RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12513
(159 letters)
>gnl|CDD|216833 pfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit. This
family includes the vacuolar ATP synthase E subunit, as
well as the archaebacterial ATP synthase E subunit.
Length = 195
Score = 51.2 bits (123), Expect = 1e-08
Identities = 24/68 (35%), Positives = 43/68 (63%)
Query: 64 FIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKYRQVELRHRTDCSNIKS 123
FI+ EA+EK ++IR + EE+++IE+ + + ++E Y KK +Q E+ + SN K+
Sbjct: 1 FIRQEAEEKAEEIRAEAEEEFEIEKAEAVEEAEKKIEEIYEKKEKQAEMEKQIIISNAKN 60
Query: 124 EGRMNVMR 131
E R+ V+
Sbjct: 61 EARLKVLN 68
>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy
production and conversion].
Length = 194
Score = 37.4 bits (87), Expect = 0.001
Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 58 IERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKYRQVELRHRTD 117
+E+++ I EA+E+ ++I + E+ + +E R+ + +++E K ++ E +
Sbjct: 4 LEKLIKKILREAEEEAEEILEEAREEAEKIKEEAKREAEEAIEEILRKAEKEAERERQRI 63
Query: 118 CSNIKSEGRMNVMRLNA 134
S+ E L A
Sbjct: 64 ISSALLE--ARRKLLEA 78
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 29.9 bits (68), Expect = 0.56
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 114 HRTDCSNIKSEGRMNVMRLNAARWSYDTGRIVPINIKSEG 153
HR DC N R+ W + G++ P++I+
Sbjct: 595 HRQDCPNFLQLAGHAPERVIDVSWGPEYGQVYPVDIEIRA 634
>gnl|CDD|217591 pfam03492, Methyltransf_7, SAM dependent carboxyl
methyltransferase. This family of plant
methyltransferases contains enzymes that act on a
variety of substrates including salicylic acid, jasmonic
acid and 7-Methylxanthine. Caffeine is synthesised
through sequential three-step methylation of xanthine
derivatives at positions 7-N, 3-N, and 1-N. The protein
7-methylxanthine methyltransferase (designated as
CaMXMT) catalyzes the second step to produce
theobromine.
Length = 331
Score = 29.2 bits (66), Expect = 0.80
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 25/91 (27%)
Query: 43 TLLGMALDDAAVEKQIERMVAFIQTEADEKLD------------DIRRKIEED--YQIER 88
LLG AL+D E IE EKLD +++ IE++ + IER
Sbjct: 198 DLLGDALNDLVSEGLIEE----------EKLDSFNIPIYAPSPEEVKEIIEKEGSFTIER 247
Query: 89 ERVTRDGKASVD-EEYAKKYRQVELRHRTDC 118
+ + V +E + + + R
Sbjct: 248 LEIIKHPNGEVPWDESDSEDKVEDGRFVASS 278
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome partitioning].
Length = 1480
Score = 29.1 bits (65), Expect = 1.1
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 57 QIERMVAFIQTEADEKLDDIRRKIEEDYQIERERV 91
Q+E+ + F + E D L RK+E DY RE+V
Sbjct: 1077 QLEKQLTFCEAEMD-NLTRKLRKLERDYFEMREQV 1110
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 28.5 bits (64), Expect = 1.8
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 50 DDAAVEKQIERMVAFIQTE-----ADEKLDDIRRKIEEDYQIERERVTRDGKASVDE 101
D E I+RM ++ L+++ R+I+ED + R + K +
Sbjct: 558 DPEVFEGLIKRMSWKFIEIEFKEISEVDLEELLREIDEDRERVRRVLEGKLKEETKD 614
>gnl|CDD|222566 pfam14134, DUF4301, Domain of unknown function (DUF4301). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 505 and 516 amino
acids in length.
