RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045702
(728 letters)
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. These proteins catalyze membrane
fission during clathrin-mediated endocytosis. Dynamin
consists of five domains; an N-terminal G domain that
binds and hydrolyzes GTP, a middle domain (MD) involved
in self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific, mediates
uptake of synaptic vesicles in presynaptic terminals;
dynamin-2 is expressed ubiquitously and similarly
participates in membrane fission; mutations in the MD,
PH and GED domains of dynamin 2 have been linked to
human diseases such as Charcot-Marie-Tooth peripheral
neuropathy and rare forms of centronuclear myopathy.
Dynamin 3 participates in megakaryocyte progenitor
amplification, and is also involved in cytoplasmic
enlargement and the formation of the demarcation
membrane system. This family also includes
interferon-induced Mx proteins that inhibit a wide range
of viruses by blocking an early stage of the replication
cycle. Dynamin oligomerizes into helical structures
around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 397 bits (1021), Expect = e-134
Identities = 164/278 (58%), Positives = 205/278 (73%), Gaps = 5/278 (1%)
Query: 43 ISLPQVAVVGSQSSGKSSVLEALVGRDFLPRGCDICTRRPLALMLVNRPR-NPGDDGREW 101
I LPQ+ VVG QSSGKSSVLEALVGRDFLPRG ICTRRPL L L P + D+ EW
Sbjct: 1 IDLPQIVVVGDQSSGKSSVLEALVGRDFLPRGSGICTRRPLELQLRRSPSESDEDEKEEW 60
Query: 102 AEFRHLPGKRFFDFTKVRQEIMAETNKEAGSNRGVSEKQIGLKISSPNVLNMTLVDLPGI 161
EF HL K F DF ++R+EI ET++ AG N+G+S + I L+I SP+V N+TLVDLPG+
Sbjct: 61 GEFLHLKSKEFTDFEELREEIEKETDRVAGENKGISPEPIRLEIESPDVPNLTLVDLPGL 120
Query: 162 TKVPVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDALQMAREADPTGSRT 221
KVPVGDQP DIE +IR M+ +YI IILAV PAN DLA S+AL++ARE DP G RT
Sbjct: 121 IKVPVGDQPEDIEEQIRSMVKSYISNPRSIILAVVPANVDLANSEALKLAREVDPEGERT 180
Query: 222 IGVITKLDIMDRGTNACNFLL---GKVVPLRLGYVGVVNRSQEDINKNRSMQDALAYEKN 278
IGV+TKLD+MD GT+A + LL GKV+PL+LGYVGVVNRSQ+DI+ +S+++AL E+
Sbjct: 181 IGVLTKLDLMDPGTDAEDILLLLQGKVIPLKLGYVGVVNRSQKDIDSGKSIEEALEAEEE 240
Query: 279 FFHDHPVYN-GLSDRCGIPQLAKKLNQILEQHIRMVLP 315
FF HP Y + R G P L K+L+++L++HIR LP
Sbjct: 241 FFETHPWYKLLPASRVGTPALRKRLSKLLQKHIRESLP 278
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 379 bits (975), Expect = e-127
Identities = 140/283 (49%), Positives = 199/283 (70%), Gaps = 1/283 (0%)
Query: 241 LLGKVVPLRLGYVGVVNRSQEDINKNRSMQDALAYEKNFFHDHPVYNGLSDRCGIPQLAK 300
L KV PL+LGYVGVVNRSQ+DIN +S+++AL E+ FF +HP Y L++RCG P LAK
Sbjct: 5 LENKVYPLKLGYVGVVNRSQQDINDKKSIKEALEDERAFFENHPHYRTLAERCGTPYLAK 64
Query: 301 KLNQILEQHIRMVLPGLKSELHSRLNAVAKELQKYGD-VMESKAEKETMLLNILTKYCEA 359
