RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy547
(282 letters)
>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain.
Length = 66
Score = 88.4 bits (220), Expect = 1e-22
Identities = 31/68 (45%), Positives = 44/68 (64%), Gaps = 4/68 (5%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ K G+GFI ++DVFVH I+ + +++L EG+ VEFDI++G KG
Sbjct: 3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTKGP 58
Query: 96 EAINVTGP 103
+A NVT
Sbjct: 59 QAANVTLL 66
Score = 80.0 bits (198), Expect = 2e-19
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ K G+GFI ++DVFVH I+ + +++L EG+ VEFDI++G KG
Sbjct: 3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQRVEFDIVEGTKGP 58
Query: 263 Q 263
Q
Sbjct: 59 Q 59
>gnl|CDD|239905 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like
cold-shock domain (CSD) that is found in eukaryotes,
prokaryotes, and archaea. CSP's include the major
cold-shock proteins CspA and CspB in bacteria and the
eukaryotic gene regulatory factor Y-box protein. CSP
expression is up-regulated by an abrupt drop in growth
temperature. CSP's are also expressed under normal
condition at lower level. The function of cold-shock
proteins is not fully understood. They preferentially
bind poly-pyrimidine region of single-stranded RNA and
DNA. CSP's are thought to bind mRNA and regulate
ribosomal translation, mRNA degradation, and the rate
of transcription termination. The human Y-box protein,
which contains a CSD, regulates transcription and
translation of genes that contain the Y-box sequence in
their promoters. This specific ssDNA-binding properties
of CSD are required for the binding of Y-box protein to
the promoter's Y-box sequence, thereby regulating
transcription.
Length = 65
Score = 79.5 bits (197), Expect = 2e-19
Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF + G+GFI EDVFVH ++ +++L EG+ VEF++ +GDKG
Sbjct: 3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALE----GDGFRSLEEGDRVEFELEEGDKGP 58
Query: 96 EAINVTG 102
+A+NV
Sbjct: 59 QAVNVRL 65
Score = 72.6 bits (179), Expect = 8e-17
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF + G+GFI EDVFVH ++ +++L EG+ VEF++ +GDKG
Sbjct: 3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALE----GDGFRSLEEGDRVEFELEEGDKGP 58
Query: 263 Q 263
Q
Sbjct: 59 Q 59
>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription].
Length = 67
Score = 68.3 bits (168), Expect = 3e-15
Identities = 29/66 (43%), Positives = 38/66 (57%), Gaps = 4/66 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ G+GFI +DVFVH I+ ++TL EG+ VEF++ QG KG
Sbjct: 4 GTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKGP 59
Query: 96 EAINVT 101
A NV
Sbjct: 60 SAANVR 65
Score = 64.9 bits (159), Expect = 5e-14
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ G+GFI +DVFVH I+ ++TL EG+ VEF++ QG KG
Sbjct: 4 GTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAG----FRTLREGQKVEFEVEQGRKGP 59
Query: 263 Q 263
Sbjct: 60 S 60
>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional.
Length = 69
Score = 64.3 bits (156), Expect = 1e-13
Identities = 34/69 (49%), Positives = 44/69 (63%), Gaps = 4/69 (5%)
Query: 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQ 58
Query: 93 KGHEAINVT 101
KG A+NVT
Sbjct: 59 KGPAAVNVT 67
Score = 57.8 bits (139), Expect = 3e-11
Identities = 30/62 (48%), Positives = 39/62 (62%), Gaps = 4/62 (6%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQ 58
Query: 260 KG 261
KG
Sbjct: 59 KG 60
>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed.
Length = 69
Score = 63.5 bits (154), Expect = 3e-13
Identities = 33/70 (47%), Positives = 43/70 (61%), Gaps = 4/70 (5%)
Query: 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91
+K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 57
Query: 92 DKGHEAINVT 101
KG A NV
Sbjct: 58 AKGPSAANVI 67
Score = 58.1 bits (140), Expect = 2e-11
Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 4/63 (6%)
Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
+K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 57
Query: 259 DKG 261
KG
Sbjct: 58 AKG 60
>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional.
