RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11790
(110 letters)
>gnl|CDD|216332 pfam01151, ELO, GNS1/SUR4 family. Members of this family are
involved in long chain fatty acid elongation systems
that produce the 26-carbon precursors for ceramide and
sphingolipid synthesis. Predicted to be integral
membrane proteins, in eukaryotes they are probably
located on the endoplasmic reticulum. Yeast ELO3 affects
plasma membrane H+-ATPase activity, and may act on a
glucose-signaling pathway that controls the expression
of several genes that are transcriptionally regulated by
glucose such as PMA1.
Length = 244
Score = 59.9 bits (146), Expect = 3e-12
Identities = 18/49 (36%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 53 WLIIGTLVVYLAFVLHIGPKYMKDRKPMNIKYIILAYNLFQTVYNAWIV 101
W +I +V+YL FV +GPK M++RKP ++K +++ +NLF + + +
Sbjct: 7 WPVILIIVLYLVFV-FLGPKIMRNRKPFDLKRLLIVHNLFLVLLSLYGF 54
>gnl|CDD|227835 COG5548, COG5548, Small integral membrane protein [Function
unknown].
Length = 105
Score = 31.4 bits (71), Expect = 0.037
Identities = 14/57 (24%), Positives = 24/57 (42%)
Query: 45 FLISSNSSWLIIGTLVVYLAFVLHIGPKYMKDRKPMNIKYIILAYNLFQTVYNAWIV 101
+L +W +I VV A ++ + ++ RKP+ L L VY +V
Sbjct: 46 YLQLQGQTWGLILATVVSAALLVFFALRLVRSRKPVPAGLTTLGGMLSLYVYVNQMV 102
>gnl|CDD|202717 pfam03647, Tmemb_14, Transmembrane proteins 14C. This family of
short membrane proteins are as yet uncharacterized.
Length = 96
Score = 26.8 bits (60), Expect = 1.1
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 45 FLISSNSSWLIIGTLVVYLAFVLHIGPKYMKDRKPM 80
+L+S N + + L+ +GP+Y+K RK M
Sbjct: 43 YLLSQNQPYGLELALLASAVLAGVMGPRYIKTRKFM 78
>gnl|CDD|238235 cd00403, Ribosomal_L1, Ribosomal protein L1. The L1 protein,
located near the E-site of the ribosome, forms part of
the L1 stalk along with 23S rRNA. In bacteria and
archaea, L1 functions both as a ribosomal protein that
binds rRNA, and as a translation repressor that binds
its own mRNA. Like several other large ribosomal
subunit proteins, L1 displays RNA chaperone activity.
L1 is one of the largest ribosomal proteins. It is
composed of two domains that cycle between open and
closed conformations via a hinge motion. The RNA-binding
site of L1 is highly conserved, with both mRNA and rRNA
binding the same binding site.
Length = 208
Score = 26.4 bits (59), Expect = 3.5
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 17 VSWAPNFIRDNVQVVLNELVEDKEVDKWFLISS 49
VS +P + +N++ V+N LV+ K I S
Sbjct: 163 VSMSPEQLVENIEAVINALVKKLPSKKGQNIKS 195
>gnl|CDD|234382 TIGR03891, thiopep_ocin, thiopeptide-type bacteriocin
biosynthesis domain. This domain occurs within longer
proteins that contain lantibiotic dehydratase domains
(see pfam04737 and pfam04738), and as single-domain
proteins in bacteriocin biosynthesis genomic contexts.
Three named genes in this family, SioK in Streptomyces
sioyaensis, TsrD in Streptomyces laurentii, and NosD in
Streptomyces actuosus, all occur in regions associated
with thiopeptide biosynthesis [Cellular processes,
Toxin production and resistance].
Length = 263
Score = 26.2 bits (58), Expect = 3.8
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 20 APNFIRDNVQVVLNELVEDKEVDKWFLI 47
A + D++ +L+EL +DKWF I
Sbjct: 13 ADELLADHLPPLLDELEAAGLIDKWFFI 40
>gnl|CDD|225716 COG3175, COX11, Cytochrome oxidase assembly factor
[Posttranslational modification, protein turnover,
chaperones].
Length = 195
Score = 26.2 bits (58), Expect = 4.0
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 66 VLHIGPKYMKDRKPMNIKYIILAYNLFQTVY 96
V + P + D + ++K I L+Y F
Sbjct: 150 VFFVDPDFADDPEMKDVKTITLSYTFFPIRE 180
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 26.2 bits (58), Expect = 4.0
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 45 FLISSNSSWLIIGTLVVYLAFVLHIGP 71
F S + ++IG+LV Y + +GP
Sbjct: 274 FFYSPTLTGVVIGSLVCYALLSVFVGP 300
>gnl|CDD|213274 cd05906, A_NRPS_TubE_like, The adenylation domain (A domain) of a
family of nonribosomal peptide synthetases (NRPSs)
synthesizing toxins and antitumor agents. The
adenylation (A) domain of NRPS recognizes a specific
amino acid or hydroxy acid and activates it as an
(amino)-acyl adenylate by hydrolysis of ATP. The
activated acyl moiety then forms a thioester to the
enzyme-bound cofactor phosphopantetheine of a peptidyl
carrier protein domain. This family includes NRPSs that
synthesize toxins and antitumor agents; for example,
TubE for Tubulysine, CrpA for cryptophycin, TdiA for
terrequinone A, KtzG for kutzneride, and Vlm1/Vlm2 for
Valinomycin. Nonribosomal peptide synthetases are large
multifunctional enzymes which 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 = 560
Score = 26.1 bits (58), Expect = 4.2
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 17 VSWAPNFIRDNVQVVLNELVEDKEVDKWFL 46
++WAPNF +LN+ +E E W L
Sbjct: 263 ITWAPNF----AFALLNDALERIEDRSWDL 288
>gnl|CDD|172795 PRK14319, glmM, phosphoglucosamine mutase; Provisional.
Length = 430
Score = 26.0 bits (57), Expect = 5.1
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 3/43 (6%)
Query: 1 MQTISTEAATGFKMALVSWAPNFIRDNVQVVLNELVEDKEVDK 43
++T+S +G K++ +S N I D QV++N V++KEV K
Sbjct: 333 LETLSVMVKSGKKLSDLS---NEIPDYPQVMINVKVKNKEVYK 372
>gnl|CDD|218089 pfam04442, CtaG_Cox11, Cytochrome c oxidase assembly protein
CtaG/Cox11. Cytochrome c oxidase assembly protein is
essential for the assembly of functional cytochrome
oxidase protein. In eukaryotes it is an integral protein
of the mitochondrial inner membrane. Cox11 is essential
for the insertion of Cu(I) ions to form the CuB site.
This is essential for the stability of other structures
in subunit I, for example haems a and a3, and the
magnesium/manganese centre. Cox11 is probably only
required in sub-stoichiometric amounts relative to the
structural units. The C terminal region of the protein
is known to form a dimer. Each monomer coordinates one
Cu(I) ion via three conserved cysteine residues (111,
208 and 210) in Saccharomyces cerevisiae. Met 224 is
also thought to play a role in copper transfer or
stabilising the copper site.
Length = 150
Score = 25.2 bits (56), Expect = 7.9
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 69 IGPKYMKDRKPMNIKYIILAYNLF 92
I P+ +D + ++K I L+Y F
Sbjct: 126 IDPELPEDPELKDVKTITLSYTFF 149
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 0.138 0.421
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,584,994
Number of extensions: 473897
Number of successful extensions: 713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 711
Number of HSP's successfully gapped: 43
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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)