RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13097
(123 letters)
>gnl|CDD|239763 cd04096, eEF2_snRNP_like_C, eEF2_snRNP_like_C: this family
represents a C-terminal domain of eukaryotic elongation
factor 2 (eEF-2) and a homologous domain of the
spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. Yeast Snu114p is essential
for cell viability and for splicing in vivo. U5-116 kD
binds GTP. Experiments suggest that GTP binding and
probably GTP hydrolysis is important for the function
of the U5-116 kD/Snu114p. In complex with GTP, EF-2
promotes the translocation step of translation. During
translocation the peptidyl-tRNA is moved from the A
site to the P site, the uncharged tRNA from the P site
to the E-site and, the mRNA is shifted one codon
relative to the ribosome.
Length = 80
Score = 98.0 bits (245), Expect = 3e-28
Identities = 31/64 (48%), Positives = 47/64 (73%)
Query: 1 KLYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
K+Y+VL +R G ++ + +G+ F ++AYLPV+ESF F ++R +TSG A PQLVFSHW
Sbjct: 17 KVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLRSATSGQAFPQLVFSHW 76
Query: 61 EVIN 64
E++
Sbjct: 77 EIVP 80
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 88.6 bits (220), Expect = 9e-22
Identities = 41/116 (35%), Positives = 60/116 (51%), Gaps = 24/116 (20%)
Query: 2 LYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
+Y+VL RR G ++ + G+ ++AYLPV ESF F +R +TSG A PQ VF HW+
Sbjct: 737 IYSVLNRRRGVVIGEEQRPGTPLSNIKAYLPVAESFGFTAALRAATSGQAFPQCVFDHWQ 796
Query: 62 VINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQ--------DKL 109
V+ DP + ++A + + S+RKRKGL + DKL
Sbjct: 797 VVPGDPL----------------EPGSKANEIVLSIRKRKGLKPEIPDLDNYLDKL 836
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 82.1 bits (203), Expect = 2e-19
Identities = 35/103 (33%), Positives = 61/103 (59%), Gaps = 18/103 (17%)
Query: 2 LYAVLGRRHGRIVYGDVTQ-GSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
+Y+VL ++ G V+ ++ + G+ + ++AYLPV+ESF F+ +R +TSG A PQ VF HW
Sbjct: 744 IYSVLNQKRGH-VFEEMQRPGTPLYNIKAYLPVIESFGFSGTLRAATSGQAFPQCVFDHW 802
Query: 61 EVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGL 103
++++ DP + ++A + + +RKRKGL
Sbjct: 803 DMMSSDPL----------------EAGSQAAQLVADIRKRKGL 829
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 73.4 bits (181), Expect = 2e-16
Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 22/103 (21%)
Query: 1 KLYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
+ L R G+I+ + G ++A +P+ E F +A ++R +T G AS + F H+
Sbjct: 617 DVIGDLNSRRGQILGMEQRPGGGLDVIKAEVPLAEMFGYATDLRSATQGRASFSMEFDHY 676
Query: 61 EVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGL 103
E + + A + + RKRKGL
Sbjct: 677 EEVP----------------------SSVAEEIIAKRRKRKGL 697
>gnl|CDD|238772 cd01514, Elongation_Factor_C, Elongation factor G C-terminus.
This domain includes the carboxyl terminal regions of
elongation factors (EFs) bacterial EF-G, eukaryotic and
archeal EF-2 and eukaryotic mitochondrial mtEFG1s and
mtEFG2s. This group also includes proteins similar to
the ribosomal protection proteins Tet(M) and Tet(O),
BipA, LepA and, spliceosomal proteins: human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and yeast counterpart Snu114p. This domain adopts
a ferredoxin-like fold consisting of an alpha-beta
sandwich with anti-parallel beta-sheets, resembling the
topology of domain III found in the elongation factors
EF-G and eukaryotic EF-2, with which it forms the
C-terminal block. The two domains however are not
superimposable and domain III lacks some of the
characteristics of this domain. EF-2/EF-G in complex
with GTP, promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome. Tet(M) and Tet(O)
mediate Tc resistance. Typical Tcs bind to the ribosome
and inhibit the elongation phase of protein synthesis,
by inhibiting the occupation of site A by
aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release
of tetracycline (Tc) from the ribosome in a
GTP-dependent manner. BipA is a highly conserved
protein with global regulatory properties in
Escherichia coli. Yeast Snu114p is essential for cell
viability and for splicing in vivo. Experiments suggest
that GTP binding and probably GTP hydrolysis is
important for the function of the U5-116 kD/Snu114p.