Length = 70
Score = 62.3 bits (151), Expect = 7e-13
Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
++ K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I
Sbjct: 1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 90 QGDKGHEAINVT 101
G KG A NVT
Sbjct: 57 SGAKGPAAGNVT 68
Score = 57.3 bits (138), Expect = 4e-11
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
++ K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I
Sbjct: 1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 257 QGDKG 261
G KG
Sbjct: 57 SGAKG 61
>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 61.5 bits (150), Expect = 1e-12
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 9/70 (12%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI--MQGDK 93
GVVKWF+ G+GFI +DVFVH +I+ K+L EG+ VEF + +G +
Sbjct: 2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPEGGE 54
Query: 94 GHEAINVTGP 103
EA NV
Sbjct: 55 KPEAENVVKL 64
Score = 55.3 bits (134), Expect = 2e-10
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI--MQGDK 260
GVVKWF+ G+GFI +DVFVH +I+ K+L EG+ VEF + +G +
Sbjct: 2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVSPEGGE 54
Query: 261 GNQ 263
+
Sbjct: 55 KPE 57
>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional.
Length = 70
Score = 59.4 bits (143), Expect = 7e-12
Identities = 30/71 (42%), Positives = 43/71 (60%), Gaps = 4/71 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
++ K+ G+VKWF+ G+GFI ++DVFVH I+ N ++TL E + VEF I
Sbjct: 1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIE 56
Query: 90 QGDKGHEAINV 100
QG +G A NV
Sbjct: 57 QGQRGPAAANV 67
Score = 55.9 bits (134), Expect = 1e-10
Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 4/65 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
++ K+ G+VKWF+ G+GFI ++DVFVH I+ N ++TL E + VEF I
Sbjct: 1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIE 56
Query: 257 QGDKG 261
QG +G
Sbjct: 57 QGQRG 61
>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD. This model
represents what appears to be a phylogenetically
distinct clade, containing E. coli CspD (SP|P24245) and
related proteobacterial proteins within the larger
family of cold shock domain proteins described by Pfam
model pfam00313. The gene symbol cspD may have been used
idependently for other subfamilies of cold shock domain
proteins, such as for B. subtilis CspD. These proteins
typically are shorter than 70 amino acids. In E. coli,
CspD is a stress response protein induced in stationary
phase. This homodimer binds single-stranded DNA and
appears to inhibit DNA replication [DNA metabolism, DNA
replication, recombination, and repair, Cellular
processes, Adaptations to atypical conditions].
Length = 68
Score = 58.3 bits (141), Expect = 1e-11
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G+VKWF+ G+GFI + D+F H I+ + Y+TL G+ V+F+++QG KG
Sbjct: 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQGPKGA 59
Query: 96 EAINV 100
A ++
Sbjct: 60 HATHI 64
Score = 57.6 bits (139), Expect = 3e-11
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G+VKWF+ G+GFI + D+F H I+ + Y+TL G+ V+F+++QG KG
Sbjct: 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG----YRTLKAGQKVQFEVVQGPKGA 59
>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible
regulatory protein CspD; Provisional.
Length = 74
Score = 57.4 bits (138), Expect = 5e-11
Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ G+GFI ED+F H I+ + Y+TL G++V+FD+ QG KGN
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGN 59
Query: 263 Q 263
Sbjct: 60 H 60
Score = 56.7 bits (136), Expect = 8e-11
Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ G+GFI ED+F H I+ + Y+TL G++V+FD+ QG KG+
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGN 59
Query: 96 EA 97
A
Sbjct: 60 HA 61
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
Length = 73
Score = 57.0 bits (137), Expect = 6e-11
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ G+GFI ED+F H I+ + Y+TL G++V FD+ QG KGN
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGN 59
Query: 263 Q 263
Sbjct: 60 H 60
Score = 56.2 bits (135), Expect = 1e-10
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ G+GFI ED+F H I+ + Y+TL G++V FD+ QG KG+
Sbjct: 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGN 59
Query: 96 EA 97
A
Sbjct: 60 HA 61
>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional.