KLNQ L HIR LP LKS+++ +L KEL++YGD E AEK LL+++T + +
Sbjct: 65 KLNQELVNHIRKSLPDLKSQINKKLQETEKELERYGDDPPEDPAEKGAFLLDLITAFNQD 124
Query: 360 FSAMVDGRSQEISTKELSGGARIRYIFQSIFVKTLEEVDPCQDLTDEDIRTAIQNATGPR 419
F ++DG ++ST ELSGGARIRYIF F K L+ +DP + L+DE+IRTAI+N G R
Sbjct: 125 FKNLIDGEEDDLSTNELSGGARIRYIFHEWFPKLLKSIDPFEKLSDEEIRTAIRNYRGRR 184
Query: 420 NALFVPEVPFEVLVRRQIARLLDPCLQCLRFVYDELIKMSHACAVTELQRFPVLRRHLDD 479
LFVPE FE+LV++QI RL +P L+C+ VY+EL ++ A EL RFP L+ + +
Sbjct: 185 LPLFVPEKAFELLVKKQIKRLEEPALKCVDLVYEELRRIFLKIASKELSRFPNLKEAIKE 244
Query: 480 VMGKFIRDSVRPAERMIDSLIEIEMDYINSSNPNFVGGKKAVE 522
V+ +R+ + P E+M+ LI++E+ YIN+++P+F+GG +AV+
Sbjct: 245 VVEDILREQLEPTEKMVRDLIDMELAYINTNHPDFIGGLQAVK 287
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 306 bits (786), Expect = e-100
Identities = 145/244 (59%), Positives = 185/244 (75%), Gaps = 8/244 (3%)
Query: 21 SVIPIINRLQDIFSPVDGELSKISLPQVAVVGSQSSGKSSVLEALVGRDFLPRGCDICTR 80
+IP++N+LQD FS + G+ + LPQ+AVVG QS+GKSSVLE VGRDFLPRG I TR
Sbjct: 3 ELIPLVNKLQDAFSAL-GQSCDLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTR 61
Query: 81 RPLALMLVNRPRNPGDDGREWAEFRHLPGKRFFDFTKVRQEIMAETNKEAGSNRGVSEKQ 140
RPL L L+ E+AEF H GK+F DF +VR EI AET++ G+N+G+S
Sbjct: 62 RPLILQLIK-------SKTEYAEFLHCKGKKFTDFDEVRNEIEAETDRVTGTNKGISGIP 114
Query: 141 IGLKISSPNVLNMTLVDLPGITKVPVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANS 200
I L++ SP+VLN+TL+DLPGITKV VGDQP DIE +I+KMI +I +E C+ILAV+PAN+
Sbjct: 115 INLRVYSPHVLNLTLIDLPGITKVAVGDQPPDIEYQIKKMIKQFISREECLILAVTPANT 174
Query: 201 DLATSDALQMAREADPTGSRTIGVITKLDIMDRGTNACNFLLGKVVPLRLGYVGVVNRSQ 260
DLA SDAL++A+E DP G RTIGVITKLD+MD GT+A + L K++PLR GY+GVVNRSQ
Sbjct: 175 DLANSDALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDILENKLLPLRRGYIGVVNRSQ 234
Query: 261 EDIN 264
+DI
Sbjct: 235 KDIE 238
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 198 bits (505), Expect = 1e-59
Identities = 88/182 (48%), Positives = 114/182 (62%), Gaps = 15/182 (8%)
Query: 48 VAVVGSQSSGKSSVLEALVGRDFLPRGCDICTRRPLALMLVNRPRNPGDDGR-EWAEFRH 106
+AVVG QS+GKSSVL AL+GRD LPRG TRRPL L L P + E+ +
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDGL- 59
Query: 107 LPGKRFFDFTKVRQEIMAETNKEAGSNRGVSEKQIGLKISSPNVLNMTLVDLPGITKVPV 166
K+F DF+++R+EI ET+K +G+ +G+S + I L+I SP V +TLVD PG+ V V
Sbjct: 60 ---KKFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPGLDSVAV 116
Query: 167 GDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDALQMAREADPTGSRTIGVIT 226
GDQ + YI+ IILAV AN DL+TS+AL +ARE DP G RTIGV+T
Sbjct: 117 GDQ---------DLTEEYIKP-ADIILAVVDANHDLSTSEALFLAREVDPNGKRTIGVLT 166
Query: 227 KL 228
K
Sbjct: 167 KD 168
>gnl|CDD|223771 COG0699, COG0699, Predicted GTPases (dynamin-related) [General
function prediction only].
