RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy291
(149 letters)
>gnl|CDD|218414 pfam05071, NDUFA12, NADH ubiquinone oxidoreductase subunit NDUFA12.
This family contains the 17.2 kD subunit of complex I
(NDUFA12) and its homologues. The family also contains a
second related eukaryotic protein of unknown function, .
Length = 100
Score = 123 bits (310), Expect = 2e-37
Identities = 45/105 (42%), Positives = 55/105 (52%), Gaps = 11/105 (10%)
Query: 42 GKYVGIDQFGNKYYENPRYFFGRNRWVIYNPDVGLNYDGSMVPAEWYGWLHYKTDYTPCE 101
G VG D+FGNKYYEN GR RWVIYN + S VP EW+GWLH+ TD P E
Sbjct: 1 GTLVGEDEFGNKYYENKDELGGRRRWVIYNGKA----EASRVPPEWHGWLHHTTDEPPTE 56
Query: 102 DPGRPVYKWMAEHTQNMSGSNKEYVPYST------TRDKIQAWTP 140
+P W H N++G+ Y PY + +AWTP
Sbjct: 57 EP-LKPRAWEKPHQPNLTGTPGAYRPYGSLLRRPRATGDYEAWTP 100
>gnl|CDD|236176 PRK08183, PRK08183, NADH dehydrogenase; Validated.
Length = 133
Score = 83.9 bits (208), Expect = 1e-21
Identities = 40/113 (35%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 40 KFGKYVGIDQFGNKYYEN--PRYFFGRN-RWVIYNPDVGLNYDGSMVPAEWYGWLHYKTD 96
+ G+ VG D+FGN YY + GR RWVIYN + S +P EW+GWLH+ D
Sbjct: 24 RKGERVGEDEFGNVYYRTKGGKPSDGRERRWVIYNGYA----EASRIPPEWHGWLHHTVD 79
Query: 97 YTPCEDPGRPVYKWMAEHTQNMSGSNKEYVP-----YSTTRDKI----QAWTP 140
P ++P P +W H N++G+ Y P R + AWTP
Sbjct: 80 VPPTKEPYPP-REWEKPHQPNLTGTPLAYRPKGSILRGGERPRATGDYDAWTP 131
>gnl|CDD|215571 PLN03095, PLN03095, NADH:ubiquinone oxidoreductase 18 kDa subunit;
Provisional.
Length = 115
Score = 75.3 bits (185), Expect = 2e-18
Identities = 38/111 (34%), Positives = 54/111 (48%), Gaps = 12/111 (10%)
Query: 40 KFGKYVGIDQFGNKYYENPRYFFGRNRWVIYNPDVGLNYDGSMVPAEWYGWLHYKTDYTP 99
+ G+ VG D+FGNKYYENP Y GR+RWV Y +Y+ S +P EW+GWLHY D
Sbjct: 8 RAGRLVGEDEFGNKYYENPSYQSGRHRWVEYADK--DDYNASNIPPEWHGWLHYVNDEPG 65
Query: 100 CEDPGRPVYKWMAEHTQNMSGSNKEYV---------PYSTTRDKIQAWTPP 141
E R ++ E + + +Y+ + W+PP
Sbjct: 66 -ELEDRTAPRYQLEFIAGGTTTGTQYMYHPKGHFLSKRPRNWKRYTPWSPP 115
>gnl|CDD|215389 PLN02732, PLN02732, Probable NADH dehydrogenase [ubiquinone] 1
alpha subcomplex subunit.
Length = 159
Score = 75.0 bits (184), Expect = 7e-18
Identities = 42/108 (38%), Positives = 60/108 (55%), Gaps = 12/108 (11%)
Query: 43 KYVGIDQFGNKYYEN-PRYFFGRNRWVIYNPDVGLNYDGSMVPAEWYGWLHYKTDYTPCE 101
VG+D+FGNKYY+ +GR+RWV Y Y+ S VPAEW+GWLH+ TD+T E
Sbjct: 50 TLVGVDKFGNKYYQKLGDTQYGRHRWVEYAEKS--RYNASQVPAEWHGWLHFITDHTGDE 107
Query: 102 DPGRPVYKWMAEHTQNMSGSNKEYVPYST-------TRD--KIQAWTP 140
++ EH +N SG +EY+ +S +D + Q+W P
Sbjct: 108 LLMLKPKRYGLEHKENFSGEGEEYIYHSKGHTLNPGQKDWTRYQSWQP 155
>gnl|CDD|226284 COG3761, COG3761, NADH:ubiquinone oxidoreductase 17.2 kD subunit
[Energy production and conversion].
