RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11490
(147 letters)
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding
protein. Members of this family are found in a range
of archaea and eukaryotes and have hypothesised ATP
binding activity.
Length = 235
Score = 64.7 bits (158), Expect = 2e-13
Identities = 22/46 (47%), Positives = 30/46 (65%)
Query: 31 VLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNVD 76
V+G AGSGKT+FV S L + YV+NLDPA ++PY ++D
Sbjct: 1 VVGPAGSGKTTFVGALSEILPLLGRSVYVVNLDPAAENLPYEADID 46
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 58.3 bits (142), Expect = 4e-11
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNVD 76
+ LG AGSGKT+ K S +L ++ + ++NLDPA +PY + D
Sbjct: 5 VFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVNLDPAVEYLPYTPDFD 52
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 49.6 bits (118), Expect = 4e-08
Identities = 18/62 (29%), Positives = 27/62 (43%)
Query: 22 FKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNVDPACRD 81
K ++VLG G GKT+ + + + + P + NLDPA PY N+ D
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 82 VP 83
Sbjct: 61 TA 62
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 36.1 bits (84), Expect = 0.003
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 28 CLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP--ACRDVPYLVNVDPACRDVPYL 85
+ + G +GSGKT+F KK S+ L P VI+LD R P + D +
Sbjct: 1 VVGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYVPRKTP---RDEDGNYDFESI 57
Query: 86 VNVGELS---MLLLNGNKLEHQILNFQK 110
+++ L+ LLNG ++E I +F+
Sbjct: 58 LDLDLLNKNLHDLLNGKEVELPIYDFRT 85
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 33.9 bits (78), Expect = 0.016
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 26 PICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
+ + G GSGKTSF+ L + + +++ DP
Sbjct: 20 GFVIGLYGAWGSGKTSFLNLLEDELKEFPEEFHIVYFDP 58
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 32.3 bits (74), Expect = 0.050
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 33 GMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDV 69
G GSGK++ K + + VI+ D R+V
Sbjct: 9 GGIGSGKSTVAKILAELGF------PVIDADDVAREV 39
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 32.0 bits (73), Expect = 0.082
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
++++G +GSGK++ +K + L + VI +DP
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLAR--GGRVIVIDP 37
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 31.5 bits (72), Expect = 0.086
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYL---YDKQDNPYVINLDPACRD 68
+I+ G AGSGKT+ ++K + QD +V L
Sbjct: 3 VILQGEAGSGKTTLLQKIALLWAQGKLPQDFDFVFFLPCRELS 45
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 31.9 bits (73), Expect = 0.087
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQD-NPYVINLD---PACRD 68
K P ++++G+ GSGKT+ K + YL KQ ++ D PA +
Sbjct: 96 KKPPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIE 145
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.1 bits (70), Expect = 0.088
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 10/79 (12%)
Query: 30 IVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNVDPACRDV-PYLVNV 88
++ G GSGK++ KK + L VI+LD D+ + +
Sbjct: 3 LITGPPGSGKSTLAKKLAEKL-----GIPVISLD----DLLREEGLAELDDGELDDIDID 53
Query: 89 GELSMLLLNGNKLEHQILN 107
EL +L+ + +++
Sbjct: 54 LELLEEILDELAKQEWVID 72
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 31.2 bits (70), Expect = 0.096
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 25 KPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
++++G GSGKT+ + + L I+ +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGE 39
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 31.8 bits (72), Expect = 0.11
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 28 CLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
++V+G + +GKTSF SY P NLDP
Sbjct: 101 TVMVVGGSQNGKTSFCFTLISYALKLGKKPLFTNLDP 137
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 31.1 bits (71), Expect = 0.16
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 25 KPICLIVLGMAGSGKTSFVKKF 46
+ I L++LG SGK++ +K+
Sbjct: 1 REIKLLLLGAGESGKSTILKQM 22
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 30.6 bits (69), Expect = 0.16
Identities = 7/26 (26%), Positives = 15/26 (57%)
Query: 28 CLIVLGMAGSGKTSFVKKFSSYLYDK 53
+++ G +G+GKTS +++ L
Sbjct: 26 SVLLTGPSGTGKTSLLRELLEGLLVA 51
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 30.7 bits (70), Expect = 0.17
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 24 SKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP-ACRDVPYLVNVDPAC 79
+K I +++ G G GKTS K ++LD + + NVD
Sbjct: 1 TKNIKVLIYGPPGIGKTSLAKTLP-------PKTLFLDLDAGTTKVLSRGDNVDIRS 50
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 30.8 bits (70), Expect = 0.18
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 20 PEFKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNVDPAC 79
PEFK LI++G G GKT+FVK+ + ++K+ Y+ L + + N P C
Sbjct: 8 PEFK-----LILVGDGGVGKTTFVKRHLTGEFEKK---YIPTLGVEVHPLKFYTNCGPIC 59
Query: 80 RDV 82
+V
Sbjct: 60 FNV 62
>gnl|CDD|223510 COG0433, COG0433, HerA helicase [Replication, recombination, and
repair].