Length = 546
Score = 168 bits (428), Expect = 8e-45
Identities = 153/620 (24%), Positives = 254/620 (40%), Gaps = 85/620 (13%)
Query: 99 REWAEFRHLPGKRFFDFTKVRQEIMAETNKEAGSNRGVSEKQIGLKISSPNVLNMTLVDL 158
E EF H P RF DF++VR E ET K+ G N G++E I LKI++ +L +T VDL
Sbjct: 1 TEEFEFTHAPIFRFLDFSRVRSEKEKETLKDDGRNSGITEVIIELKIAAERLLQLTDVDL 60
Query: 159 PGITKVPVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDALQMAREADPTG 218
PG+ KVP+ +P DI + + I EN +IL N+D ++++ READ
Sbjct: 61 PGLRKVPLSLEPEDIAQEDELLDLGKIEIENALILLGIAPNADEEAELSIEVIREADR-- 118
Query: 219 SRTIGVITKLDIMDRGTNACNFLLGKVVPLRLGYVGVVNRSQEDINKNRSMQDALAYEKN 278
V TK++ ++ GTN + L G V VV+ + DI ++ +AL E
Sbjct: 119 -----VPTKINFLNGGTNL-------TLILGNGDVLVVDALETDIQLLKTALEALVKELE 166
Query: 279 FFHDHPVYNGLSDRCGIPQLAKKLNQILEQHIRMVLPGLKSELHSRLNAVAKELQKYGDV 338
+F +HP+ +P L K L++ILE H+R++ + + +Q D+
Sbjct: 167 YFAEHPLLEDNEKLVLLPYLKKLLSKILELHLRLLPK---------YDKLQDVIQLSQDL 217
Query: 339 MESKAEKETMLLNILTKYCEAFSAMVDGRSQEISTKELSGGARIRYIFQSIFVKTLEEVD 398
E++ L ++ + S EL GARIR
Sbjct: 218 FENEV------LAVIQTLLKRLS-------------ELVRGARIRLNIILF--------S 250
Query: 399 PCQDLTDEDIRTAIQNATGPRNALFVPEVPFEVLVRRQIARLLDPCLQCLRFVYDELIKM 458
++++D + + G R +L + LV I + Q LR + EL+++
Sbjct: 251 DLEEVSDSPVLLKELASKGERPSLLSGLTLLDTLVETPIGQFDTQINQLLRKLISELVRI 310
Query: 459 SHACA-VTELQRFPVLRRHLDDVMGKFIRDSVRPAERMIDSLIEIEMDYINSSNPNFVGG 517
FP L L++V+ + E + ++I+IE YIN+ +P F+
Sbjct: 311 LLKELESASSSPFPKLSEALEEVVNQLKNKVDSGLESGLLAIIDIEERYINTKHPLFLSL 370
Query: 518 KKAVEVAMQQLKSSQDGTDGEKGTLSEIGQRFGLTSQGRHSQSNNQRAASVGGNSSSRTW 577
+ A L D E R S+ R S G +S +
Sbjct: 371 R----QAAAILSKVLD--------NLEALLRSLDDSR--------LRELSDMGLNSLLS- 409
Query: 578 GFPIIFGGKVQAGESPASRSP--HETLHNVEQLPSTIQLTEPPSIL--GPLEMTEQEAVE 633
+ S S +E L + L L + E++ +E
Sbjct: 410 --NNLEE---HLLGSDFSLYKFLNEFLELKKLDAL---LATLGEALRRLTGLLPERKTLE 461
Query: 634 ILVTKLLLQSYYDVVRKNVQDLVPKSIMHFLVNHAKRNLHNTFIQKLYRENHVEELLQEH 693
+ K LL+S + + ++D V K+I L N KR +++LY E +ELL+
Sbjct: 462 KQLIKSLLESLLI-LAQKIRDSVLKAIFELLKNKRKRLAQKQRLKRLYLEQLEDELLRTA 520
Query: 694 DEVAANRRQVKEVSLVLQQA 713
+E+ R +++ L+ A
Sbjct: 521 EEILELRLLLEQFLEALKLA 540
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 106 bits (267), Expect = 1e-27
Identities = 35/90 (38%), Positives = 62/90 (68%)
Query: 631 AVEILVTKLLLQSYYDVVRKNVQDLVPKSIMHFLVNHAKRNLHNTFIQKLYRENHVEELL 690
+E+ + LL+SY+++VRK + D +PK+IM+FLVN +K +L +Q LY++ ++ELL
Sbjct: 1 ELEVEEIRRLLKSYFNIVRKRIADQIPKAIMYFLVNESKESLQKELLQLLYKKEDLDELL 60
Query: 691 QEHDEVAANRRQVKEVSLVLQQAVQTLDEV 720
+E E+A R+++K+ L++A + L EV
Sbjct: 61 KEDPEIAQKRKELKKRLERLKKAREILAEV 90
>gnl|CDD|128597 smart00302, GED, Dynamin GTPase effector domain.