Length = 513
Score = 28.3 bits (64), Expect = 2.1
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 48 ALDDAAV-EKQIERMVAFIQTEADEKLDDIRRKIEEDYQIER 88
LD V E+++E +V F++ E KL + K ++ IE
Sbjct: 327 LLDKGKVSEEELEEIVDFLEDELCIKLPEDFEKFSDEELIEY 368
>gnl|CDD|217072 pfam02503, PP_kinase, Polyphosphate kinase middle domain.
Polyphosphate kinase (Ppk) catalyzes the formation of
polyphosphate from ATP, with chain lengths of up to a
thousand or more orthophosphate molecules.
Length = 204
Score = 27.5 bits (62), Expect = 2.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 79 KIEEDYQIERERVTRDGKASVDEEYAKKYRQV---ELRHR 115
++ Y RVTRD +DEE A+ + EL+ R
Sbjct: 98 EVLGAYAF---RVTRDADLEIDEEEAEDLLEAIEKELKKR 134
>gnl|CDD|219342 pfam07227, DUF1423, Protein of unknown function (DUF1423). This
family represents a conserved region approximately 500
residues long within a number of Arabidopsis thaliana
proteins of unknown function.
Length = 446
Score = 27.8 bits (62), Expect = 3.0
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 57 QIERMVAFIQTEAD---EKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 112
++E +V Q EAD K D+ RR+ E +R+ +EEYA KY ++ L
Sbjct: 354 ELESIVRLKQAEADMFQLKADEARREAER-----LQRIALAKTEKSEEEYASKYLKLRL 407
>gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional.
Length = 214
Score = 27.3 bits (60), Expect = 3.5
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 76 IRRKIEED------YQIERERVTRDGKASVDEEYAKKYRQVELRHRTDCSNIKSEGRMNV 129
+RR++ E Y+ E R+ R+G + D + + + HR + +KS R+ +
Sbjct: 10 LRRRLAETHLRAEVYREETLRLHREGVGTQDPRFVGAFMAAKAAHRELEARLKSRARLEM 69
Query: 130 MRLNAA 135
+R +AA
Sbjct: 70 LRQHAA 75
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13. This model
describes bacterial ribosomal protein S13, to the
exclusion of the homologous archaeal S13P and eukaryotic
ribosomal protein S18. This model identifies some (but
not all) instances of chloroplast and mitochondrial S13,
which is of bacterial type [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 113
Score = 26.3 bits (59), Expect = 3.8
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 70 DEKLDDIRRKIEEDYQIE---RERVTRDGKASVDEEYAKKYRQVELRHR 115
+E+L+ IR +IE Y++E R V+ + K +D YR LRHR
Sbjct: 48 EEELNAIREEIEAKYKVEGDLRREVSLNIKRLMD---IGCYRG--LRHR 91
>gnl|CDD|187614 cd05356, 17beta-HSD1_like_SDR_c, 17-beta-hydroxysteroid
dehydrogenases (17beta-HSDs) types -1, -3, and -12,
-like, classical (c) SDRs. This subgroup includes
various 17-beta-hydroxysteroid dehydrogenases and
3-ketoacyl-CoA reductase, these are members of the SDR
family, and contain the canonical active site tetrad
and glycine-rich NAD-binding motif of the classical
SDRs. 3-ketoacyl-CoA reductase (KAR, aka 17beta-HSD
type 12, encoded by HSD17B12) acts in fatty acid
elongation; 17beta- hydroxysteroid dehydrogenases are
isozymes that catalyze activation and inactivation of
estrogen and androgens, and include members of the SDR
family. 17beta-estradiol dehydrogenase (aka 17beta-HSD
type 1, encoded by HSD17B1) converts estrone to
estradiol. Estradiol is the predominant female sex
hormone. 17beta-HSD type 3 (aka testosterone
17-beta-dehydrogenase 3, encoded by HSD17B3) catalyses
the reduction of androstenedione to testosterone, it
also accepts estrogens as substrates. This subgroup
also contains a putative steroid dehydrogenase let-767
from Caenorhabditis elegans, mutation in which results
in hypersensitivity to cholesterol limitation. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 239
Score = 27.2 bits (61), Expect = 4.1
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 71 EKLDDIRRKIEEDYQIE 87
EKLD + ++IEE Y +E
Sbjct: 36 EKLDAVAKEIEEKYGVE 52
>gnl|CDD|179208 PRK01026, PRK01026, tetrahydromethanopterin S-methyltransferase
subunit G; Provisional.
