RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13777
(121 letters)
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 184 bits (470), Expect = 2e-57
Identities = 58/121 (47%), Positives = 82/121 (67%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60
++L+LAQYRE+ AFAQFGSDLD AT+ L RG RL ELLKQ QY P+ +EEQV ++Y G
Sbjct: 382 LRLDLAQYRELEAFAQFGSDLDEATRAQLERGQRLVELLKQPQYSPLPVEEQVVILYAGT 441
Query: 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFT 120
G+LD + K+ FE E LA+++S+ LLE I++ ++++ +AKLK + F F
Sbjct: 442 NGYLDDVPVEKVRRFEAELLAYLRSNHADLLEEIRETKDLSDEIEAKLKAAIEEFKKTFA 501
Query: 121 G 121
Sbjct: 502 A 502
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 150 bits (382), Expect = 1e-44
Identities = 59/119 (49%), Positives = 83/119 (69%)
Query: 2 KLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVR 61
+L LAQYRE+ AF+QFGSDLD AT++ L RG RLTELLKQ QY P+++EEQV ++Y G
Sbjct: 383 RLILAQYRELEAFSQFGSDLDKATRKQLERGKRLTELLKQPQYSPLSVEEQVLILYAGTN 442
Query: 62 GHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFT 120
G+LD + K+ FEKE LA+++S + LLE I+ ++ ++ +AKLK + F F
Sbjct: 443 GYLDDVPVEKVADFEKELLAYLRSDHKELLEEIRTTKELDDEIEAKLKAAIKEFKKTFA 501
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 145 bits (369), Expect = 8e-43
Identities = 57/119 (47%), Positives = 83/119 (69%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60
++LELAQYRE+ AF+QF SDLD AT++ L RG R+ ELLKQ QY P+++EEQV +++ G
Sbjct: 381 LRLELAQYRELEAFSQFASDLDEATKKQLERGQRVVELLKQPQYKPLSVEEQVVILFAGT 440
Query: 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANF 119
+G+LD + KI FE+ LA++ ++ +LE I K+TE+ +AKLK + NF F
Sbjct: 441 KGYLDDIPVDKIRKFEQALLAYLDANHPDILEEINTTKKLTEELEAKLKEALKNFKKTF 499
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 128 bits (323), Expect = 3e-36
Identities = 55/119 (46%), Positives = 72/119 (60%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60
+KLELAQ+ E+ AFAQF SDLD ATQ L RG RL ELLKQ Q P+ +EEQVA IY G
Sbjct: 361 LKLELAQFAELEAFAQFASDLDKATQNQLARGQRLRELLKQSQSAPLTVEEQVATIYTGT 420
Query: 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANF 119
G+LD L+ ++ F E ++K+++ E I TE+ +A LK + L F
Sbjct: 421 NGYLDSLEIGQVRKFLVELRTYLKTNKPQFQEIISSTKTFTEEAEALLKEAIQEQLELF 479
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 120 bits (303), Expect = 3e-33
Identities = 41/120 (34%), Positives = 69/120 (57%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60
++L+ AQ+ E+ AF +FG LDA TQ+ + RG RL ELLKQ ++ P+++EEQ+A++Y
Sbjct: 382 LRLDYAQFLELEAFTRFGGLLDAGTQKQITRGRRLRELLKQPRFSPLSVEEQIALLYALN 441
Query: 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITEDTDAKLKTVVTNFLANFT 120
G LD + A I FE+ L + + L +++ ++ E A L+ ++ F
Sbjct: 442 EGLLDAVPLANIQAFEERLLEKLDARFAALSLALESPRELDEAWLAALEEILREAGERFA 501
>gnl|CDD|215848 pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal
domain.