The function of LepA proteins is unknown.
Length = 79
Score = 66.4 bits (163), Expect = 1e-15
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 1 KLYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
+ L +R G I+ G +G+ ++A LP+ E F FA ++R T G AS + FSH+
Sbjct: 17 AVIGDLSKRRGEIL-GMEPRGTGRVVIKAELPLAEMFGFATDLRSLTQGRASFSMEFSHY 75
Query: 61 EVIN 64
E +
Sbjct: 76 EPVP 79
>gnl|CDD|239765 cd04098, eEF2_C_snRNP, eEF2_C_snRNP: This family includes a
C-terminal portion of the spliceosomal human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and, its yeast counterpart Snu114p. This domain is
homologous to the C-terminal domain of the eukaryotic
translational elongation factor EF-2. Yeast Snu114p is
essential for cell viability and for splicing in vivo.
U5-116 kD binds GTP. Experiments suggest that GTP
binding and probably GTP hydrolysis is important for
the function of the U5-116 kD/Snu114p. In complex
with GTP, EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome.
Length = 80
Score = 59.6 bits (145), Expect = 4e-13
Identities = 25/63 (39%), Positives = 39/63 (61%)
Query: 2 LYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
+Y VL RR G ++Y G+ + V+A++PV+ESF F ++R T G A Q VF HW+
Sbjct: 18 VYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLRVHTQGQAFCQSVFDHWQ 77
Query: 62 VIN 64
++
Sbjct: 78 IVP 80
>gnl|CDD|197906 smart00838, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 85
Score = 59.4 bits (145), Expect = 4e-13
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 3 YAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
L R G+I + Q ++A +P+ E F +A ++R +T G A+ + FSH+E
Sbjct: 21 IGDLNSRRGKIE--GMEQRGGAQVIKAKVPLSEMFGYATDLRSATQGRATWSMEFSHYE 77
>gnl|CDD|201388 pfam00679, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 89
Score = 53.7 bits (130), Expect = 8e-11
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 1 KLYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
+ L +R G I+ G ++A +P+ E F F+ E+R T G S + FS +
Sbjct: 20 DVIGDLNQRRGEIL-DMEPDGGGRVVIEAEVPLAELFGFSTELRSLTQGRGSFSMEFSGY 78
Query: 61 EVINIDP 67
E + D
Sbjct: 79 EPVPGDI 85
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 52.9 bits (128), Expect = 3e-09
Identities = 26/101 (25%), Positives = 40/101 (39%), Gaps = 24/101 (23%)
Query: 4 AVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWEVI 63
+ R G+I+ D+ Q ++A PV E F FA EIR +T G A F+ +E +
Sbjct: 644 REIQGRRGKIL--DMEQEGDMAIIEAEAPVAEMFGFAGEIRSATEGRALWSTEFAGFEPV 701
Query: 64 NIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLP 104
P + + +R+RKGL
Sbjct: 702 -------PD---------------SLQLDIVRQIRERKGLK 720
>gnl|CDD|239683 cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the
C-terminal domain of the bacterial translational
elongation factor (EF) EF-G. Included in this group is
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells
harbor 2 protein synthesis systems: one localized in
the cytoplasm, the other in the mitochondria. Most
factors regulating mitochondrial protein synthesis are
encoded by nuclear genes, translated in the cytoplasm,
and then transported to the mitochondria. The
eukaryotic system of elongation factor (EF) components
is more complex than that in prokaryotes, with both
cytoplasmic and mitochondrial elongation factors and
multiple isoforms being expressed in certain species.
During the process of peptide synthesis and tRNA site
changes, the ribosome is moved along the mRNA a
distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic mtEFG1 proteins show significant homology to
bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects
and a tendency to lose mitochondrial DNA. No clear
phenotype has been found for mutants in the yeast
homologue of mtEFG2, MEF2.
Length = 78
Score = 38.7 bits (91), Expect = 4e-05
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
L R G+I+ ++A +P+ E F ++ ++R T G S + FSH+E
Sbjct: 22 LSSRRGQIL--GTESRGGWKVIKAEVPLAEMFGYSTDLRSLTQGRGSFTMEFSHYE 75
>gnl|CDD|239764 cd04097, mtEFG1_C, mtEFG1_C: C-terminus of mitochondrial
Elongation factor G1 (mtEFG1)-like proteins found in
eukaryotes. Eukaryotic cells harbor 2 protein
synthesis systems: one localized in the cytoplasm, the
other in the mitochondria. Most factors regulating
mitochondrial protein synthesis are encoded by nuclear
genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. Eukaryotic EF-2
operates in the cytosolic protein synthesis machinery
of eukaryotes, EF-Gs in protein synthesis in bacteria.