Length = 92
Score = 93.8 bits (234), Expect = 4e-23
Identities = 35/92 (38%), Positives = 60/92 (65%)
Query: 629 QEAVEILVTKLLLQSYYDVVRKNVQDLVPKSIMHFLVNHAKRNLHNTFIQKLYRENHVEE 688
E E+ K L++SY+ +V K + D VPK+IM+ LVN +K +L N + LY+E ++E
Sbjct: 1 YEDSELEEIKSLVKSYFTIVSKTLADQVPKAIMYLLVNESKDSLQNELLALLYKEELLDE 60
Query: 689 LLQEHDEVAANRRQVKEVSLVLQQAVQTLDEV 720
LL+E E+A+ R+++K+ +L++A Q + V
Sbjct: 61 LLEEDPEIASKRKELKKRLELLKKARQIIAAV 92
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The
dynamin family of large mechanochemical GTPases
includes the classical dynamins and dynamin-like
proteins (DLPs) that are found throughout the Eukarya.
This family also includes bacterial DLPs. These
proteins catalyze membrane fission during
clathrin-mediated endocytosis. Dynamin consists of five
domains; an N-terminal G domain that binds and
hydrolyzes GTP, a middle domain (MD) involved in
self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific,
mediates uptake of synaptic vesicles in presynaptic
terminals; dynamin-2 is expressed ubiquitously and
similarly participates in membrane fission; mutations
in the MD, PH and GED domains of dynamin 2 have been
linked to human diseases such as Charcot-Marie-Tooth
peripheral neuropathy and rare forms of centronuclear
myopathy. Dynamin 3 participates in megakaryocyte
progenitor amplification, and is also involved in
cytoplasmic enlargement and the formation of the
demarcation membrane system. This family also includes
mitofusins (MFN1 and MFN2 in mammals) that are involved
in mitochondrial fusion. Dynamin oligomerizes into
helical structures around the neck of budding vesicles
in a GTP hydrolysis-dependent manner.
Length = 180
Score = 38.7 bits (91), Expect = 0.004
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 48 VAVVGSQSSGKSSVLEALVGRDFLPRGCDICT 79
+AVVG S+GKS++L AL+G + LP G T
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTT 34
>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 = 35.9 bits (83), Expect = 0.030
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 49 AVVGSQSSGKSSVLEALVGRDFLPRG-CDICTRRP 82
VVG GKSS+L AL+G + TR P
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDP 35
Score = 30.9 bits (70), Expect = 1.5
Identities = 23/115 (20%), Positives = 42/115 (36%), Gaps = 11/115 (9%)
Query: 152 NMTLVDLPGITKVPVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDALQMA 211
+ LVD PG+ + E R +R + I+L V + + L +
Sbjct: 48 KLVLVDTPGLDEF----GGLGREELARL----LLRGADLILLVVDSTDRESEEDAKLLIL 99
Query: 212 READPTGSRTIGVITKLDIMDRGTNACNFLLGKVVPLRLG--YVGVVNRSQEDIN 264
R G I V K+D+++ L + + LG V ++ E ++
Sbjct: 100 RRLRKEGIPIILVGNKIDLLEEREVE-ELLRLEELAKILGVPVFEVSAKTGEGVD 153
>gnl|CDD|212684 cd11734, Ssq1_like_NBD, Nucleotide-binding domain of Saccharomyces
cerevisiae Ssq1 and similar proteins. Ssq1p (also
called Stress-seventy subfamily Q protein 1, Ssc2p,
Ssh1p, mtHSP70 homolog) belongs to the heat shock
protein 70 (HSP70) family of chaperones that assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). S. cerevisiae Ssq1p is a mitochondrial
chaperone that is involved in iron-sulfur (Fe/S) center
biogenesis. Ssq1p plays a role in the maturation of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia).