Length = 110
Score = 81.9 bits (203), Expect = 2e-21
Identities = 39/108 (36%), Positives = 48/108 (44%), Gaps = 13/108 (12%)
Query: 1 MKLELAQYREVAAFAQ-FGSD-LDAATQQLLNRGVRLTELLKQGQYVPM-------AIEE 51
+KLELAQYRE+ A Q G D L + L R R+ E LKQ QY P +EE
Sbjct: 7 LKLELAQYRELQAIVQLVGEDALSEEDKLTLERARRIEEFLKQNQYSPEPVEKQYVPVEE 66
Query: 52 QVAVIYCGVRGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGK 99
+ + Y +RG D L + LA K L E KK K
Sbjct: 67 TIDLFYALLRGKFDDLPEDALYRIGTIDLAKYKD----LEEKFKKLKK 110
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 70.2 bits (172), Expect = 2e-15
Identities = 30/103 (29%), Positives = 54/103 (52%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGV 60
+KL AQ+ E+ FA+FG+ LD T++ + G R+ LKQ Q P+ + +Q+A++
Sbjct: 382 LKLAYAQFEELETFARFGARLDENTRKTIEHGRRIRACLKQTQSSPLTVPQQIAILLALT 441
Query: 61 RGHLDKLDPAKITTFEKEFLAHIKSSERGLLESIKKEGKITED 103
G D +D + E A + S L E ++ K++++
Sbjct: 442 NGLFDGVDLDAMPEAESAIRAAVTSLPADLRERLQSGKKLSDE 484
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 28.9 bits (65), Expect = 0.62
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 9/43 (20%)
Query: 64 LDKLDPAKITTFEKEF---------LAHIKSSERGLLESIKKE 97
L +L +I FEKE+ L I SSE+ LL+ IKKE
Sbjct: 440 LYRLTGLEIVAFEKEYKELEKLIKKLTKILSSEKELLKVIKKE 482
>gnl|CDD|211353 cd07263, Glo_EDI_BRP_like_16, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 120
Score = 27.9 bits (63), Expect = 0.81
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 19 SDLDAATQQLLNRGVRLTELLKQGQYVPMAI 49
D+DA ++L RGV TE ++ Y +A+
Sbjct: 77 DDIDATYEELKARGVEFTEEPREMPYGTVAV 107
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 28.0 bits (63), Expect = 1.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 12 AAFAQFGSDLDAATQQLLNRGVRL 35
A A+ G LDA T +L+ GV+L
Sbjct: 332 ADLAEAGISLDAVTDKLVAEGVQL 355
>gnl|CDD|131749 TIGR02702, SufR_cyano, iron-sulfur cluster biosynthesis
transcriptional regulator SufR. All members of this
cyanobacterial protein family are the transcriptional
regulator SufR and regulate the SUF system, which makes
possible iron-sulfur cluster biosynthesis despite
exposure to oxygen. In all cases, the sufR gene is
encoded near SUF system genes but in the opposite
direction. This DNA-binding protein belongs to the the
DeoR family of helix-loop-helix proteins. All members
also have a probable metal-binding motif
C-X(12)-C-X(13)-C-X(14)-C near the C-terminus
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Regulatory functions, DNA
interactions].
Length = 203
Score = 27.9 bits (62), Expect = 1.3
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 35 LTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKLDPAKITTFEKE 78
L+ LLKQGQ A+ E +A+ VR HL L+ + +E
Sbjct: 7 LSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAV 50
>gnl|CDD|184685 PRK14453, PRK14453, chloramphenicol/florfenicol resistance protein;
Provisional.
Length = 347
Score = 26.6 bits (59), Expect = 3.3
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 11 VAAFAQFGSDLDAATQQLL 29
V QFGSD+ AA QL
Sbjct: 322 VTVRTQFGSDISAACGQLY 340
>gnl|CDD|152724 pfam12289, Rotavirus_VP1, Rotavirus VP1 structural protein. This
domain family is found in viruses, and is approximately
50 amino acids in length. The family is found in
association with pfam02123. VP1 is a structural protein
of the inner core layer of the rotavirus virion. It
complexes with VP2 and Vp3 to form this layer.
Length = 51
Score = 25.0 bits (54), Expect = 3.7
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 30 NRGVRLTELLKQGQYVPMAIEEQVAVI 56
+ G+ LTE K Y P+A+E++ A I
Sbjct: 1 SDGIALTEKAKLNSYAPIALEKRRAQI 27
>gnl|CDD|203376 pfam06016, Reovirus_L2, Reovirus core-spike protein lambda-2 (L2).
This family consists of several Reovirus core-spike
protein lambda-2 (L2) sequences. The reovirus L2 genome
segment encodes the core spike protein lambda-2, which
mediates enzymatic reactions in 5' capping of the viral
plus-strand transcripts.
Length = 1290
Score = 26.7 bits (59), Expect = 4.0
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 12 AAFAQFGSDLDAATQQLLNR 31
AA A G LDA QQL+
Sbjct: 895 AAAAGAGMTLDAGVQQLIKV 914
>gnl|CDD|233314 TIGR01211, ELP3, histone acetyltransferase, ELP3 family. The
Saccharomyces cerevisiae member YPL086C has been
characterized in vitro as an N-terminal
acetyltransferase for all four core histones. It is a
component of the RNA polymerase II holoenzyme,
designated Elp3p for Elongator Protein 3. Members of
this family are found in eukaryotes and archaea. These
proteins are part of the larger set of GNAT
acetyltransferases [Transcription, DNA-dependent RNA
polymerase].