Length = 520
Score = 31.1 bits (70), Expect = 0.19
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 31 VLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
+LG GSGK++ K L K VI DP
Sbjct: 173 ILGSTGSGKSNLAKVLLEELLGKDGATVVI-FDP 205
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 30.5 bits (69), Expect = 0.23
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 20 PEFKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYV 59
P FK L+++G G+GKT+FVK+ + ++K+ P +
Sbjct: 12 PSFK-----LVIVGDGGTGKTTFVKRHLTGEFEKKYEPTI 46
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 30.5 bits (70), Expect = 0.27
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 16/50 (32%)
Query: 31 VLGMAGSGKTSFVKKFSS-------------YLY--DKQDNPYVINLDPA 65
VLG G+G+T+ V+++ Y+ D D P + L PA
Sbjct: 35 VLGEPGTGRTTLVRRYLEERAKKEPTPDDWCYVNNFDDPDRPRALRL-PA 83
>gnl|CDD|216796 pfam01935, DUF87, Domain of unknown function DUF87. The function
of this prokaryotic domain is unknown. It contains
several conserved aspartates and histidines that could
be metal ligands.
Length = 218
Score = 30.4 bits (69), Expect = 0.29
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 31 VLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
+LG GSGK++ V L +K+ +I DP
Sbjct: 28 ILGSTGSGKSNTVAVLLEELLEKKGATVLI-FDP 60
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 29.9 bits (68), Expect = 0.33
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 24 SKPICLIVLGMAG---SGKTSFVKKFSSYLYDKQDNPYVINLD 63
KP +I++G+AG SGKT+ K+ S L + VI+LD
Sbjct: 3 KKPEKVIIIGIAGGSGSGKTTVAKELSEQL--GVEKVVVISLD 43
>gnl|CDD|226648 COG4185, COG4185, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 187
Score = 29.7 bits (67), Expect = 0.36
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 26 PICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
IV G GSGK++ +S L +N D
Sbjct: 2 KRLDIVAGPNGSGKSTVY---ASTLAPLLPGIVFVNAD 36
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 30.2 bits (69), Expect = 0.39
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 14 SSGDHGPEFKSKPICLIVL-GMAGSGKTSFVKKFSSYLYDKQDNPYVINLD---PA 65
+ KP +I++ G+ GSGKT+ K + YL K ++ D PA
Sbjct: 87 GGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADTYRPA 142
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 29.8 bits (68), Expect = 0.40
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 24 SKPICLIVLGMAGSGKTSFVKKFSSYL 50
S+P+ +++ G G+GKT+ VKK L
Sbjct: 53 SRPLNVLIYGPPGTGKTTTVKKVFEEL 79
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 29.6 bits (67), Expect = 0.41
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 29 LIVL-GMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
LI++ G+ GSGK++F ++ ++ V++ D
Sbjct: 1 LILMVGLPGSGKSTFARR-----LLRELGAVVLSSD 31
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 29.5 bits (67), Expect = 0.42
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 28 CLIVLGMAGSGKTSFVKKFSSYL 50
+ + G G GKT+ VKK L
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELL 23
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 30.1 bits (67), Expect = 0.43
Identities = 24/105 (22%), Positives = 50/105 (47%), Gaps = 15/105 (14%)
Query: 17 DHGPEFKSKPICLIVLGMAGSGKT----SFVKKFSSYLYDKQDNPYVINLDPACRDVPYL 72
D P+ P + V+G G+GK+ S V++F+ D+ P + + R + +L
Sbjct: 60 DRTPKDLPPPFIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGPITV-VSGKTRRITFL 118
Query: 73 VNVDPACR-DVPYLVNVGELS---MLLLNGN-KLEHQILNFQKLA 112
C D+ +++V +++ +LL++GN E + + F +
Sbjct: 119 -----ECPSDLHQMIDVAKIADLVLLLIDGNFGFEMETMEFLNIL 158
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 29.9 bits (68), Expect = 0.46
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKFSSYLYDK 53
K KP+ ++ +G+ G+GKT+ + K + YL
Sbjct: 137 KGKPVVIVFVGVNGTGKTTTIAKLAYYLKKN 167
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 29.1 bits (66), Expect = 0.53
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
+++ G GKT+ + +F L + N INLD
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSE--NILYINLD 37
>gnl|CDD|237453 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 29.3 bits (66), Expect = 0.66
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
L++LG GSGK++ K ++ L + YV LD
Sbjct: 39 LVILGRNGSGKSTIAKHMNALLIPSEGKVYVDGLD 73
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 28.8 bits (65), Expect = 0.67
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 26 PICLIVLGMAGSGKTSFVKKFSSYLYDK 53
+ + + G G GKT+ V K + L +K
Sbjct: 5 AMKIFITGRPGVGKTTLVLKIAEKLREK 32
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 29.2 bits (66), Expect = 0.68
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 29 LIVL-GMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
LI+L G+ SGK++ K+ + YL +K + VI+ +
Sbjct: 1 LIILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDE 36
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.4 bits (64), Expect = 0.69
Identities = 6/19 (31%), Positives = 13/19 (68%)
Query: 28 CLIVLGMAGSGKTSFVKKF 46
++ G +GSGKT+ +++
Sbjct: 6 IGVLTGESGSGKTTLLRRL 24
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles
at different stages of viral RNA replication, as
dissected by mutational analysis.
