RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13494
(143 letters)
>gnl|CDD|148383 pfam06747, CHCH, CHCH domain. we have identified a conserved
motif in the LOC118487 protein that we have called the
CHCH motif. Alignment of this protein with related
members showed the presence of three subgroups of
proteins, which are called the S (Small), N (N-terminal
extended) and C (C-terminal extended) subgroups. All
three sub-groups of proteins have in common that they
contain a predicted conserved [coiled coil 1]-[helix
1]-[coiled coil 2]-[helix 2] domain (CHCH domain).
Within each helix of the CHCH domain, there are two
cysteines present in a C-X9-C motif. The N-group
contains an additional double helix domain, and each
helix contains the C-X9-C motif. This family contains a
number of characterized proteins: Cox19 protein - a
nuclear gene of Saccharomyces cerevisiae, codes for an
11-kDa protein (Cox19p) required for expression of
cytochrome oxidase. Because cox19 mutants are able to
synthesise the mitochondrial and nuclear gene products
of cytochrome oxidase, Cox19p probably functions
post-translationally during assembly of the enzyme.
Cox19p is present in the cytoplasm and mitochondria,
where it exists as a soluble intermembrane protein.
This dual location is similar to what was previously
reported for Cox17p, a low molecular weight copper
protein thought to be required for maturation of the
CuA centre of subunit 2 of cytochrome oxidase. Cox19p
have four conserved potential metal ligands, these are
three cysteines and one histidine. Mrp10 - belongs to
the class of yeast mitochondrial ribosomal proteins
that are essential for translation. Eukaryotic
NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit.
The CHCH domain was previously called DUF657.
Length = 35
Score = 34.5 bits (80), Expect = 9e-04
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 59 CGVQFREAFSCFHYSTDEPKGVNCFEAFKTMQDCMAQ 95
CG +F+ C ++DE C + F + C+ +
Sbjct: 1 CGEEFKAFLKCLKENSDE--LSKCRKEFDAFRQCVKK 35
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 32.2 bits (74), Expect = 0.085
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 104 DDDDEDLDDVKDESIRKEAQEKADRIIEQADSG 136
D + +D KDE + EA+ ++I Q + G
Sbjct: 590 GRKDIEAEDEKDEIVI-EAEGSVLKLILQYEEG 621
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the CF(0)
(base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the ab
CF(1) proteins (in the head of the ATP synthase) which
are found in pfam00006.
Length = 132
Score = 30.7 bits (70), Expect = 0.14
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 116 ESIRKEAQEKADRIIEQA 133
E I EAQ+ A+R++E A
Sbjct: 83 EEILAEAQKDAERLLESA 100
>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
Length = 156
Score = 30.5 bits (70), Expect = 0.17
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 116 ESIRKEAQEKADRIIEQADS 135
E + EA+ +A RI QA +
Sbjct: 88 EEAKAEAEAEAARIKAQAQA 107
>gnl|CDD|218640 pfam05565, Sipho_Gp157, Siphovirus Gp157. This family contains
both viral and bacterial proteins which are related to
the Gp157 protein of the Streptococcus thermophilus SFi
bacteriophages. It is thought that bacteria possessing
the gene coding for this protein have an increased
resistance to the bacteriophage.
Length = 162
Score = 30.3 bits (69), Expect = 0.22
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 91 DCMAQYPTLYKQNDDDDEDLDDVKD--ESIRKEAQEKADRIIEQADS 135
+ QY L + +D D D + + D ESI +E ++K + I + +
Sbjct: 5 ELTGQYKELLELLEDGDLDPEALADTLESIEEEFEDKVENIAKVIKN 51
>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 = 30.4 bits (69), Expect = 0.23
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 118 IRKEAQEKADRIIEQAD 134
IR+EA+EKA+ I +A+
Sbjct: 2 IRQEAEEKAEEIRAEAE 18
>gnl|CDD|180481 PRK06231, PRK06231, F0F1 ATP synthase subunit B; Validated.
Length = 205
Score = 30.2 bits (68), Expect = 0.24
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 116 ESIRKEAQEKADRIIEQA 133
+ KEA +A+ II QA
Sbjct: 132 SELEKEANRQANLIIFQA 149
>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy
production and conversion].
Length = 194
Score = 29.6 bits (67), Expect = 0.42
Identities = 9/26 (34%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 109 DLDDVKDESIRKEAQEKADRIIEQAD 134
+L+ + + I +EA+E+A+ I+E+A
Sbjct: 3 ELEKLIKK-ILREAEEEAEEILEEAR 27
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 28.8 bits (65), Expect = 0.78
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 101 KQNDDDDEDLDDVKDESIRKEAQEKADRIIEQA 133
+ ++ L + + E +EA+E+A IIEQA
Sbjct: 51 RLKEEAQALLAEYEQE--LEEAREQASEIIEQA 81
Score = 27.6 bits (62), Expect = 1.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 116 ESIRKEAQEKADRIIEQA 133
E I+ EA+E+ +RI E A
Sbjct: 90 EEIKAEAEEELERIKEAA 107
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 28.4 bits (64), Expect = 0.96
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 6/30 (20%)
Query: 110 LDDVKDES------IRKEAQEKADRIIEQA 133
++D++DE+ IR EA E+A+ II +A
Sbjct: 7 VEDIRDEARARASEIRAEADEEAEEIIAEA 36
>gnl|CDD|179204 PRK01005, PRK01005, V-type ATP synthase subunit E; Provisional.