Length = 70
Score = 40.3 bits (94), Expect = 5e-05
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
++ K+ G+VK F KSG G I +DV VH + + + L G VEF +
Sbjct: 1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRI 56
Query: 90 QGDKGHEAINV 100
G +G A NV
Sbjct: 57 NGLRGPTAANV 67
Score = 36.4 bits (84), Expect = 0.001
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
++ K+ G+VK F KSG G I +DV VH + + + L G VEF +
Sbjct: 1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDA----EELTTGLRVEFCRI 56
Query: 257 QGDKG 261
G +G
Sbjct: 57 NGLRG 61
>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional.
Length = 70
Score = 32.0 bits (72), Expect = 0.041
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
++ K+ G+VK F KSG GFI ++V VH I PR + L G VEF +
Sbjct: 1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVH---ISAFTPRDA-EVLIPGLRVEFCRV 56
Query: 90 QGDKGHEAINV 100
G +G A NV
Sbjct: 57 NGLRGPTAANV 67
Score = 28.9 bits (64), Expect = 0.61
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVH 229
++ K+ G+VK F KSG GFI ++V VH
Sbjct: 1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVH 33
>gnl|CDD|212580 cd11707, DHR2_DOCK1, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 1. Dock1, also called
Dock180, is an atypical guanine nucleotide exchange
factor (GEF) that lacks the conventional Dbl homology
(DH) domain. As a GEF, it activates small GTPases by
exchanging bound GDP for free GTP. Dock1 interacts with
the scaffold protein Elmo and the resulting complex
functions upstream of Rac in many biological events
including phagocytosis of apoptotic cells, cell
migration and invasion. In the nervous system, it
mediates attractive responses to netrin-1 and thus,
plays a role in axon outgrowth and pathfinding. DOCK
proteins are divided into four classes (A-D) based on
sequence similarity and domain architecture; class A
includes Dock1, 2 and 5. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Dock1,
which contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock1, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 400
Score = 32.3 bits (73), Expect = 0.26
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 9 KAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSN 56
K E P N AN ++ V A K+ G+++WF VKS + +P N
Sbjct: 233 KGEKDPDNEFANMWIERTTYVTAYKLPGILRWFEVKSVFMVEISPLEN 280
Score = 31.2 bits (70), Expect = 0.61
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 141 FGVKYQLEIPMEFSSKTMPFFMILFCCL------QMCDSGTKAEATPSNPSASESPKKEP 194
F VK LE+P +F +K + ++ F + Q K E P N A+ ++
Sbjct: 192 FTVKPLLELPPKFQNKPVSEQIVSFYRVNEVQRFQYSRPVRKGEKDPDNEFANMWIERTT 251
Query: 195 VVLATKVCGVVKWFSVKSGYGFIATPSSN 223
V A K+ G+++WF VKS + +P N
Sbjct: 252 YVTAYKLPGILRWFEVKSVFMVEISPLEN 280
>gnl|CDD|176206 cd08244, MDR_enoyl_red, Possible enoyl reductase. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 30.4 bits (69), Expect = 0.84
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 71 PRKLYKTLAEGE-TVEFDIMQGDKGHEAINVTGPDGRHV 108
P ++ + L G TV D + G G A+ + P GR +
Sbjct: 200 PDQVREALGGGGVTVVLDGVGGAIGRAALALLAPGGRFL 238
>gnl|CDD|224513 COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic
diacylglycerol kinase [Lipid metabolism / General
function prediction only].
Length = 301
Score = 30.0 bits (68), Expect = 1.2
Identities = 10/54 (18%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 215 GFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL 268
G + ++N F + I ++ + + GET + D+ G + F+
Sbjct: 87 GILPGGTAN--DFARALGIPLDDIEAALELIKSGETRKVDL--GQVNGRRYFIN 136
Score = 29.6 bits (67), Expect = 1.8
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 48 GFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102
G + ++N F + I ++ + + GET + D+ Q + IN G
Sbjct: 87 GILPGGTAN--DFARALGIPLDDIEAALELIKSGETRKVDLGQVNGRRYFINNAG 139
>gnl|CDD|143197 cd05720, Ig_CD8_alpha, Immunoglobulin (Ig) like domain of CD8 alpha
chain. Ig_CD8_alpha: immunoglobulin (Ig)-like domain in
CD8 alpha. The CD8 glycoprotein plays an essential role
in the control of T-cell selection, maturation and the
T-cell receptor (TCR)-mediated response to peptide
antigen. CD8 is comprised of alpha and beta subunits and
is expressed as either an alphaalpha or alphabeta dimer.