Length = 226
Score = 29.3 bits (66), Expect = 0.70
Identities = 6/18 (33%), Positives = 13/18 (72%)
Query: 29 LIVLGMAGSGKTSFVKKF 46
++V G+ G GK++ ++K
Sbjct: 1 IVVHGVPGCGKSTLIRKL 18
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 29.0 bits (65), Expect = 0.75
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 29 LIVLGMAGSGKTSFVKKFSS 48
++VLG+ G+GKTS + SS
Sbjct: 2 ILVLGLDGAGKTSLLHSLSS 21
>gnl|CDD|147018 pfam04656, Pox_E6, Pox virus E6 protein. Family of pox virus E6
proteins.
Length = 566
Score = 29.2 bits (66), Expect = 0.78
Identities = 9/20 (45%), Positives = 17/20 (85%)
Query: 42 FVKKFSSYLYDKQDNPYVIN 61
++K++++YLY +D+PYVI
Sbjct: 415 YIKEYNTYLYLNEDDPYVIY 434
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 0.86
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 30 IVLGMAGSGKTSFVKKF 46
+V G G+GKT KF
Sbjct: 277 LVSGATGTGKTLLASKF 293
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase.
Members of this protein family are the bacterial
polynucleotide kinase-phosphatase (Pnkp) whose genes
occur paired with genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis
is that the combination of Pnkp (RNA repair) and Hen1
(RNA modification) serves to first repair RNA damage
from ribotoxins and then perform a modification that
prevents the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 29.2 bits (66), Expect = 0.88
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 6/27 (22%)
Query: 20 PEFKSKPICLIVL-GMAGSGKTSFVKK 45
PE L+VL G +GSGK++F +K
Sbjct: 6 PEL-----SLVVLVGASGSGKSTFARK 27
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. Arf (ADP-ribosylation factor)/Arl
(Arf-like) small GTPases. Arf proteins are activators
of phospholipase D isoforms. Unlike Ras proteins they
lack cysteine residues at their C-termini and therefore
are unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a
unique structural device, interswitch toggle, that
implements front-back communication from N-terminus to
the nucleotide binding site. Arf-like (Arl) proteins
are close relatives of the Arf, but only Arl1 has been
shown to function in membrane traffic like the Arf
proteins. Arl2 has an unrelated function in the folding
of native tubulin, and Arl4 may function in the
nucleus. Most other Arf family proteins are so far
relatively poorly characterized. Thus, despite their
significant sequence homologies, Arf family proteins
may regulate unrelated functions.
Length = 158
Score = 28.7 bits (65), Expect = 0.88
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 28 CLIVLGMAGSGKTSFVKKF 46
+++LG+ G+GKT+ + K
Sbjct: 1 RILMLGLDGAGKTTILYKL 19
>gnl|CDD|177505 PHA03000, PHA03000, Hypothetical protein; Provisional.
Length = 566
Score = 28.8 bits (65), Expect = 1.0
Identities = 7/20 (35%), Positives = 17/20 (85%)
Query: 42 FVKKFSSYLYDKQDNPYVIN 61
F+K++++YLY +++P V++
Sbjct: 415 FIKEYNTYLYLNEEDPLVLD 434
>gnl|CDD|169051 PRK07667, PRK07667, uridine kinase; Provisional.
Length = 193
Score = 28.5 bits (64), Expect = 1.1
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 33 GMAGSGKTSFVKKFSSYLYDKQDNP--YVINLD 63
G++ SGKT+FV + KQ+ ++ ++D
Sbjct: 24 GLSRSGKTTFVANLKENM--KQEGIPFHIFHID 54
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small
guanosine triphosphatases (GTPases). Rab GTPases form
the largest family within the Ras superfamily. There
are at least 60 Rab genes in the human genome, and a
number of Rab GTPases are conserved from yeast to
humans. Rab GTPases are small, monomeric proteins that
function as molecular switches to regulate vesicle
trafficking pathways. The different Rab GTPases are
localized to the cytosolic face of specific
intracellular membranes, where they regulate distinct
steps in membrane traffic pathways. In the GTP-bound
form, Rab GTPases recruit specific sets of effector
proteins onto membranes. Through their effectors, Rab
GTPases regulate vesicle formation, actin- and
tubulin-dependent vesicle movement, and membrane
fusion. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 28.2 bits (64), Expect = 1.1
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNP 57
++++G +G GKTS + +F + +
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKS 31
>gnl|CDD|225398 COG2842, COG2842, Uncharacterized ATPase, putative transposase
[General function prediction only].