Length = 373
Score = 36.7 bits (85), Expect = 0.040
Identities = 18/65 (27%), Positives = 28/65 (43%)
Query: 429 FEVLVRRQIARLLDPCLQCLRFVYDELIKMSHACAVTELQRFPVLRRHLDDVMGKFIRDS 488
FE L + R + PC QCL+ + V + R P ++ + ++ GK S
Sbjct: 296 FEQLRKSICKRTIYPCKQCLKDAGLRKKDIDEVILVGGMTRMPYIQNVVQEIFGKKPSKS 355
Query: 489 VRPAE 493
V P E
Sbjct: 356 VNPDE 360
>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 = 34.9 bits (81), Expect = 0.077
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 50 VVGSQSSGKSSVLEALVGRDF 70
V+G++ SGKS++L+A +GR F
Sbjct: 9 VLGAKGSGKSALLQAFLGRSF 29
>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 = 33.5 bits (77), Expect = 0.100
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 48 VAVVGSQSSGKSSVLEALVGRDFLP 72
V V+G + SGKSS+L LVG +F P
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPP 26
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 33.2 bits (77), Expect = 0.25
Identities = 19/41 (46%), Positives = 23/41 (56%), Gaps = 8/41 (19%)
Query: 28 RLQDI-FSPVDGELSKISLPQVAVVGSQSSGKSSVLEALVG 67
L+DI GEL VA+VG SGKSS+L AL+G
Sbjct: 20 TLKDINLEVPKGEL-------VAIVGPVGSGKSSLLSALLG 53
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter
family is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 33.3 bits (77), Expect = 0.28
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 6 SFSNKNVAASTTIGSSVIPIINRLQDIFSPVDGELSKISLPQVAVVGSQSSGKSSVLEAL 65
SF N V ++ S ++ + P GEL A++G +GKS++L AL
Sbjct: 5 SFRNLTVTVKSSPSKSGKQLLKNVSGKAKP--GEL-------TAIMGPSGAGKSTLLNAL 55
Query: 66 VGR 68
GR
Sbjct: 56 AGR 58
>gnl|CDD|234064 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of
this family are homodimeric ferredoxins from nitrogen
fixation regions of many nitrogen-fixing bacteria. As
characterized in Rhodobacter capsulatus, these proteins
are homodimeric, with two 4Fe-4S clusters bound per
monomer. Although nif-specific, this protein family is
not usiveral, as other nitrogenase systems may
substitute flavodoxins, or different types of ferredoxin
[Central intermediary metabolism, Nitrogen fixation].
Length = 91
Score = 30.4 bits (69), Expect = 0.75
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 9/58 (15%)
Query: 138 EKQIG----LKISSPNVLNMTLVDLPGITKVPVGDQPTDIEARIRKMIMAYIRQENCI 191
EK IG K+ +VL + GI + D + I + +M NCI
Sbjct: 21 EKCIGCGRCYKVCGRDVLTLK-----GINEEGELVASDDDDDEIERKVMVVANPGNCI 73
>gnl|CDD|191308 pfam05596, Taeniidae_ag, Taeniidae antigen. This family consists
of several antigen proteins from Taenia and Echinococcus
(tapeworm) species.
Length = 64
Score = 29.6 bits (67), Expect = 0.77
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 13/62 (20%)
Query: 266 NRSMQDALAYEKNFFHDHPVYNGLSDRCGIPQLAKKLN---QILEQHIRMVLP----GLK 318
+S+ L + FF + P L + + QLAK+L Q IR L GLK
Sbjct: 9 KKSVMKQLGEVRRFFREDP----LGQK--LAQLAKELKEICQEARLKIRTSLKEYVKGLK 62
Query: 319 SE 320
+E
Sbjct: 63 NE 64
>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 = 31.4 bits (71), Expect = 0.94
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 26 INRLQDIFSPVDGELSKISLPQVAVVGSQSSGKSSVLEALV-GRDFLPRGCDICTRRP 82
+ RL D P V + G +GK+S+L L+ G CD R P
Sbjct: 9 LERLLDALRRA----RSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNP 62
>gnl|CDD|218112 pfam04497, Pox_E2-like, Poxviridae protein. This family of
proteins is restricted to Poxviridae. It contains a
number of differently named uncharacterized proteins.
Length = 727
Score = 32.4 bits (74), Expect = 0.97
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 304 QILEQHIRMVLPGLKSELHSRLNAVAKELQKYGDVME-----SKAEKETMLLNILTKYC 357
+I+ + +HSRL V E Y D+++ + LT Y
Sbjct: 333 RIVVCDSGKKVRIKSLPIHSRLVMVMCEEMGYEDIVDFLDNLDVDTLVKKGADPLTDYL 391
>gnl|CDD|218237 pfam04738, Lant_dehyd_C, Lantibiotic dehydratase, C terminus.
Lantibiotics are ribosomally synthesised antimicrobial
agents derived from ribosomally synthesised peptides.
They are produced by bacteria of the Firmicutes phylum,
and include mutacin, subtilin, and nisin. Lantibiotic
peptides contain thioether bridges termed lanthionines
that are thought to be generated by dehydration of
serine and threonine residues followed by addition of
cysteine residues. This family constitutes the
C-terminus of the enzyme proposed to catalyze the
dehydration step.