Eukaryotic mtEFG1 proteins show significant homology to
bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects
and a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 78
Score = 36.1 bits (84), Expect = 4e-04
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
L +R G IV D + FT++A +P+ + F ++ E+R T G + FS +
Sbjct: 22 LNKRKGTIVDTDTGEDE--FTLEAEVPLNDMFGYSTELRSMTQGKGEFSMEFSRY 74
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 36.4 bits (85), Expect = 0.002
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
L RR G+I + G+ V+A++P+ E F +A ++R +T G A+ + F H+E
Sbjct: 621 LNRRRGQIQGMEARGGAQI--VKAFVPLSEMFGYATDLRSATQGRATFSMEFDHYE 674
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 35.9 bits (84), Expect = 0.003
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
L R GRI+ G ++G V+A +P+ E F +A ++R T G S + FSH+E
Sbjct: 603 LSSRRGRIL-GMESRGGGD-VVRAEVPLAEMFGYATDLRSLTQGRGSFSMEFSHYE 656
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 34.2 bits (79), Expect = 0.010
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 5 VLG---RRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
VLG +R GRI G +G V+A P+ E F +A +R T G S + FSH++
Sbjct: 616 VLGDLSQRRGRIE-GTEPRGDGEVLVKAEAPLAELFGYATRLRSMTKGRGSFTMEFSHFD 674
Query: 62 V 62
Sbjct: 675 P 675
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 33.7 bits (77), Expect = 0.014
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 24/95 (25%)
Query: 9 RHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWEVINIDPY 68
R G+I+ ++ Q T+ A PV E F FA IR +TSG + +E++
Sbjct: 647 RRGQIL--EMKQEGDMVTIIAKAPVAEMFGFAGAIRGATSGRCLWSTEHAGFELV----- 699
Query: 69 WEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGL 103
P+ N ++++ VRKRKGL
Sbjct: 700 --PQ---------------NLQQEFVMEVRKRKGL 717
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 32.9 bits (75), Expect = 0.034
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHW 60
L R G I G +G+V ++A +P+ E F +A ++R T G + + F H+
Sbjct: 621 LSSRRGIIE-GMEARGNVQ-KIKAEVPLSEMFGYATDLRSFTQGRGTYSMEFLHY 673
>gnl|CDD|182681 PRK10727, PRK10727, DNA-binding transcriptional regulator GalR;
Provisional.
Length = 343
Score = 30.9 bits (70), Expect = 0.12
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 84 ADTENRARKYMDSVRKRKGLPVQDKLVAHAE 114
+D E+R + Y D++ + G+P D+LV E
Sbjct: 189 SDAEDRLQGYYDALAES-GIPANDRLVTFGE 218
>gnl|CDD|226068 COG3538, COG3538, Uncharacterized conserved protein [Function
unknown].
Length = 434
Score = 30.8 bits (70), Expect = 0.13
Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 15/76 (19%)
Query: 27 VQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWEVINIDPYWEPRTEEEYLHFGDKADT 86
V+ YLP+ + E+R+ +GL V I +DPY E G + D
Sbjct: 70 VRPYLPLAKE---DEELRRLIAGL-----VKRQARYILLDPYANAFNETANGA-GHQTDH 120
Query: 87 ENRA-----RKY-MDS 96
RKY +DS
Sbjct: 121 TEMNPWVWERKYEIDS 136
>gnl|CDD|201347 pfam00619, CARD, Caspase recruitment domain. Motif contained in
proteins involved in apoptotic signaling. Predicted to
possess a DEATH (pfam00531) domain-like fold.
Length = 85
Score = 28.3 bits (64), Expect = 0.39
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 73 TEEEYLHFGDKADTENRARKYMDSVRKR 100
TEEEY ++AR+ +D V+K+
Sbjct: 32 TEEEYEKIKANTTRRDKARELLDLVQKK 59
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 28.6 bits (65), Expect = 0.95
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 6 LGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWE 61
L R G+I + G+ ++A +P+ E F +A ++R T G A+ + F H+E
Sbjct: 624 LNSRRGQIEGMEDRGGAKV--IRAEVPLSEMFGYATDLRSMTQGRATYSMEFDHYE 677
>gnl|CDD|182179 PRK09980, ompL, outer membrane porin L; Provisional.
