RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17997
(120 letters)
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 68.7 bits (168), Expect = 5e-15
Identities = 39/108 (36%), Positives = 60/108 (55%), Gaps = 3/108 (2%)
Query: 3 ENVTDLPALFSQPSQDLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYKYEPTIKMIDGPD 62
+N L +P + P FS+GI++G + L VP + K E LY Y+P +GP
Sbjct: 203 KNSVKLEMQVEKPKPEKPNTFSTGIKMGYQISL-VP-VQKSEE-ALYPYQPLNIETEGPP 259
Query: 63 YPSWDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRALNDAFAGLYHT 110
P+ +++ R YL HVR + ++ AGGY +A RAL +AF+GL+
Sbjct: 260 VPTLEELVRQGYLNHVRAASPQDIAGGYTSNLACERALQEAFSGLFWQ 307
>gnl|CDD|234091 TIGR03022, WbaP_sugtrans, Undecaprenyl-phosphate galactose
phosphotransferase, WbaP. The WbaP (formerly RfbP)
protein has been characterized as the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose to a
polyprenyl carrier (utilizing the highly conserved
C-terminal sugar transferase domain, pfam02397) a
reaction which takes place at the cytoplasmic face of
the inner membrane. The N-terminal hydrophobic domain is
then believed to facilitate the "flippase" function of
transferring the liposaccharide unit from the
cytoplasmic face to the periplasmic face of the inner
membrane. This model includes the enterobacterial
enzymes, where the function is presumed to be identical
to the S. typhimurium enzyme as well as a somewhat
broader group which are likely to catalyze the same or
highly similar reactions based on a phylogenetic
tree-building analysis of the broader sugar transferase
family. Most of these genes are found within large
operons dedicated to the production of complex
exopolysaccharides such as the enterobacterial
O-antigen. The most likely heterogeneity would be in the
precise nature of the sugar molecule transferred.
Length = 456
Score = 28.9 bits (65), Expect = 0.62
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 4 NVTDLPALFSQPSQDLPKHFSSG---IRIGSNLGLSVPAIVK 42
NV +P+LF P+ + F G +R+ +NL L ++K
Sbjct: 218 NVLIVPSLFGLPNLWISPRFIGGVLGLRVRNNLLLPSARLIK 259
>gnl|CDD|143231 cd05754, Ig3_Perlecan_like, Third immunoglobulin (Ig)-like domain
found in Perlecan and similar proteins.
Ig3_Perlecan_like: domain similar to the third
immunoglobulin (Ig)-like domain found in Perlecan.
Perlecan is a large multi-domain heparin sulfate
proteoglycan, important in tissue development and
organogenesis. Perlecan can be represented as 5 major
portions; its fourth major portion (domain IV) is a
tandem repeat of immunoglobulin-like domains (Ig2-Ig15),
which can vary in size due to alternative splicing.
Perlecan binds many cellular and extracellular ligands.
Its domain IV region has many binding sites. Some of
these have been mapped at the level of individual
Ig-like domains, including a site restricted to the Ig5
domain for heparin/sulfatide, a site restricted to the
Ig3 domain for nidogen-1 and nidogen-2, a site
restricted to Ig4-5 for fibronectin, and sites
restricted to Ig2 and to Ig13-15 for fibulin-2.
Length = 85
Score = 26.4 bits (58), Expect = 2.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 85 EKAGGYVCAIATMRALNDAFAGLY 108
AG YVC + M ++A A LY
Sbjct: 62 SDAGTYVCTGSNMLDTDEATATLY 85
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 26.5 bits (59), Expect = 4.0
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 16 SQDLPKHFSSGIRIGSNLGLSV 37
S DL F++GIR N+G+SV
Sbjct: 324 SADL---FNAGIRPAINVGISV 342
>gnl|CDD|187781 cd09650, Cas7_I, CRISPR/Cas system-associated RAMP superfamily
protein Cas7. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas7 is a RAMP superfamily protein; Subunit of the
Cascade complex; also known as MJ0381 family.
Length = 189
Score = 26.2 bits (58), Expect = 4.1
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 16/63 (25%)
Query: 54 TIKMIDGPDYPSWDDVRRGNYLKHVRTETVEEKAGGYVCAIATMRALNDAFAGLYHTNKR 113
+++ DG P G LKH + E G+ M A T +R
Sbjct: 22 KVRVGDGRVVP----YVSGEALKHALRVILVEDLFGF------MSAKKGG------TVRR 65
Query: 114 TSP 116
TSP
Sbjct: 66 TSP 68
>gnl|CDD|205259 pfam13078, DUF3942, Protein of unknown function (DUF3942). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 130 amino acids in
length.
Length = 126
Score = 25.6 bits (56), Expect = 5.5
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 48 LYKYEPTIKMIDGPDYPSWDDVRRGNYLKHVRTETVEEK 86
L K E I ++ PD+ + R H+ E V+ K
Sbjct: 33 LKKLENEIGVVKNPDFLFFTSGRN----SHIVIENVKFK 67
>gnl|CDD|180567 PRK06452, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 566
Score = 26.0 bits (57), Expect = 5.7
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 59 DGPDYPSWDDVRRGNYL 75
D PDY ++D V+ G+YL
Sbjct: 63 DNPDYMTYDTVKGGDYL 79
>gnl|CDD|181955 PRK09561, nhaA, pH-dependent sodium/proton antiporter; Reviewed.
Length = 388
Score = 26.0 bits (58), Expect = 6.4
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 76 KHVRTETVEEKAGGYVCAIATMRAL---NDAFAGLYH 109
KH+R E +GG + IA A+ N +G Y
Sbjct: 3 KHIRRFLSSEASGGILLIIAAALAMLMANSPTSGWYQ 39
>gnl|CDD|187723 cd08821, FMT_core_like_1, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 211
Score = 25.4 bits (56), Expect = 8.1
Identities = 8/22 (36%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 44 ELGPLYKYEPTIKMIDGPDYPS 65
L +Y + I+M+D YPS
Sbjct: 173 NLEKIYDF---IRMLDADGYPS 191
>gnl|CDD|218455 pfam05133, Phage_prot_Gp6, Phage portal protein, SPP1 Gp6-like.
This protein forms a hole, or portal, that enables DNA
passage during packaging and ejection. It also forms the
junction between the phage head (capsid) and the tail
proteins. During SPP1 morphogenesis, Gp6 participates in
the procapsid assembly reaction. This family also
includes the old Pfam family Phage_min_cap (PF05126).
Length = 435
Score = 25.4 bits (56), Expect = 8.1
Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 6/70 (8%)
Query: 18 DLPKHFSSGIRIGSNLGLSVPAIVKPELGPLYKYEPTIKMIDGPD-YPSWDDVRRGNYLK 76
D S + G + + E G EP I+++ +P +DD
Sbjct: 91 DFDDKLSELHKDALIYGRAYELVYIDEDG-----EPRIRVVSPEQAFPIYDDTIDRELAA 145
Query: 77 HVRTETVEEK 86
VR T ++
Sbjct: 146 AVRYYTDKDG 155
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
0.315 0.134 0.400
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,217,070
Number of extensions: 539479
Number of successful extensions: 380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 380
Number of HSP's successfully gapped: 19
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 53 (24.4 bits)