Length = 207
Score = 28.2 bits (63), Expect = 1.1
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 98 TLYKQNDDDDEDLDDVKD--ESIRKEAQEKADRIIEQADSGSSHTNKK 143
TL ++ + + K+ + I EAQE+A++II A+ + K+
Sbjct: 21 TLKPAEEEAGAIVHNAKEQAKRIIAEAQEEAEKIIRSAEETADQKLKQ 68
>gnl|CDD|215121 PLN02189, PLN02189, cellulose synthase.
Length = 1040
Score = 28.8 bits (64), Expect = 1.2
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 83 FEAFKTMQDCMAQYPTLYK--------QNDDDDEDLDDVKDESIRKEAQEKADRIIE 131
+E + Q+C Q T YK + DDD+ED+DD++ E + Q+K I E
Sbjct: 70 YERREGTQNC-PQCKTRYKRLKGSPRVEGDDDEEDIDDIEHEFNIDDEQDKNKHITE 125
>gnl|CDD|233860 TIGR02421, QEGLA, conserved hypothetical protein. Members of this
family include a possible metal-binding motif HEXXXH
and, nearby, a perfectly conserved motif QEGLA. All
members belong to the Proteobacteria, including
Agrobacterium tumefaciens and several species of Vibrio
and Pseudomonas, and are found in only one copy per
chromosome (Vibrio vulnificus, with two chromosomes, has
two). The function is unknown.
Length = 366
Score = 28.1 bits (63), Expect = 1.5
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 71 HYSTDEPKGVNCFEAFKTMQDCMAQY 96
+E V+ EA + +Q + Y
Sbjct: 125 AMEEEEQAPVSATEAAEILQQRLEDY 150
>gnl|CDD|237138 PRK12563, PRK12563, sulfate adenylyltransferase subunit 2;
Provisional.
Length = 312
Score = 27.8 bits (62), Expect = 2.0
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 104 DDDDEDLDDVKDESIRKEAQEKADRIIEQADSGSSHTNKK 143
+ D + ++ + E E+ R+I+Q + S KK
Sbjct: 269 ESDADTVEKIIQEMAVTRISERQGRMIDQDSAASMEKKKK 308
>gnl|CDD|176962 CHL00019, atpF, ATP synthase CF0 B subunit.
Length = 184
Score = 27.5 bits (62), Expect = 2.1
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 99 LYKQNDDDDEDLDDVKDESIRKEAQEKADRIIEQ 132
L Q +D E L++ K+E+IR E Q R I Q
Sbjct: 110 LINQAKEDLERLENYKNETIRFEQQ----RAINQ 139
>gnl|CDD|145928 pfam03040, CemA, CemA family. Members of this family are probable
integral membrane proteins. Their molecular function is
unknown. CemA proteins are found in the inner envelope
membrane of chloroplasts but not in the thylakoid
membrane. A cyanobacterial member of this family has
been implicated in CO2 transport, but is probably not a
CO2 transporter itself. They are predicted to be
haem-binding however this has not been proven
experimentally.
Length = 230
Score = 27.5 bits (62), Expect = 2.4
Identities = 5/33 (15%), Positives = 13/33 (39%)
Query: 108 EDLDDVKDESIRKEAQEKADRIIEQADSGSSHT 140
++ + +R E +KA + + + S
Sbjct: 75 KESPPTSLQELRIEIHKKAIELAKIYNEESIQA 107
>gnl|CDD|225368 COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy
production and conversion].
Length = 108
Score = 26.6 bits (59), Expect = 3.0
Identities = 14/31 (45%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 105 DDDEDLDDVKDES--IRKEAQEKADRIIEQA 133
DE++++ K+E+ I KEA+E+A IIE+A
Sbjct: 18 SADEEIEEAKEEAEQIIKEAREEAREIIEEA 48
Score = 26.2 bits (58), Expect = 3.6
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 115 DESIRKEAQEKADRIIEQADSGSSHTNKK 143
E R+EA+E+A+ I+ +A+ +S K
Sbjct: 60 LEEAREEAEEEAEEILAEAEKEASAILSK 88
>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model
describes the F1/F0 ATP synthase b subunit in bacteria
only. Scoring just below the trusted cutoff are the
N-terminal domains of Mycobacterial b/delta fusion
proteins and a subunit from an archaeon, Methanosarcina
barkeri, in which the ATP synthase homolog differs in
architecture and is not experimentally confirmed. This
model helps resolve b from the related b' subunit.
Within the family is an example from a
sodium-translocating rather than proton-translocating
ATP synthase [Energy metabolism, ATP-proton motive force
interconversion].