Length = 297
Score = 28.5 bits (64), Expect = 1.2
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 21 EFKSKPICL-IVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPA 65
SK L +V G AG GKT K ++ N +I DP+
Sbjct: 88 RPASKTGSLVVVYGYAGLGKTQAAKNYAP----SNPNALLIEADPS 129
>gnl|CDD|216591 pfam01591, 6PF2K, 6-phosphofructo-2-kinase. This enzyme occurs
as a bifunctional enzyme with
fructose-2,6-bisphosphatase. The bifunctional enzyme
catalyzes both the synthesis and degradation of
fructose-2,6-bisphosphate, a potent regulator of
glycolysis. This enzyme contains a P-loop motif.
Length = 219
Score = 28.5 bits (64), Expect = 1.2
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 19 GPEFKSKPICLIVLGMAGSGKTSFVKKFSSYL 50
GP F + ++++G+ GKT KK + YL
Sbjct: 3 GPNFTNSKTLIVMVGLPARGKTYISKKLTRYL 34
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 28.8 bits (65), Expect = 1.3
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 2 AEEKVSDNSGPASSGDHGPEFKSKPI-CLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVI 60
A E VSD A +G P ++PI + LG G GKT K + L+ + I
Sbjct: 499 AVEAVSDAIRRARAGLGDP---NRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRI 555
Query: 61 N 61
+
Sbjct: 556 D 556
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
This model describes the DndB protein encoded by an
operon associated with a sulfur-containing modification
to DNA. The operon is sporadically distributed in
bacteria, much like some restriction enzyme operons.
DndD is described as a putative ATPase. The small
number of examples known so far include species from
among the Firmicutes, Actinomycetes, Proteobacteria,
and Cyanobacteria [DNA metabolism,
Restriction/modification].
Length = 650
Score = 28.5 bits (64), Expect = 1.4
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQ 54
KPI LI G+ G+GKT+ + LY K+
Sbjct: 26 SPKPIILIG-GLNGAGKTTLLDAIQLALYGKR 56
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily
consists of a set of proteins characterized only in
Xenopus leavis, to date. In Xenopus Ras-dva expression
is activated by the transcription factor Otx2 and
begins during gastrulation throughout the anterior
ectoderm. Ras-dva expression is inhibited in the
anterior neural plate by factor Xanf1. Downregulation
of Ras-dva results in head development abnormalities
through the inhibition of several regulators of the
anterior neural plate and folds patterning, including
Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation
of Ras-dva also interferes with the FGF-8a signaling
within the anterior ectoderm. Most Ras proteins contain
a lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Ras proteins.
Length = 197
Score = 28.3 bits (63), Expect = 1.4
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 3/24 (12%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYD 52
L+ +G AG GKT+ +++F LYD
Sbjct: 2 LVFMGAAGVGKTALIQRF---LYD 22
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.
Members of this protein are L-seryl-tRNA(Sec) kinase.
This enzyme is part of a two-step pathway in Eukaryota
and Archaea for performing selenocysteine biosynthesis
by changing serine misacylated on selenocysteine-tRNA
to selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 28.2 bits (63), Expect = 1.5
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDK 53
+I+ G+ G GK++F K+ + L +K
Sbjct: 2 IILTGLPGVGKSTFSKELAKKLSEK 26
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 28.0 bits (63), Expect = 1.6
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDK--QDNPYVIN 61
L+V G GSGKT+ V+ + LY ++N N
Sbjct: 39 LLVQGPPGSGKTAAVRALARELYGDPWENNFTEFN 73
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 28.0 bits (63), Expect = 1.6
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDP 64
++V G GKT+ +++F L + VI DP
Sbjct: 23 IVVYGPRRCGKTALLREFLEELREL--GYRVIYYDP 56
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7
is a small Rab GTPase that regulates vesicular traffic
from early to late endosomal stages of the endocytic
pathway. The yeast Ypt7 and mammalian Rab7 are both
involved in transport to the vacuole/lysosome, whereas
Ypt7 is also required for homotypic vacuole fusion.
Mammalian Rab7 is an essential participant in the
autophagic pathway for sequestration and targeting of
cytoplasmic components to the lytic compartment.