Length = 77
Score = 25.7 bits (57), Expect = 4.2
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 68 EADEKLDDIRRKIE----EDYQIERERVTRD 94
E ++LD+I K+E E +Q ++V RD
Sbjct: 19 EIQKRLDEIEEKVEFTNAEIFQRIGKKVGRD 49
>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
functions primarily to fill DNA gaps that arise during
DNA repair, recombination and replication. DNA-dependent
DNA polymerases can be classified in six main groups
based upon phylogenetic relationships with E. coli
polymerase I (classA), E. coli polymerase II (class B),
E.coli polymerase III (class C), euryarchaaeota
polymerase II (class D), human polymerase beta (class
x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma
pigmentosum variant (class Y). Family A polymerase are
found primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I ,mitochondrial
polymerase delta, and several bacteriphage polymerases
including those from odd-numbered phage (T3, T5, and
T7). Prokaryotic Pol Is have two functional domains
located on the same polypeptide; a 5'-3' polymerase and
5'-3' exonuclease. Pol I uses its 5' nuclease activity
to remove the ribonucleotide portion of newly
synthesized Okazaki fragments and DNA polymerase
activity to fill in the resulting gap. A combination of
phylogenomic and signature sequence-based (or phonetic)
approaches is used to understand the evolutionary
relationships among bacteria. DNA polymerase I is one of
the conserved proteins that is used to search for
protein signatures. The structure of these polymerases
resembles in overall morphology a cupped human right
hand, with fingers (which bind an incoming nucleotide
and interact with the single-stranded template), palm
(which harbors the catalytic amino acid residues and
also binds an incoming dNTP) and thumb (which binds
double-stranded DNA) subdomains.
Length = 429
Score = 27.0 bits (60), Expect = 5.5
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 74 DDIRRKIEEDYQIERERVTRDGKASVDEEYAKK 106
I ++++ Y E + T G+ VDE+ K
Sbjct: 71 KHIAKRLKAKYGWEPQEFTESGEPKVDEDVLSK 103
>gnl|CDD|218215 pfam04696, Pinin_SDK_memA, pinin/SDK/memA/ protein conserved
region. Members of this family have very varied
localisations within the eukaryotic cell. pinin is known
to localise at the desmosomes and is implicated in
anchoring intermediate filaments to the desmosomal
plaque. SDK2/3 is a dynamically localised nuclear
protein thought to be involved in modulation of
alternative pre-mRNA splicing. memA is a tumour marker
preferentially expressed in human melanoma cell lines. A
common feature of the members of this family is that
they may all participate in regulating protein-protein
interactions.
Length = 131
Score = 26.3 bits (58), Expect = 6.0
Identities = 13/47 (27%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 67 TEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKYRQVELR 113
T +++ +I +K+EE + ERE + ++ + +E ++ +Q+ELR
Sbjct: 31 TSKEKRRAEIEQKLEEQEKQEREELRKEKRELFEE---RRRKQLELR 74
>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase.
Length = 455
Score = 26.7 bits (59), Expect = 6.4
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 40 PPPTLLGMALDDAAV-EKQIERMVAFIQTEADEKLDDIRRKIEEDYQIE 87
P P LL D EK I + I+ E +++++ + ++ E ++
Sbjct: 358 PEPPLLERLEKDVEEGEKTIVKEARQIEEELEKEVEKLGKEEESLFKRV 406
>gnl|CDD|113000 pfam04210, MtrG, Tetrahydromethanopterin S-methyltransferase,
subunit G. The N5-methyltetrahydromethanopterin:
coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is
a membrane-associated, corrinoid-containing protein
that uses a transmethylation reaction to drive an
energy-conserving sodium ion pump.
