RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9580
(71 letters)
>gnl|CDD|234676 PRK00172, rpmI, 50S ribosomal protein L35; Reviewed.
Length = 65
Score = 66.7 bits (164), Expect = 7e-17
Identities = 34/63 (53%), Positives = 43/63 (68%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
K+KTKS A KRF + G +KR A KRHILTKKSTK KR+LRG V K++ V+ M+
Sbjct: 3 KMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRML 62
Query: 69 PNS 71
P +
Sbjct: 63 PYA 65
>gnl|CDD|223368 COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal
structure and biogenesis].
Length = 65
Score = 57.2 bits (139), Expect = 4e-13
Identities = 33/61 (54%), Positives = 40/61 (65%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
K+KTK A KRF I G IKR A KRHILTKKSTK KR LR A V K+++ V+ ++
Sbjct: 3 KMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRLL 62
Query: 69 P 69
Sbjct: 63 L 63
>gnl|CDD|129113 TIGR00001, rpmI_bact, ribosomal protein L35. This ribosomal
protein is found in bacteria and organelles only. It is
not closely related to any eukaryotic or archaeal
ribosomal protein [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 63
Score = 54.6 bits (132), Expect = 4e-12
Identities = 30/61 (49%), Positives = 40/61 (65%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
K+KT +A KRF I G IKR +A KRH+LTKKS+K KR LR A V ++ V+ ++
Sbjct: 2 KMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLLL 61
Query: 69 P 69
P
Sbjct: 62 P 62
>gnl|CDD|145004 pfam01632, Ribosomal_L35p, Ribosomal protein L35.
Length = 61
Score = 48.4 bits (116), Expect = 9e-10
Identities = 30/60 (50%), Positives = 38/60 (63%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
K+KT +A KRF G IKR +A KRH+LTKKSTK KR+LR V KS+ V ++
Sbjct: 2 KMKTVKAAAKRFKRTASGKIKRRKAGKRHLLTKKSTKRKRRLRKKVLVSKSDAKRVDKLL 61
>gnl|CDD|214367 CHL00103, rpl35, ribosomal protein L35.
Length = 65
Score = 39.7 bits (93), Expect = 4e-06
Identities = 26/61 (42%), Positives = 37/61 (60%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
K+KT+ +A KR+ G R +AFK H+L KKS+K KRKL V K + S++ M+
Sbjct: 3 KLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLML 62
Query: 69 P 69
P
Sbjct: 63 P 63
>gnl|CDD|218463 pfam05141, DIT1_PvcA, Pyoverdine/dityrosine biosynthesis protein.
This family includes DIT1 that is involved in
synthesising dityrosine. Dityrosine is a
sporulation-specific component of the yeast ascospore
wall that is essential for the resistance of the spores
to adverse environmental conditions. P. aeruginosa pvcA
is involved in the biosynthesis of pyoverdine.
Length = 274
Score = 26.0 bits (58), Expect = 1.7
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 11 KTKSSAKKRFFIRTGGVIKRGQAF 34
+K + KK R G+IKRG+AF
Sbjct: 178 GSKKALKKDAKARAYGMIKRGKAF 201
>gnl|CDD|236826 PRK11031, PRK11031, guanosine pentaphosphate phosphohydrolase;
Provisional.
Length = 496
Score = 25.3 bits (56), Expect = 3.1
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 44 TKVKRKLRGLASVHKSNIASVRAM 67
++KRK+R A + N S AM
Sbjct: 34 ARIKRKVRLAAGLDSDNALSNEAM 57
>gnl|CDD|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase. The
eukaryotic RPB11 subunit of RNA polymerase (RNAP), as
well as its archaeal (L subunit) and bacterial (alpha
subunit) counterparts, is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III, for the synthesis of
ribosomal RNA precursor, mRNA precursor, and 5S and
tRNA, respectively. A single distinct RNAP complex is
found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. The assembly
of the two largest eukaryotic RNAP subunits that
provide most of the enzyme's catalytic functions
depends on the presence of RPB3/RPB11 heterodimer
subunits. This is also true for the archaeal (D/L
subunits) and bacterial (alpha subunit) counterparts.
Length = 83
Score = 24.4 bits (53), Expect = 3.3
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 4 LFSVFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHI 38
F+ + IK K + I+T IK A KR +
Sbjct: 37 DFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAV 71
>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 25.2 bits (56), Expect = 3.3
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 16 AKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLR 51
+KR +R G K G K L K + ++ L
Sbjct: 211 PRKRIEVRAGETSK-GVTVKDPELFKLAERLAEALG 245
>gnl|CDD|151880 pfam11441, MxiM, Pilot protein MxiM. MxiM, a Shigella pilot
protein, is essential for the assembly and membrane
association of the Shigella secretin MxiD. MxiM contains
an orthologous secretin component and has a specific
binding domain for the acyl chains of bacterial lipids.
The C terminal domain of MxiD hinders lipid binding to
MxiM.
Length = 115
Score = 24.3 bits (52), Expect = 5.4
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 1 MKELFSVFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKL-RGL 53
+KE+ F K + K F + GV+ +G IL +K +VK KL RG+
Sbjct: 62 VKEVDGCFMDAQKIAIDKLFSMLKDGVVLKGNKINDTILIEKDGEVKLKLIRGI 115
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
0.322 0.131 0.348
Gapped
Lambda K H
0.267 0.0528 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,314,692
Number of extensions: 236650
Number of successful extensions: 248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 12
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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: 40 (21.5 bits)
S2: 53 (24.7 bits)