Length = 118
Score = 64.2 bits (156), Expect = 3e-14
Identities = 39/113 (34%), Positives = 51/113 (45%), Gaps = 18/113 (15%)
Query: 40 KFGKYVGIDQFGNKYYE--NPRYFFGRNRWVIYNPDVGLNY-DGSMVPAEWYGWLHYKTD 96
+F K VG D+FGN YYE N RWVIYN Y + S +P W+GWLH++ D
Sbjct: 11 RFHKKVGEDEFGNVYYEGRNIDSEGRTRRWVIYN-----GYAEASKIPPGWHGWLHHRVD 65
Query: 97 YTPCEDPGRPVYKWMAEHTQNMSGSNKEYVPYS---------TTRDKIQAWTP 140
P + P +W H N++G+ Y P AWTP
Sbjct: 66 EPPKSEQLFP-REWQKPHLPNLTGTPHAYRPKGSLARAGERPRVTGDYDAWTP 117
>gnl|CDD|168631 PRK06630, PRK06630, hypothetical protein; Provisional.
Length = 99
Score = 34.9 bits (80), Expect = 0.003
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 41 FGKYVGIDQFGNKYYE--NPRYFFGRNRWVIYNPDVGLNYDGSMVPAEWYGWLHYKTDYT 98
F K VG D+F N+YYE N Y R+VIY +N + + +P W+ WLH+ +
Sbjct: 12 FHKKVGEDEFLNQYYESRNIDYLGRPRRFVIYK---NVN-EPTKIPPSWHAWLHHLVNEI 67
Query: 99 P 99
P
Sbjct: 68 P 68
>gnl|CDD|162081 TIGR00874, talAB, transaldolase. This family includes the majority
of known and predicted transaldolase sequences,
including E. coli TalA and TalB. It excluded two other
families. The first includes E. coli transaldolase-like
protein TalC. The second family includes the putative
transaldolases of Helicobacter pylori and Mycobacterium
tuberculosis [Energy metabolism, Pentose phosphate
pathway].
Length = 317
Score = 28.6 bits (64), Expect = 1.3
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 16/64 (25%)
Query: 72 PDVGLNYDGSMVPAEWYGWLHYKTDYTPCEDPG----RPVYKWMAEH---TQNMSGS--N 122
P VG D WY K +Y+ EDPG + +Y + +H T+ M S N
Sbjct: 175 PFVGRILD-------WYKAATGKKEYSIEEDPGVASVKKIYNYYKKHGYPTEVMGASFRN 227
Query: 123 KEYV 126
KE +
Sbjct: 228 KEEI 231
>gnl|CDD|129658 TIGR00567, 3mg, DNA-3-methyladenine glycosylase (3mg). This
families are based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University). All
proteins in this family for which the function is known
are involved in the base excision repair of alkylation
damage to DNA. The exact specificty of the type of
alkylation damage repaired by each of these varies
somewhat between species. Substrates include 3-methyl
adenine, 7-methyl-guanaine, and 3-methyl-guanine [DNA
metabolism, DNA replication, recombination, and repair].
Length = 192
Score = 27.1 bits (60), Expect = 3.6
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 2 SKLKNFLGINVLENLRKIYKENGGLKNCW-KTLYLTDDLKFGKYVGIDQFGNKYYENPRY 60
KL LGI + N R + + + W + L G VGID G + R+
Sbjct: 128 GKLCQALGITMSFNGRDLIQPSA----LWLERGPLEHSAPAGPRVGIDYAGEWDIKPWRF 183
Query: 61 FFGRNRWV 68
+ N WV
Sbjct: 184 YVTGNPWV 191
>gnl|CDD|200522 cd11261, Sema_4F, The Sema domain, a protein interacting module, of
semaphorin 4F (Sema4F). Sema4F plays role in
heterotypic cell-cell contacts and controls cell
proliferation and suppresses tumorigenesis. In
neurofibromatosis type 1 (NF1) patients, reduced Sema4F
level disrupts Schwann cell/axonal interactions.