Mammalian Rab7 is also proposed to function as a tumor
suppressor. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 172
Score = 27.6 bits (62), Expect = 1.7
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 5/26 (19%)
Query: 29 LIVLGMAGSGKTSFV-----KKFSSY 49
+I+LG +G GKTS + KKFS+
Sbjct: 3 VIILGDSGVGKTSLMNQYVNKKFSNQ 28
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 27.7 bits (62), Expect = 1.8
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKF 46
K + + +++LG+ +GKT+ +KKF
Sbjct: 11 KEREMRILMLGLDNAGKTTILKKF 34
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 27.7 bits (62), Expect = 2.1
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 24 SKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYV--INLDPACRDVPYLVNV 75
+P +I+ G G+GKT+ VK L + N V IN C ++ V
Sbjct: 40 ERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYIN----CLELRTPYQV 89
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 27.8 bits (62), Expect = 2.2
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 7/51 (13%)
Query: 18 HGPEFKSKPICLIVLGMAGSGKTSFVKKFSSYL----YDKQDNPYVINLDP 64
E +K L++LG GSGKT+F+++ + +L + +D P + L+
Sbjct: 217 EALEKYAK---LLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNA 264
>gnl|CDD|234914 PRK01184, PRK01184, hypothetical protein; Provisional.
Length = 184
Score = 27.6 bits (62), Expect = 2.3
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 29 LIVLGMAGSGKTSFVKKFSSY 49
+ V+GM GSGK F K
Sbjct: 4 IGVVGMPGSGKGEFSKIAREM 24
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity.
The Ras superfamily is divided into at least four
families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf
families. This superfamily also includes proteins like
the GTP translation factors, Era-like GTPases, and
G-alpha chain of the heterotrimeric G proteins. Members
of the Ras superfamily regulate a wide variety of
cellular functions: the Ras family regulates gene
expression, the Rho family regulates cytoskeletal
reorganization and gene expression, the Rab and
Sar1/Arf families regulate vesicle trafficking, and the
Ran family regulates nucleocytoplasmic transport and
microtubule organization. The GTP translation factor
family regulates initiation, elongation, termination,
and release in translation, and the Era-like GTPase
family regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 27.4 bits (61), Expect = 2.3
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 31 VLGMAGSGKTSFVKKF 46
V+G G GK+S +
Sbjct: 2 VVGRGGVGKSSLLNAL 17
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 27.5 bits (62), Expect = 2.4
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 28 CLIVLGMAGSGKTSFVKK-FSSYLYDKQDNPY 58
++V+G +G GK++F+ F + LY + P
Sbjct: 6 NIMVVGESGLGKSTFINTLFGTKLYPSKYPPA 37
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 27.9 bits (63), Expect = 2.5
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 20 PEFKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
KP ++++G+ GSGKT+ K + Y K ++ D
Sbjct: 89 LVLPLKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAAD 132
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.1 bits (58), Expect = 2.6
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 29 LIVL-GMAGSGKTSFVKKFSSYLYDKQDNPYVI 60
+I + G +GSGK++ KK + L + V+
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGG--RSVVVL 31
>gnl|CDD|238980 cd02022, DPCK, Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24)
catalyzes the phosphorylation of dephosphocoenzyme A
(dCoA) to yield CoA, which is the final step in CoA
biosynthesis.
Length = 179
Score = 27.1 bits (61), Expect = 2.6
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 6/37 (16%)
Query: 33 GMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDV 69
G GSGK++ K VI+ D +V
Sbjct: 6 GGIGSGKSTVAKLLKELGI------PVIDADKIAHEV 36
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it
a potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 170
Score = 27.1 bits (60), Expect = 2.6
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQ 54
KS + +I+LG G GK+S + ++ + +D Q
Sbjct: 2 KSSLLKVILLGDGGVGKSSLMNRYVTNKFDTQ 33
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 27.2 bits (61), Expect = 2.7
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 24 SKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
+P+ +++ G G+GKT + L N I+ D
Sbjct: 10 ERPVAVLLGGQPGAGKTELARALLEEL--GGGNVVRIDPD 47
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 27.7 bits (62), Expect = 2.7
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 25 KPI-CLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
+PI + G G GKT K +SY + +D +I LD
Sbjct: 537 RPIASFLFSGPTGVGKTELTKALASYFFGSEDA--MIRLD 574
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 322
Score = 27.3 bits (61), Expect = 2.8
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPA 65
+ G G GKT+ + L + +++ DPA
Sbjct: 5 VFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPA 41
>gnl|CDD|226986 COG4639, COG4639, Predicted kinase [General function prediction
only].
Length = 168
Score = 27.0 bits (60), Expect = 2.8
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 29 LIVL-GMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACR 67
L+VL G +GSGK++F K+ + YV++LD
Sbjct: 4 LVVLRGASGSGKSTFAKE------NFL-QNYVLSLDDLRL 36
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 27.5 bits (61), Expect = 2.9
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 24 SKPI-CLIVLGMAGSGKTSFVKKFSSYLYDKQD 55
++PI + LG G GKT K +++++D D
Sbjct: 595 NRPIGSFLFLGPTGVGKTELCKALANFMFDSDD 627
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 27.5 bits (61), Expect = 3.0
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 23 KSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
K K ++ +G+ GSGKT+ K + Y K P ++ D
Sbjct: 97 KGKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCAD 137
>gnl|CDD|235498 PRK05541, PRK05541, adenylylsulfate kinase; Provisional.