Length = 522
Score = 25.9 bits (57), Expect = 6.1
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 1 MKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVI 56
+ +L +RE+ +F D+ L+ RG L EL K+G+Y P EE V +I
Sbjct: 271 FERDLEMFREIFEDPRFKPDMLKIYPTLVTRGTELYELWKRGEYKPYTTEEAVELI 326
>gnl|CDD|180627 PRK06569, PRK06569, F0F1 ATP synthase subunit B'; Validated.
Length = 155
Score = 25.6 bits (56), Expect = 6.7
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 64 LDKLDPAKITTFEKEFLAHIKSSERGLLESIKK 96
+D+L KI + E EFL K+ E+ L SI +
Sbjct: 78 IDRLKKEKIDSLESEFLIKKKNLEQDLKNSINQ 110
>gnl|CDD|236791 PRK10902, PRK10902, FKBP-type peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 269
Score = 25.9 bits (57), Expect = 6.8
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 70 AKITTFEKEFLAH--IKSSERGLLESIKKEGKITEDTDAKLKTVVTNF 115
AK + ++F +K++ GLL ++KEG D+ TVV N+
Sbjct: 126 AKGKKYREKFAKEKGVKTTSTGLLYKVEKEGTGEAPKDS--DTVVVNY 171
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 25.7 bits (57), Expect = 7.6
Identities = 17/43 (39%), Positives = 19/43 (44%)
Query: 8 YREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIE 50
EVA A AA Q L G L ELL G+ P+ IE
Sbjct: 256 VHEVALGAAHDHGDPAAWQDLRYAGEELLELLAAGKLEPLVIE 298
>gnl|CDD|234699 PRK00241, nudC, NADH pyrophosphatase; Reviewed.
Length = 256
Score = 25.6 bits (57), Expect = 8.0
Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 10/45 (22%)
Query: 20 DLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHL 64
DLD QLL R V+L E + ++ YCG H
Sbjct: 77 DLDDGLFQLLGRAVQLAEFYRSHRFCG----------YCGHPMHP 111
>gnl|CDD|200523 cd11262, Sema_4G, The Sema domain, a protein interacting module,
of semaphorin 4G (Sema4G). The Sema4G and Sema4C genes
are expressed in the developing cerebellar cortex.
Sema4G and Sema4C proteins specifically bind to Plexin
B2 expressed in the cerebellar granule cells. Sema4G
and Sema4C are involved in neural tube closure and
cerebellar granule cell development through Plexin
B2.Sema4G belongs to the class 4 transmembrane
semaphorin family of proteins. Semaphorins are
regulatory molecules involved in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 457
Score = 25.5 bits (56), Expect = 8.0
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 44 YVPMAIEEQVAVIYCGVRGHLDKLDPAKITT 74
Y + +E++ +Y G RG + L+ + I+
Sbjct: 10 YSTLLLEDESGRLYVGARGAIFSLNASDISD 40
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 25.6 bits (57), Expect = 8.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 8 YREVAAFAQFGSDLDAATQQLLNRGVR 34
YR + A + +LD T++LL R +R
Sbjct: 86 YRALKAVDEKNEELDPETRRLLERLLR 112
>gnl|CDD|224670 COG1756, Mra1, Uncharacterized conserved protein [Function
unknown].
Length = 223
Score = 25.4 bits (56), Expect = 8.9
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 88 RGLLESIKKEGKITEDTDAKLKTVVTNFLANF 119
GL+E + K+G+I + L V N L +
Sbjct: 111 IGLMEQLLKKGRIPSNGGETLLEVEKNPLTDL 142
>gnl|CDD|188642 cd00955, Transaldolase_like, Transaldolase-like proteins from
plants and bacteria. Transaldolase-like proteins from
plants and bacteria. Transaldolase is found in the
non-oxidative branch of the pentose phosphate pathway,
that catalyze the reversible transfer of a
dihydroxyacetone group from fructose-6-phosphate to
erythrose-4-phosphate yielding sedoheptulose-7-phosphate
and glyceraldehyde-3-phosphate. They are members of the
class I aldolases, who are characterized by using a
Schiff-base mechanism for stabilization of the reaction
intermediates.
Length = 338
Score = 25.4 bits (56), Expect = 9.4
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 8 YREVAAFAQFGSDLDAATQQLLNRGVRL 35
R +A + G DLDA T++LL GV+
Sbjct: 304 ERVLAELERLGIDLDAVTEKLLKEGVKK 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
0.318 0.134 0.363
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,042,496
Number of extensions: 532161
Number of successful extensions: 583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 581
Number of HSP's successfully gapped: 48
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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 (21.7 bits)
S2: 53 (24.1 bits)