Experiments using a yeast two-hybrid system show that
the extreme C-terminus of Sema4F interacts with the PDZ
domains of post-synaptic density protein SAP90/PSD-95,
indicating possible functional involvement of Semas4F at
glutamatergic synapses. Recent work also suggests a role
for Sema4F in the injury response of intramedullary
axotomized motoneuron. Sema4F belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulator 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 = 460
Score = 26.8 bits (59), Expect = 5.9
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 109 KWMAEHTQNMS------GSNKEYVPYSTTRDKIQAWTPPSSSGRNK 148
++ A HT N S S+ YV RD I A T P S R +
Sbjct: 5 RFSAPHTYNYSVLLVDPASHTLYV---GARDAIFALTLPFSGERPR 47
>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor. This sigma
factor is restricted to certain lineages of the order
Bacillales including Staphylococcus , Listeria and
Bacillus.
Length = 255
Score = 26.4 bits (58), Expect = 6.6
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 94 KTDYTPCEDPGRPVYKWMAEHTQNMSGSNKE 124
+ P V +W+AE QN +G +E
Sbjct: 2 EIQSQPTNLTKEDVIQWIAEFQQNQNGEAQE 32
>gnl|CDD|222859 PHA02535, P, terminase ATPase subunit; Provisional.
Length = 581
Score = 26.6 bits (59), Expect = 7.2
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 44 YVGIDQFGNKY--YENPRYFFGRNRWVIYNPDV 74
Y+GID G Y+ + FF + Y+P+V
Sbjct: 463 YIGIDATGIGAGVYQLVKKFFPAAVAINYSPEV 495
>gnl|CDD|184446 PRK14000, PRK14000, potassium-transporting ATPase subunit C;
Provisional.
Length = 185
Score = 26.1 bits (57), Expect = 7.8
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 42 GKYVGIDQFGNKYYENPRYFFGRNRWVIYN 71
GK +G G ++ P+YF GR V YN
Sbjct: 47 GKVIGSKLIGQQW-TEPKYFHGRISAVNYN 75
>gnl|CDD|239829 cd04337, Rieske_RO_Alpha_Cao, Cao (chlorophyll a oxygenase) is a
rieske non-heme iron-sulfur protein located within the
plastid-envelope inner and thylakoid membranes, that
catalyzes the conversion of chlorophyllide a to
chlorophyllide b. CAO is found not only in plants but
also in chlorophytes and prochlorophytes. This domain
represents the N-terminal rieske domain of the
oxygenase alpha subunit. ROs comprise a large class of
aromatic ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or
ferredoxin component and transfers them to the
mononuclear iron for catalysis. Cao is closely related
to several other plant RO's including Tic 55, a 55 kDa
protein associated with protein transport through the
inner chloroplast membrane; Ptc 52, a novel 52 kDa
protein isolated from chloroplasts; and LLS1/Pao
(Lethal-leaf spot 1/pheophorbide a oxygenase).
Length = 129
Score = 25.5 bits (56), Expect = 8.6
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 13 LENLRKIYKENGGLKNCWKTLYLTDDLKFGKYVGIDQFG 51
L + GL+N W + + DLK V + FG
Sbjct: 1 SRVLGSSLELEPGLRNFWYPVEFSKDLKMDTMVPFELFG 39
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 26.2 bits (58), Expect = 9.4
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 108 YKWMAEHTQNMSGS-----NKEYVPYSTTR 132
Y MA T++MSG ++++ Y
Sbjct: 742 YAEMASRTESMSGQMSENLSQQFAQYVMKH 771
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 0.138 0.460
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,943,721
Number of extensions: 707612
Number of successful extensions: 586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 30
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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 (21.6 bits)
S2: 54 (24.8 bits)