Length = 176
Score = 26.9 bits (60), Expect = 3.1
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 22 FKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPY--VINLD 63
K + + G+AGSGKT+ K LY++ Y VI LD
Sbjct: 3 MKPNGYVIWITGLAGSGKTTIAKA----LYERLKLKYSNVIYLD 42
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
Miro is one of few Rho subfamilies that lack this
feature.
Length = 180
Score = 26.8 bits (60), Expect = 3.3
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 31 VLGMAGSGKTSFVKKFSSYLYDKQDNP------YVIN 61
VLG GSGK++ ++ F + + Y +N
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVN 45
>gnl|CDD|185387 PRK15490, PRK15490, Vi polysaccharide biosynthesis protein TviE;
Provisional.
Length = 578
Score = 27.4 bits (60), Expect = 3.4
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 35 AGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVPYLVNV 75
AG F++ S ++ D + +NLD ACR LVN+
Sbjct: 504 AGGSAECFIEGVSGFILD---DAQTVNLDQACRYAEKLVNL 541
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 27.0 bits (60), Expect = 3.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 22 FKSKPICLIVLGMAGSGKTSFVKKFS 47
K ++V+G G+GKT+FV+ S
Sbjct: 6 NKMIETKIVVIGPVGAGKTTFVRALS 31
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 26.7 bits (60), Expect = 3.7
Identities = 7/14 (50%), Positives = 10/14 (71%), Gaps = 1/14 (7%)
Query: 29 LIVL-GMAGSGKTS 41
IVL G G+GK++
Sbjct: 6 NIVLIGFMGAGKST 19
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs
is not yet characterized. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 26.6 bits (59), Expect = 4.0
Identities = 10/29 (34%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLY-DKQDN 56
+I++G + GKT V++F S + ++Q N
Sbjct: 6 IILIGDSNVGKTCVVQRFKSGTFSERQGN 34
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 27.0 bits (60), Expect = 4.0
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 28 CLIVL-GMAGSGKTSFVKKFSSYL 50
LI++ G+ G GK++ K + L
Sbjct: 4 KLIIIEGLPGFGKSTTAKMLNDIL 27
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 26.4 bits (59), Expect = 4.0
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACRDVP 70
+ + G G GKT+ + YL +K I+ DP D+P
Sbjct: 2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPD--DLP 41
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 116
Score = 26.2 bits (58), Expect = 4.1
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 29 LIVLGMAGSGKTSFVKKF 46
++V+G GSGK+S + +
Sbjct: 2 VVVIGDKGSGKSSLLSQL 19
>gnl|CDD|215856 pfam00318, Ribosomal_S2, Ribosomal protein S2.
Length = 205
Score = 26.8 bits (60), Expect = 4.3
Identities = 5/20 (25%), Positives = 13/20 (65%)
Query: 44 KKFSSYLYDKQDNPYVINLD 63
K Y+Y +++ ++I+L+
Sbjct: 17 PKMKPYIYGERNGIHIIDLE 36
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is
not ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a
95-base pair insertion, producing an alternative
sequence for the 30 amino acids at the C-terminus. The
two human isoforms are presumably the result of
alternative splicing. Since they differ at the
C-terminus but not in the GTP-binding region, they are
predicted to be targeted to different cellular
locations. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins.
Length = 213
Score = 26.7 bits (59), Expect = 4.3
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQ 54
++VLG SGKTS +++F+ + K
Sbjct: 3 IVVLGDGASGKTSLIRRFAQEGFGKS 28
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 27.2 bits (61), Expect = 4.4
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 24 SKPI-CLIVLGMAGSGKTSFVKKFSSYLYDKQDN 56
++PI + LG G GKT K + +L+D +D
Sbjct: 592 NRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDA 625
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 26.9 bits (60), Expect = 4.6
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 29 LIVLGMAGSGKTSFVKK-FSSYLYDKQDNP 57
L+V+G +G GKT+ + F + L ++ P
Sbjct: 7 LMVVGESGLGKTTLINTLFLTDLIPERGIP 36
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed
in a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 201
Score = 26.5 bits (59), Expect = 4.8
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 29 LIVLGMAGSGKTSFVKKF 46
++V+G G GKTS +K++
Sbjct: 3 VLVIGDLGVGKTSIIKRY 20
>gnl|CDD|129254 TIGR00150, T6A_YjeE, tRNA threonylcarbamoyl adenosine
modification protein YjeE. This protein family belongs
to a four-gene system responsible for the
threonylcarbamoyl adenosine (t6A) tRNA modification.