Length = 500
Score = 31.9 bits (73), Expect = 1.2
Identities = 32/170 (18%), Positives = 53/170 (31%), Gaps = 35/170 (20%)
Query: 295 IPQLAKKLNQILEQHIRMVLPGLKSELHSRLNAVAKELQKYGDVMESKAEKETMLLNI-- 352
I + K L ++ E+ + + P + L+ L A+E+ +V E A +LL +
Sbjct: 86 IGEGRKLLQEL-EEKMSQLTPSRRGPLYVDLRLDAEEVTLGENVAEEIARAAELLLRLSP 144
Query: 353 -------LTKYCEAFSAMVDGRSQEISTKEL-----------------------SGGARI 382
L Y E F G + + EL
Sbjct: 145 NPAGRPYLRDYHERFLERY-GENALVPLLELLDPDLGLGAPAGYLGPENAPNTSLDQKEF 203
Query: 383 RYIFQSIFVKTLEEVDPCQDLTDEDIRTAIQNATGPRNALFVPEVPFEVL 432
R + L LTD+D+ ++ PE+ FEV
Sbjct: 204 RQLLAEAQEAALRGGREIV-LTDDDLEDLARDDGDDPFVPPSPELMFEVK 252
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 31.8 bits (73), Expect = 1.2
Identities = 38/134 (28%), Positives = 51/134 (38%), Gaps = 21/134 (15%)
Query: 302 LNQILEQHIRMVLPGLKSELH--------SRLNAVAKEL--------QKYGDVMESKAEK 345
LN I+E VLP LK L + + L +K DV + K
Sbjct: 174 LNAIMEILKEEVLPPLK--LWEFYVLDVEKAVEQFKEALKSGKPKLPKKGSDVSLADILK 231
Query: 346 ETMLLNILTKYCEAFSAMVD-GRSQEISTKELSGGARIRYIFQSIFVKTLEEV-DPCQDL 403
+ LL I E F A VD ++ EI RI + F K L+E+ P
Sbjct: 232 KEELLIIQDPLYERFGATVDMEKAAEIFNSHRGDEERIEECLER-FRKALDELNVPLYRE 290
Query: 404 TDEDIRTAIQNATG 417
DED+ A+ N G
Sbjct: 291 YDEDLNAAVNNIIG 304
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 30.7 bits (70), Expect = 1.4
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 48 VAVVGSQSSGKSSVLEALVGR 68
V VVG GKSS++ AL GR
Sbjct: 102 VGVVGYPKVGKSSIINALKGR 122
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 31.7 bits (73), Expect = 1.4
Identities = 13/26 (50%), Positives = 20/26 (76%), Gaps = 2/26 (7%)
Query: 47 QVAVVGSQSSGKSSVLEALVGRDFLP 72
++A+VG +GK+S+L AL+G FLP
Sbjct: 378 RIALVGPSGAGKTSLLNALLG--FLP 401
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 31.7 bits (72), Expect = 1.4
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 39 ELSKISLPQ--VAVVGSQSSGKSSVLEALVGRDFLP 72
EL KIS + +A+VG+ +GKS+ + A+VG + LP
Sbjct: 61 ELRKISRLEMVLAIVGTMKAGKSTTINAIVGTEVLP 96
>gnl|CDD|148168 pfam06400, Alpha-2-MRAP_N, Alpha-2-macroglobulin RAP, N-terminal
domain. The alpha-2-macroglobulin receptor-associated
protein (RAP) is a intracellular glycoprotein that binds
to the 2-macroglobulin receptor and other members of the
low density lipoprotein receptor family. The protein
inhibits binding of all currently known ligands of these
receptors. The N-terminal domain is predominately alpha
helical. Two different studies have provided conflicted
domain boundaries.
Length = 121
Score = 30.1 bits (68), Expect = 1.5
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 301 KLNQILEQHIRMVLPGLK-SELHSRLNAVAKELQKY----GDVMESKAEKETMLLN---- 351
KLNQ+ E+ R+ L +K ELHS L K+ + + ++ EKE L
Sbjct: 45 KLNQVWEKAQRLRLSEVKLKELHSDLKIQEKDELAWKKLKAEGLDKDGEKEAKLRRKLNV 104
Query: 352 ILTKY 356
I++KY
Sbjct: 105 IMSKY 109
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 30.6 bits (70), Expect = 1.5
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 10/40 (25%)
Query: 48 VAVVGSQSSGKSSVLEAL----------VGRDFLPRGCDI 77
+ + G S+GK+++LEAL GR+++
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVVPEYGREYIEEQLAD 41
>gnl|CDD|109649 pfam00601, Flu_NS2, Influenza non-structural protein (NS2). NS2
may play a role in promoting normal replication of the
genomic RNAs by preventing the replication of
short-length RNA species.