Length = 70
Score = 25.1 bits (55), Expect = 6.5
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 68 EADEKLDDIRRKIE----EDYQIERERVTRD 94
E ++LD+I K+E E YQ ++V RD
Sbjct: 16 EIHKRLDEIEEKVEFVNGEVYQRIGKKVGRD 46
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 26.8 bits (60), Expect = 6.9
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 50 DDAAVEKQIERMVAFIQ----TEADE-KLDDIRRKIEEDYQIERERVTRDGKASVD 100
D+ E +++ + E L+++ R+I+ED RER+ R ++
Sbjct: 548 DEKLFESLKKKLRWLLPEIEFKPLSEVDLEELLREIDED----RERIRRVERSKDL 599
>gnl|CDD|239823 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein
(RNP) domain. RpoE (subunit E) is a subunit of the
archaeal RNA polymerase (RNAP) that is homologous to
Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP
III, and Rpa43 of eukaryotic RNAP I. RpoE
heterodimerizes with RpoF, another RNA polymerase
subunit. RpoE has an elongated two-domain structure
that includes an N-terminal RNP domain and a C-terminal
oligonucleotide-binding (OB) domain. Both domains of
RpoE bind single-stranded RNA.
Length = 80
Score = 25.2 bits (56), Expect = 7.4
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 36 DIFRPPPTLLGMALDDAAVE 55
D+ R PP L G L++A +E
Sbjct: 8 DVVRVPPELFGEDLEEAVLE 27
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 26.4 bits (58), Expect = 7.7
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 52 AAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRD--GKASVDEEYAKK 106
AAVE+++ +V I +E+ D+R++ E + +ER+ D G+ S D E +
Sbjct: 218 AAVERRLAELVEMINWNLEERRRDLRKEQELEENVERDSDDEDEHGEDSEDGETKPE 274
>gnl|CDD|220397 pfam09781, NDUF_B5, NADH:ubiquinone oxidoreductase, NDUFB5/SGDH
subunit. Members of this family mediate the transfer of
electrons from NADH to the respiratory chain. The
immediate electron acceptor for the enzyme is believed
to be ubiquinone, the reaction that occurs being: NADH +
ubiquinone = NAD(+) + ubiquinol.
Length = 182
Score = 25.9 bits (57), Expect = 7.9
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 15/61 (24%)
Query: 55 EKQIERMVAFIQTEADEKLD------DIRRKIEE--DYQ------IERERVTRDGKASVD 100
+K+ E+M+A IQ E EK + ++RR + E D I++E + KA+ D
Sbjct: 123 QKEYEKMLALIQEEN-EKAEIRLLELEVRRLMRERGDGPWYYYRTIDKELIDHSPKATPD 181
Query: 101 E 101
Sbjct: 182 N 182
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 26.5 bits (59), Expect = 8.6
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 57 QIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVT 92
Q+E+ + F + E D +R K+E DY RE+V
Sbjct: 1078 QLEKQLTFCEAEMDNLTKKLR-KLERDYHEMREQVV 1112
>gnl|CDD|150099 pfam09320, DUF1977, Domain of unknown function (DUF1977). Members
of this family of functionally uncharacterized domains
are predominantly found in dnaj-like proteins.
Length = 107
Score = 25.3 bits (56), Expect = 9.1
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 14/64 (21%)
Query: 71 EKLDDIRRKIEEDY------QIERERVTRDGKA-----SVDEEYAKKYRQVELRHRTDCS 119
KL ++ +K+EEDY ERE+ +D DE+ KK +E C
Sbjct: 46 SKLAELEKKVEEDYVQNLRNNCEREKQRKDQLLNRARFFGDEDLLKKAESMETPS---CE 102
Query: 120 NIKS 123
+
Sbjct: 103 KLND 106
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
0.319 0.134 0.374
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: 8,139,514
Number of extensions: 761635
Number of successful extensions: 1104
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1097
Number of HSP's successfully gapped: 109
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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 (21.8 bits)
S2: 55 (24.9 bits)