Members of this family have a conserved
nucleotide-binding motif GXXGXGKT and a
nucleotide-binding fold. Member protein YjeE of
Haemophilus influenzae (HI0065) was shown to have
(weak) ATPase activity [Protein synthesis, tRNA and
rRNA base modification].
Length = 133
Score = 26.3 bits (58), Expect = 4.9
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 22 FKSKPICLIVL--GMAGSGKTSFVKKF 46
K +VL G G+GKT+ V+
Sbjct: 16 AKPLDFGTVVLLKGDLGAGKTTLVQGL 42
>gnl|CDD|221211 pfam11760, CbiG_N, Cobalamin synthesis G N-terminal. Members of
this family are involved in cobalamin synthesis. The
cbiH precorrin methylase gene of Synechocystis sp. PCC
6803 represents a fusion between cbiH and cbiG. As
other multi-functional proteins involved in cobalamin
biosynthesis catalyze adjacent steps in the pathway,
including CysG, CobL (CbiET), CobIJ and CobA-HemD, it
is therefore possible that CbiG catalyzes a reaction
step adjacent to CbiH. In the anaerobic pathway such a
step could be the formation of a gamma lactone, which
is thought to help to mediate the anaerobic ring
contraction process. Within the cobalamin synthesis
pathway CbiG catalyzes the both the opening of the
lactone ring and the extrusion of the two-carbon
fragment of cobalt-precorrin-5A from C-20 and its
associated methyl group (deacylation) to give
cobalt-precorrin-5B. The N-terminal of the enzyme is
conserved in this family, and the C-terminal and the
mid-sections are conserved independently in other
families, CbiG_C and CbiG_mid, although the distinct
function of each region is unclear.
Length = 82
Score = 25.5 bits (57), Expect = 4.9
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 28 CLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLDPACR 67
+I + AG V+ + L DK +P V+ +D R
Sbjct: 12 AIIFIMAAGI----VVRLIAPLLKDKDTDPAVVVVDEDGR 47
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 26.5 bits (59), Expect = 4.9
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
+I++G GSGK++ ++ L N V +LD
Sbjct: 4 IILIGSGGSGKSTLARQLGEKL-----NIPVHHLD 33
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 26.5 bits (59), Expect = 5.1
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 29 LIVL-GMAGSGKTSFVKKFSSYL 50
IV+ G+ G+GKT+ + L
Sbjct: 5 FIVIEGIDGAGKTTQAELLKERL 27
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions,
Prophage functions].
Length = 220
Score = 26.7 bits (59), Expect = 5.1
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 21 EFKSKPICLIVLGMAGSGKTSFVKKF 46
K P ++ G G+GKTS +K
Sbjct: 7 NIKRIPNMYLIYGKPGTGKTSTIKYL 32
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 26.0 bits (58), Expect = 5.6
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 30 IVL-GMAGSGKTSFVKKFSSYL 50
IVL GM G+GKT+ + + L
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKAL 23
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 169
Score = 26.4 bits (58), Expect = 6.0
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLY 51
++++G AG GKT V++F+ L+
Sbjct: 10 IVLIGNAGVGKTCLVRRFTQGLF 32
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 26.1 bits (58), Expect = 6.5
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 22 FKSKPICLIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
K + G++GSGK++ L+ K + Y+ LD
Sbjct: 19 KGQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYL--LD 58
>gnl|CDD|165416 PHA03145, PHA03145, helicase-primase primase subunit; Provisional.
Length = 1058
Score = 26.5 bits (58), Expect = 6.6
Identities = 13/24 (54%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 64 PAC-RDVPYLVNVDPACRDVPYLV 86
AC R +P V V PAC DVP V
Sbjct: 833 LACGRLLPVFV-VPPACPDVPAFV 855
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 26.3 bits (59), Expect = 7.2
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 29 LIVL-GMAGSGKTSFVKK 45
L+VL G GSGKT ++
Sbjct: 143 LVVLGGNTGSGKTELLQA 160
>gnl|CDD|181536 PRK08674, PRK08674, bifunctional phosphoglucose/phosphomannose
isomerase; Validated.
Length = 337
Score = 26.1 bits (58), Expect = 7.3
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD---PACRDVPYLV 73
+++ GM GSG + L+D+ P +N D PA D LV
Sbjct: 37 IVISGMGGSGIGGDL--LRILLFDELKVPVFVNRDYTLPAFVDEKTLV 82
>gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional.
Length = 684
Score = 26.5 bits (59), Expect = 7.4
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 29 LIVLGMAGSGKTS 41
L+VL AGSGKTS
Sbjct: 212 LLVLAGAGSGKTS 224
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 26.2 bits (58), Expect = 7.7
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLY 51
+VLG GSG ++ +K +S
Sbjct: 90 TVVLGRPGSGCSTLLKTIASNTD 112
>gnl|CDD|172457 PRK13951, PRK13951, bifunctional shikimate
kinase/3-dehydroquinate synthase; Provisional.