Length = 94
Score = 29.6 bits (66), Expect = 1.6
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 654 DLVPKSIMHFLVNHAKRNLHNTFIQKLYRE-NHVEELLQEHDEVAANRRQVKEVSLVLQQ 712
D + + +M H+ + + + ++LY++ + L+ EH V AN E + Q
Sbjct: 16 DSLGELVMRTGDLHSLQERNRLWREELYQKFEEIRWLILEHRTVLANTENSFEQ-ITFLQ 74
Query: 713 AVQTLDEVESE 723
A+Q L EVE E
Sbjct: 75 ALQLLYEVEDE 85
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 31.0 bits (71), Expect = 1.6
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 155 LVDLPG--ITKVPVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDA-LQMA 211
LVDLPG KVP + + +K+I Y+ + + V ++ D +M
Sbjct: 74 LVDLPGYGYAKVPKEVK-----EKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMI 128
Query: 212 READPTGSRTIGVITKLD 229
G I V+TK D
Sbjct: 129 EFLLELGIPVIVVLTKAD 146
Score = 28.7 bits (65), Expect = 8.1
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 44 SLPQVAVVGSQSSGKSSVLEALVGRDFLPR 73
LP++A G + GKSS++ AL + L R
Sbjct: 23 DLPEIAFAGRSNVGKSSLINALTNQKNLAR 52
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 30.4 bits (69), Expect = 2.1
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 12/65 (18%)
Query: 151 LNMTLVDLPGIT-KV-PVGDQPTDIEARIRKMIMAYIRQENCIILAVSPANSDLATSDAL 208
NM V +T KV +G QP R R M Y R N I+ V D A + L
Sbjct: 34 FNMRKVTKGNVTIKVWDLGGQP-----RFRSMWERYCRGVNAIVYVV-----DAADREKL 83
Query: 209 QMARE 213
++A+
Sbjct: 84 EVAKN 88
>gnl|CDD|206650 cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal
domain). Guanylate-binding protein (GBP), N-terminal
domain. Guanylate-binding proteins (GBPs) define a
group of proteins that are synthesized after activation
of the cell by interferons. The biochemical properties
of GBPs are clearly different from those of Ras-like
and heterotrimeric GTP-binding proteins. They bind
guanine nucleotides with low affinity (micromolar
range), are stable in their absence and have a high
turnover GTPase. In addition to binding GDP/GTP, they
have the unique ability to bind GMP with equal affinity
and hydrolyze GTP not only to GDP, but also to GMP.
Furthermore, two unique regions around the base and the
phosphate-binding areas, the guanine and the phosphate
caps, respectively, give the nucleotide-binding site a
unique appearance not found in the canonical
GTP-binding proteins. The phosphate cap, which
constitutes the region analogous to switch I,
completely shields the phosphate-binding site from
solvent such that a potential GTPase-activating protein
(GAP) cannot approach.
Length = 224
Score = 30.8 bits (70), Expect = 2.2
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 48 VAVVGSQSSGKSSVLEALVGR 68
V+V GSQSSGKS +L L G
Sbjct: 10 VSVFGSQSSGKSFLLNHLFGT 30
>gnl|CDD|227858 COG5571, COG5571, Autotransporter protein or domain, integral
membrane beta-barrel involved in protein secretion [Cell
motility and secretion].
Length = 239
Score = 30.9 bits (70), Expect = 2.2
Identities = 11/39 (28%), Positives = 13/39 (33%)
Query: 545 IGQRFGLTSQGRHSQSNNQRAASVGGNSSSRTWGFPIIF 583
G F L S + +QR S N T G F
Sbjct: 201 AGADFLLNSSIGAFAAASQRENSTENNQYLYTLGVSARF 239
>gnl|CDD|140213 PTZ00186, PTZ00186, heat shock 70 kDa precursor protein;
Provisional.
Length = 657
Score = 31.2 bits (70), Expect = 2.2
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 414 NATGPRNA-LFVPEVPFEVLVRRQIARLLDPCLQCLRFVYDELIKMSHACAVTELQRFPV 472
NA G ++ + + FE + +R I R + PC QC++ EL +++ V + R P
Sbjct: 309 NADGAQHIQMHISRSKFEGITQRLIERSIAPCKQCMKDAGVELKEINDVVLVGGMTRMPK 368
Query: 473 LRRHLDDVMGKFIRDSVRPAE 493
+ + K V P E
Sbjct: 369 VVEEVKKFFQKDPFRGVNPDE 389
>gnl|CDD|219768 pfam08267, Meth_synt_1, Cobalamin-independent synthase, N-terminal
domain. The N-terminal domain and C-terminal domains of
cobalamin-independent synthases together define a
catalytic cleft in the enzyme. The N-terminal domain is
thought to bind the substrate, in particular, the
negatively charged polyglutamate chain. The N-terminal
domain is also thought to stabilise a loop from the
C-terminal domain.