Length = 230
Score = 27.6 bits (61), Expect = 1.8
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 36 SFSFAPEIRKSTSGLASPQLVFSHWEVIN-----IDPYWEPRTEEEYL--HFGDKADTEN 88
S++F P + + S HWE+ N I+ +W P E +L + +N
Sbjct: 161 SYTFEPHYFYNVNDFNSSNGTKHHWEITNTFRYRINEHWLPYFELRWLDRNVNPYHREQN 220
Query: 89 RAR 91
+ R
Sbjct: 221 QIR 223
>gnl|CDD|107285 cd06290, PBP1_LacI_like_9, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 265
Score = 26.5 bits (59), Expect = 3.9
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 82 DKADTENRARKYMDSVRKRKGLPVQDKLVAHAE 114
D +R Y ++ + GL VQ L+ +
Sbjct: 126 GHIDARDRLAGYRKALEEA-GLEVQPDLIVQGD 157
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 26.3 bits (58), Expect = 5.2
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 2/63 (3%)
Query: 6 LGRRHGRI--VYGDVTQGSVTFTVQAYLPVVESFSFAPEIRKSTSGLASPQLVFSHWEVI 63
+GRR+ R V + + +F RK ++ S L + WE
Sbjct: 48 VGRRYNRAGDALAAVPGEAPLLDCSYPTNAAYAENFEGLARKYSNKHVSSALFSATWEFF 107
Query: 64 NID 66
++
Sbjct: 108 DLA 110
>gnl|CDD|224966 COG2055, COG2055, Malate/L-lactate dehydrogenases [Energy
production and conversion].
Length = 349
Score = 25.7 bits (57), Expect = 6.7
Identities = 8/43 (18%), Positives = 17/43 (39%)
Query: 79 HFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTVKR 121
FGD + + R Y+D +R + + E++ +
Sbjct: 277 AFGDGDEFDERLSAYLDELRASEPADGFQGVRLPGEREFAARE 319
>gnl|CDD|217587 pfam03479, DUF296, Domain of unknown function (DUF296). This
putative domain is found in proteins that contain
AT-hook motifs pfam02178, which strongly suggests a
DNA-binding function for the proteins as a whole. There
are three highly conserved histidine residues, eg at
117, 119 and 133 in Reut_B5223, which should be a
structurally conserved metal-binding unit, based on
structural comparison with known metal-binding
structures. The proteins should work as trimers.
Length = 120
Score = 25.2 bits (56), Expect = 7.1
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 2 LYAVLGRRHGRIVYGDVTQGSVTFTVQAYLPVVESFSFAPEIR 44
L+ L G++V G + +G+V T + VV SF R
Sbjct: 81 LHVSLADPDGQVVGGHLAEGTVFATGEV---VVTELSFENARR 120
>gnl|CDD|234438 TIGR03999, thiol_BshA, N-acetyl-alpha-D-glucosaminyl L-malate
synthase BshA. Members of this protein family are BshA,
a glycosyltransferase required for bacillithiol
biosynthesis. This enzyme combines UDP-GlcNAc and
L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate
synthase. Bacillithiol is a low-molecular-weight thiol,
an analog of glutathione and mycothiol, and is found
largely in the Firmicutes [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 374
Score = 25.6 bits (57), Expect = 7.3
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 85 DTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTVKR 121
DT+ RK +++++ G P +K++ H R VKR
Sbjct: 177 DTDRYRRKNDPALKRKLGAPEDEKVLIHISNFRPVKR 213
>gnl|CDD|238931 cd01971, Nitrogenase_VnfN_like, Nitrogenase_vnfN_like: VnfN subunit
of the VnfEN complex-like. This group in addition to
VnfN contains a subset of the beta subunit of the
nitrogenase MoFe protein and NifN-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protien
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 427
Score = 25.8 bits (57), Expect = 7.3
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 47 TSGLASPQLVFSHWEVINIDPYWEPRTEEEYLHF 80
+ A LV S W + + E + + Y+H
Sbjct: 204 SIPKAQFNLVLSPWVGLEFAQHLEEKYGQPYIHS 237
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 25.6 bits (56), Expect = 8.7
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 23 VTFTVQAYLPVVESF---SFAPEIRKSTSGLASPQLVFSHWEVINIDPYWEPRTEEEYLH 79
+++T Q +L + + + E+ K+ +G SP + +++ P EE+L
Sbjct: 338 LSWTAQGFLSPMAAAVGGVVSQEVLKAVTGKFSPLCQWFYFDSAESLPSLGKPECEEFLP 397
Query: 80 FGDKAD 85
GD+ D
Sbjct: 398 RGDRYD 403
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 0.395
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,338,863
Number of extensions: 551728
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 510
Number of HSP's successfully gapped: 36
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (24.0 bits)