Length = 488
Score = 26.4 bits (58), Expect = 7.8
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYL 50
+ ++GM GSGK++ K+ S L
Sbjct: 3 IFLVGMMGSGKSTIGKRVSEVL 24
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast
Ypt6p, the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 161
Score = 25.7 bits (57), Expect = 7.9
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPY 58
L+ LG GKTS + +F +YD DN Y
Sbjct: 3 LVFLGDQSVGKTSIITRF---MYDTFDNQY 29
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 160
Score = 25.6 bits (57), Expect = 8.0
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 17/54 (31%)
Query: 29 LIVLGMAGSGKTSFVKKF------SSY------LYDKQ----DNPYVIN-LDPA 65
L+VLG G GK++ +F Y Y KQ Y ++ LD A
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTA 55
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 25.6 bits (57), Expect = 8.6
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 33 GMAGSGKTSFVKKFSSYLYDKQDN 56
G G GKT+ V K + L ++
Sbjct: 7 GPPGVGKTTLVLKIAELLKEEGYK 30
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain.
Length = 173
Score = 25.6 bits (57), Expect = 8.6
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLYDKQDNPYVINLD 63
++++G+ G GKT+ K + YL K ++ D
Sbjct: 3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAAD 37
>gnl|CDD|130724 TIGR01663, PNK-3'Pase, polynucleotide 5'-kinase 3'-phosphatase.
This model represents the metazoan
5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is
believed to be involved in repair of oxidative DNA
damage. Removal of 3' phosphates is essential for the
further processing of the break by DNA polymerases. The
central phosphatase domain is a member of the IIIA
subfamily (TIGR01662) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. As is
common in this superfamily, the enzyme is magnesium
dependent. A difference between this enzyme and other
HAD-superfamily phosphatases is in the third conserved
catalytic motif which usually contains two conserved
aspartate residues believed to be involved in binding
the magnesium ion. Here, the second aspartate is
replaced by a conserved arginine residue which may
indicate an interaction with the phosphate backbone of
the substrate. Very close relatives of this domain are
also found separate from the N- and C-terminal domains
seen here, as in the 3'-phosphatase found in plants. The
larger family of these domains is described by
TIGR01664. Outside of the phosphatase domain is a P-loop
ATP-binding motif associated with the kinase activity.
The entry for the mouse homolog, GP|7108591, appears to
be missing a large piece of sequence corresponding to
the first conserved catalytic motif of the phosphatase
domain as well as the conserved threonine of the second
motif. Either this is a sequencing artifact or this may
represent a pseudo- or non-functional gene. Note that
the EC number for the kinase function is: 2.7.1.78.
Length = 526
Score = 26.1 bits (57), Expect = 8.9
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 17 DHGPEFKSKPICLIVLGMAGSGKTSFVKKF 46
D E +I +G G+GK+ F KKF
Sbjct: 366 DAPCEM------VIAVGFPGAGKSHFCKKF 389
>gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated.
Length = 226
Score = 25.8 bits (57), Expect = 9.0
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 6 VSD-NSGPASSGDHGPEFKSKPICLIVLGMAGSGKTSF 42
V++ N S DH P + S P+ ++ G GSGKT
Sbjct: 25 VTESNRAAVSLVDHWPNWPS-PVVVLA-GPVGSGKTHL 60
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 25.8 bits (57), Expect = 9.0
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 29 LIVLGMAGSGKTSFVKKFSSYLY 51
LI+ G GSGK++F+KK +
Sbjct: 55 LILQGAQGSGKSTFLKKLGGEWF 77
>gnl|CDD|218480 pfam05176, ATP-synt_10, ATP10 protein. ATP 10 is essential for the
assembly of a functional mitochondrial ATPase complex.
Length = 255
Score = 25.7 bits (57), Expect = 9.4
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 38 GKTSFVKKFSSYLYDKQDNPYVINLDP 64
GK S V+ FSS +KQ Y N
Sbjct: 124 GKVSVVRLFSSAWGEKQARSYFKNPFL 150
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 26.0 bits (58), Expect = 9.6
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 29 LIVL-GMAGSGKTSFVKK 45
LIVL GM GSGKT +
Sbjct: 129 LIVLGGMTGSGKTELLHA 146
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
0.320 0.138 0.421
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,367,784
Number of extensions: 630433
Number of successful extensions: 965
Number of sequences better than 10.0: 1
Number of HSP's gapped: 965
Number of HSP's successfully gapped: 114
Length of query: 147
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 59
Effective length of database: 7,034,450
Effective search space: 415032550
Effective search space used: 415032550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.0 bits)