a CX6C motif that forms an
          intrasubunit disulfide bond, and a C-terminal heptad
          repeat. N-terminal to HR1-HR2 region is a fusion
          peptide (FP), and C-terminal, is a membrane-spanning
          region (MSR). Viral infection involves the formation of
          a trimer-of-hairpins structure (three HR1s helices,
          buttressed by three HR2 helices lying in antiparallel
          orientation). In this structure, the FP (inserted in
          the host cell membrane) and MSR (inserted in the viral
          membrane) are in close proximity. ERVs are likely to
          originate from ancient germ-line infections by active
          retroviruses. Some modern ERVs, those that integrated
          into the host genome post-speciation, have a currently
          active exogenous counterpart, such as FeLV. Some ERVs
          play specific roles in the host, including placental
          development, protection of the host from infection by
          related pathogenic and exogenous retroviruses, and
          genome plasticity. Syncytin-1 and Syncytin-2 are
          expressed in the placenta, and are fusogenic, although
          they have a different cell specificity for fusion.
          Syncytin-2, but not Syncytin-1, is immunosuppressive;
          its immunosuppressive domain may protect the fetus from
          the mother's immune system. Syncytin-1 may participate
          in the formation of the placental trophoblast; it is
          also implicated in cell fusions between cancer and host
          cells and between cancer cell, and in human osteclast
          fusion. This subfamily also contains a mouse envelope
          protein encoded by the Fv-4 env gene, that blocks
          infection by exogenous MuLV.
          Length = 78

 Score = 24.1 bits (53), Expect = 8.0
 Identities = 10/47 (21%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 33 FRAVQKTIDREVSYVQSAANELEKTIASSAQVLAKN---LEVLFILQ 76
          ++++   +D ++  +  + ++L+K + S A+V+ +N   L++L + Q
Sbjct: 3  YKSLSHALDADIQRLAQSISKLQKQLTSLAEVVLQNRRGLDLLTLEQ 49


>gnl|CDD|238409 cd00794, NOS_oxygenase_prok, Nitric oxide synthase (NOS)
          prokaryotic oxygenase domain. NOS produces nitric oxide
          (NO) by catalyzing a five-electron heme-based oxidation
          of a guanidine nitrogen of L-arginine to L-citrulline
          via two successive monooxygenation reactions producing
          N(omega)-hydroxy-L-arginine (NHA) as an intermediate.
          Nitric oxide synthases are homodimers. Most prokaryotes
          produce NO as a byproduct of denitrification, using a
          completely different set of enzymes than NOS. However,
          a few prokaryotes also have a NOS, consisting solely of
          the NOS oxygenase domain. Prokaryotic NOS binds to the
          substrate L-Arg, zinc, and to the cofactors heme and
          tetrahydrofolate.
          Length = 353

 Score = 24.7 bits (54), Expect = 8.1
 Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 1/31 (3%)

Query: 25 PYEILNKKFRAVQKTIDREVSYVQSAANELE 55
              LNK+  AV+  ID   +Y  +   EL 
Sbjct: 19 ETGELNKRLAAVESEIDETGTYTHTTE-ELV 48


>gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain.  This is a family of PrkA
          bacterial and archaeal serine kinases approximately 630
          residues long. This is the N-terminal AAA domain.
          Length = 358

 Score = 24.7 bits (54), Expect = 8.4
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 31 KKFRAVQKTIDREVSYVQSAANELE 55
            F  +++TI+R V+Y + AA  LE
Sbjct: 58 ADFFGMEETIERIVNYFRHAAQGLE 82


>gnl|CDD|217540 pfam03408, Foamy_virus_ENV, Foamy virus envelope protein.
           Expression of the envelope (Env) glycoprotein is
           essential for viral particle egress. This feature is
           unique to the Spumavirinae, a subclass of the
           Retroviridae.
          Length = 985

 Score = 24.7 bits (54), Expect = 9.7
 Identities = 8/15 (53%), Positives = 12/15 (80%)

Query: 17  LEHSTLKVPYEILNK 31
           L H T++ PYEI+N+
Sbjct: 733 LTHVTIQHPYEIINQ 747


  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
   0.325    0.136    0.401 

Gapped
Lambda     K      H
   0.267   0.0788    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,503,587
Number of extensions: 342191
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 486
Number of HSP's successfully gapped: 31
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)