Both dimeric isoforms can serve as a coreceptor for T
cell activation and differentiation, however they have
distinct physiological roles, different cellular
distributions, unique binding partners etc. Each CD8
subunit is comprised of an extracellular domain
containing a v-type Ig-like domain, a single pass
transmembrane portion and a short intracellular domain.
The Ig domain of CD8 alpha binds to antibodies.
Length = 104
Score = 28.6 bits (64), Expect = 1.3
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 259 DKGNQFCFVLKNIVLYFS-FVP 279
++G FC V N VLYFS FVP
Sbjct: 80 NEGYYFCSVASNSVLYFSSFVP 101
>gnl|CDD|206208 pfam14038, YqzE, YqzE-like protein. The YqzE-like protein family
includes the B. subtilis YqzE protein, which is
functionally uncharacterized. It is a part of the ComG
operon, which is regulated by the competence
transcription factor ComK. This family of proteins is
found in bacteria. Proteins in this family are typically
between 49 and 66 amino acids in length.
Length = 54
Score = 27.2 bits (61), Expect = 1.4
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 116 NKPKYNRRKAKANKRKRKSRRNNRLFGVKYQLEIPMEFS 154
+ PK R++ K +++ K + R FGV IP FS
Sbjct: 18 DTPKEERKEKKEERKEEKPPFSYRWFGV-----IPYSFS 51
>gnl|CDD|176680 cd07257, THT_oxygenase_C, The C-terminal domain of
2,4,5-Trihydroxytoluene (THT) oxygenase, which is an
extradiol dioxygenease in the 2,4-dinitrotoluene (DNT)
degradation pathway. This subfamily contains the
C-terminal, catalytic, domain of THT oxygenase. THT
oxygenase is an extradiol dioxygenase in the
2,4-dinitrotoluene (DNT) degradation pathway. It
catalyzes the conversion of 2,4,5-trihydroxytoluene to
an unstable ring fission product,
2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The
native protein was determined to be a dimer by gel
filtration. The enzyme belongs to the type I family of
extradiol dioxygenases which contains two structurally
homologous barrel-shaped domains at the N- and
C-terminus of each monomer. The active-site metal is
located in the C-terminal barrel. Fe(II) is required for
its catalytic activity.
Length = 153
Score = 28.8 bits (65), Expect = 2.1
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 9/37 (24%)
Query: 82 ETVEFD-IMQG-----DKGHEAINVTGPDGRHVQGSQ 112
E +FD G +KG+E +V G GRH+ GSQ
Sbjct: 74 EVHDFDAQGLGHDYLREKGYE--HVWGV-GRHILGSQ 107
>gnl|CDD|177341 PHA02091, PHA02091, hypothetical protein.
Length = 72
Score = 26.8 bits (59), Expect = 3.3
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 73 KLYKTLAE-GETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKPKY 120
KL +++ + +T E I+Q D+G +NV GP G+ +Q ++ K+
Sbjct: 23 KLARSIVDFAKTRELQIIQRDRGMWTLNVYGPLGK----AQICRDQQKF 67
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 26.2 bits (58), Expect = 5.2
Identities = 10/62 (16%), Positives = 20/62 (32%), Gaps = 3/62 (4%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G V S+ F+ + VH + + + G+ VE +++ D
Sbjct: 3 GKVV--SITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
Query: 263 QF 264
Sbjct: 60 GR 61
>gnl|CDD|189055 cd09885, PIN_Smg6, PIN domain of human telomerase-binding protein
EST1, Smg6, and other similar eukaryotic homologs.
Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are
essential to the post-transcriptional regulatory
pathway, NMD, which recognizes and rapidly degrades
mRNAs containing premature translation termination
codons. In vivo, the Smg6 PIN (PilT N terminus) domain
elicits degradation of bound mRNAs, as well as, metal
ion dependent, degradation of single-stranded RNA, in
vitro. These PIN domains are structural homologs of flap
endonuclease-1 (FEN1)-like PIN domains, but lack the
extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule. Point mutation studies of the conserved
aspartate residues in the catalytic center of the Smg6
PIN domain revealed that Smg6 is the endonuclease
involved in human NMD. However, Smg5 lacks several of
these key catalytic residues and does not degrade
single-stranded RNA, in vivo. Eukaryotic Smg6 PIN
domains are present at the C-terminal end of the
telomerase activating proteins, Est1.