Length = 147
Score = 26.6 bits (59), Expect = 3.3
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 116 ESIRKEAQEKADRIIEQA 133
E + EA+E+ ++I QA
Sbjct: 79 EEAKAEAREEREKIKAQA 96
>gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional.
Length = 445
Score = 27.4 bits (61), Expect = 3.4
Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 110 LDDVKDES--IRKEAQEKADRIIEQ 132
++D K E+ + +EA+E A+RI EQ
Sbjct: 62 VEDAKAEAARVVEEAREDAERIAEQ 86
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 27.1 bits (61), Expect = 3.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 115 DESIRKEAQEKADRIIEQA 133
DE I +EA+E+ D IIE+A
Sbjct: 651 DEDIPEEAKEEIDEIIEEA 669
Score = 26.4 bits (59), Expect = 6.1
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 106 DDEDLDDVKDESIRK---EAQEKADRIIEQADSG 136
DDED+ + E I + EA+++ + +IE ++G
Sbjct: 650 DDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENG 683
>gnl|CDD|184695 PRK14471, PRK14471, F0F1 ATP synthase subunit B; Provisional.
Length = 164
Score = 26.3 bits (58), Expect = 4.9
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 84 EAFKTMQDCMAQYPTLYKQ----NDDDDEDLDDVKDESI---RKEAQEKADRIIEQA 133
EA K MQ+ A L K+ D ++ ++K++ I ++EAQ + D++IEQA
Sbjct: 53 EARKEMQNLQADNERLLKEARAERDAILKEAREIKEKMIADAKEEAQVEGDKMIEQA 109
>gnl|CDD|240400 PTZ00396, PTZ00396, Casein kinase II subunit beta; Provisional.
Length = 251
Score = 26.5 bits (59), Expect = 4.9
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 103 NDDDDEDLDDVKDESIRKEAQE 124
DDEDL+D + + +EA +
Sbjct: 71 EPPDDEDLEDEQFLEVYQEASD 92
>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1220
Score = 26.9 bits (60), Expect = 5.4
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 102 QNDDDDEDLDDVKDESIRKEAQEKADRIIEQ 132
++DDDD+ L+ + + A + A++I+E+
Sbjct: 929 EDDDDDDALEALIEAPAAARAVQVAEKIVER 959
>gnl|CDD|218434 pfam05103, DivIVA, DivIVA protein. The Bacillus subtilis divIVA1
mutation causes misplacement of the septum during cell
division, resulting in the formation of small, circular,
anucleate mini-cells. Inactivation of divIVA produces a
mini-cell phenotype, whereas overproduction of DivIVA
results in a filamentation phenotype. These proteins
appear to contain coiled-coils.
Length = 131
Score = 26.1 bits (58), Expect = 5.6
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 116 ESIRKEAQEKADRIIEQA 133
E I KEA+ KA+RI+ A
Sbjct: 88 ELIIKEAEAKAERIVNDA 105
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 26.2 bits (58), Expect = 6.3
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 9/43 (20%)
Query: 102 QNDDDDEDLDDVKDES---------IRKEAQEKADRIIEQADS 135
+ DDD D DD +DE+ I+KE E+ +R E+ +
Sbjct: 129 DSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAA 171
>gnl|CDD|216038 pfam00639, Rotamase, PPIC-type PPIASE domain. Rotamases increase
the rate of protein folding by catalyzing the
interconversion of cis-proline and trans-proline.
Length = 94
Score = 25.3 bits (56), Expect = 6.4
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 112 DVKDESIRKEAQEKADRIIEQADSG 136
+ + R A+ KA+ I+EQ SG
Sbjct: 5 KPPESADRAAAKAKAEEILEQLQSG 29
>gnl|CDD|173880 cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 460
Score = 26.4 bits (59), Expect = 6.4
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 100 YKQNDDDD-----EDLDDVKDESIRKEAQEKADRIIEQ 132
+ + D + E + D + RK A +KA +II +
Sbjct: 399 WFKARDAEFDELLEKAETTTDPAKRKAAYKKALKIIAE 436
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 25.8 bits (58), Expect = 8.4
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 104 DDDDEDLDDVKDESIRKEAQEKADRIIEQADSGS 137
++D E L D K +E + + ++ A G
Sbjct: 177 EEDIEFLSDEKILEKLEELIAELEALLASARQGE 210
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 26.0 bits (57), Expect = 8.9
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 72 YSTDEPKGVNCFEAFKTMQDCMAQYPTLYKQNDDDDEDLDDVKDESIRKEA 122
Y D K VN F+A T + Y N+ D+ D ++D R+
Sbjct: 288 YQVDVQKAVNDFKAHWTQ-------ESSYVTNNIKDQSSDIIQDPEYRRFG 331
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 0.417
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,216,132
Number of extensions: 628174
Number of successful extensions: 882
Number of sequences better than 10.0: 1
Number of HSP's gapped: 874
Number of HSP's successfully gapped: 54
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 42 (22.0 bits)
S2: 54 (24.6 bits)