Length = 182
Score = 27.7 bits (62), Expect = 5.4
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 162 MILFCCLQMCDSGTKAEATPSNPSASESPKK--EPVVLAT 199
+IL CCL C K +A P + P K VVL T
Sbjct: 121 VILACCLHFC----KDKAKDFMPREKDQPTKLVREVVLLT 156
>gnl|CDD|235025 PRK02290, PRK02290, 3-dehydroquinate synthase; Provisional.
Length = 344
Score = 27.9 bits (63), Expect = 5.6
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 79 AEGETVEFDIMQGDKGHEAINVTGPDGRHV 108
G+ + I+Q E I + PDG+ V
Sbjct: 286 YGGKRIRT-ILQNA---ETIRLVTPDGKPV 311
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. This RNA
helicase, the transcription termination factor Rho,
occurs in nearly all bacteria but is missing from the
Cyanobacteria, the Mollicutes (Mycoplasmas), and
various Lactobacillales including Streptococcus. It is
also missing, of course, from the Archaea, which also
lack Nus factors. Members of this family from
Micrococcus luteus, Mycobacterium tuberculosis, and
related species have a related but highly variable
long, highly charged insert near the amino end. Members
of this family differ in the specificity of RNA binding
[Transcription, Transcription factors].
Length = 415
Score = 27.7 bits (62), Expect = 7.7
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 12/45 (26%)
Query: 46 GYGFIATPSSN-----EDVFVHSKRIKYNNPRKLYKTLAEGETVE 85
G+GF+ +P S+ +D++V +I+ N R G+T+E
Sbjct: 61 GFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRT-------GDTIE 98
Score = 27.7 bits (62), Expect = 7.7
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 12/45 (26%)
Query: 213 GYGFIATPSSN-----EDVFVHSKRIKYNNPRKLYKTLAEGETVE 252
G+GF+ +P S+ +D++V +I+ N R G+T+E
Sbjct: 61 GFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRT-------GDTIE 98
>gnl|CDD|176251 cd08291, ETR_like_1, 2-enoyl thioester reductase (ETR) like
proteins, child 1. 2-enoyl thioester reductase (ETR)
like proteins. ETR catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity has
been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the 2-enoyl
thioester reductase (ETR) like proteins. ETR catalyzes
the NADPH-dependent dependent conversion of
trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA)
to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in Candida
tropicalis as essential in maintaining mitiochondrial
respiratory function. This ETR family is a part of the
medium chain dehydrogenase/reductase family, but lack
the zinc coordination sites characteristic of the
alcohol dehydrogenases in this family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. Candida
tropicalis enoyl thioester reductase (Etr1p) catalyzes
the NADPH-dependent reduction of trans-2-enoyl
thioesters in mitochondrial fatty acid synthesis. Etr1p
forms homodimers, with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 324
Score = 27.6 bits (62), Expect = 8.2
Identities = 17/50 (34%), Positives = 20/50 (40%), Gaps = 11/50 (22%)
Query: 176 KAEATPSNPS-------ASESPKKEPVVLATKVCGVVKWFSVKSGYGFIA 218
K EA P NPS S K PV + G V V +G G +A
Sbjct: 36 KVEAAPINPSDLGFLKGQYGSTKALPVPPGFEGSGTV----VAAGGGPLA 81
>gnl|CDD|234005 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA repair
is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and in
alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1076
Score = 27.5 bits (61), Expect = 9.9
Identities = 12/23 (52%), Positives = 12/23 (52%)
Query: 93 KGHEAINVTGPDGRHVQGSQFAA 115
G AIN DGR VQG Q A
Sbjct: 1022 SGRFAINPYTEDGRSVQGDQLKA 1044
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
0.316 0.132 0.391
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,720,784
Number of extensions: 1240914
Number of successful extensions: 1246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1219
Number of HSP's successfully gapped: 48
Length of query: 282
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 186
Effective length of database: 6,679,618
Effective search space: 1242408948
Effective search space used: 1242408948
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: 58 (26.0 bits)