Length = 310
Score = 30.7 bits (70), Expect = 2.7
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 9/70 (12%)
Query: 612 IQLTEP-------PSILGPLEMTEQEAVEILVTKLLLQSYYDVVRKNVQDLV--PKSIMH 662
+Q+ EP L + E KLLL +Y+ V ++ L P +
Sbjct: 198 VQIDEPALVLDLPKEWLEAFKEAYAELASKGGLKLLLATYFGSVADALELLASLPVDGLG 257
Query: 663 FLVNHAKRNL 672
+ NL
Sbjct: 258 LDLVRGPENL 267
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members
commonly are called EngB based on homology to EngA, one
of several other GTPases of ribosome biogenesis.
Cutoffs as set find essentially all bacterial members,
but also identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about
80 percent of bacterial genomes [Protein synthesis,
Other].
Length = 178
Score = 29.7 bits (68), Expect = 3.1
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 44 SLPQVAVVGSQSSGKSSVLEALVGR 68
P++A G + GKSS++ AL R
Sbjct: 17 DGPEIAFAGRSNVGKSSLINALTNR 41
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 29.7 bits (68), Expect = 3.6
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 42 KISLPQVAVVGSQSSGKSSVLEALVGRD 69
+ +P VA+VG ++GKS++ AL G D
Sbjct: 38 RSGVPTVALVGYTNAGKSTLFNALTGAD 65
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.9 bits (65), Expect = 3.9
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 46 PQVAVVGSQSSGKSSVLEALV 66
P V VVG + SGK++++ L+
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLL 21
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase.
The Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show
sequence conservation in the region between the Walker
A and B motifs (G1 and G3 box motifs), to the exclusion
of other GTPases. TrmE is ubiquitous in bacteria and is
a widespread mitochondrial protein in eukaryotes, but
is absent from archaea. The yeast member of TrmE
family, MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein
involved in cell division control. Era is characterized
by a distinct derivative of the KH domain (the
pseudo-KH domain) which is located C-terminal to the
GTPase domain. EngA and its orthologs are composed of
two GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct
GTPases, gave rise to this family.
Length = 161
Score = 29.1 bits (66), Expect = 4.2
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 49 AVVGSQSSGKSSVLEALVGRD 69
A+ G + GKSS+L AL+G++
Sbjct: 1 AIFGRPNVGKSSLLNALLGQN 21
>gnl|CDD|235325 PRK04974, PRK04974, glycerol-3-phosphate acyltransferase;
Validated.
Length = 818
Score = 30.2 bits (69), Expect = 4.3
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 670 RNLHNTFIQKLYRENHV---EELLQEHDEVAANRRQVK-----EVSLVLQQAVQTLDEVE 721
+ L ++FIQ L E ++ + E +E +K EV L ++Q Q +E E
Sbjct: 757 KALFSSFIQTLREEGYIRDDDSGDLEFEETLEIYAILKRLLSPEVRLTIEQVAQAEEEEE 816
Query: 722 SE 723
++
Sbjct: 817 AK 818
>gnl|CDD|236272 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
Length = 167
Score = 29.2 bits (66), Expect = 4.6
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 317 LKSELHSRLNAVAKELQKYGD-VMESKAEKETML 349
LK+ SR+N ++K L++ + + ESK +KE L
Sbjct: 47 LKNFYKSRINKISKRLEEIQEKLKESKEKKEDAL 80
>gnl|CDD|239517 cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase
is a prototypical Nudix hydrolase that catalyzes the
hydrolysis of nucleoside and deoxynucleoside
triphosphates (NTPs and dNTPs) by substitution at a
beta-phosphorus to yield a nucleotide monophosphate
(NMP) and inorganic pyrophosphate (PPi). This enzyme
requires two divalent cations for activity; one
coordinates the phosphoryl groups of the NTP/dNTP
substrate, and the other coordinates to the enzyme. It
also contains the Nudix motif, a highly conserved
23-residue block (GX5EX7REUXEEXGU, where U = I, L or V),
that functions as metal binding and catalytic site. MutT
pyrophosphohydrolase is important in preventing errors
in DNA replication by hydrolyzing mutagenic nucleotides
such as 8-oxo-dGTP (a product of oxidative damage),
which can mispair with template adenine during DNA
replication, to guanine nucleotides.
Length = 124
Score = 28.2 bits (64), Expect = 5.9
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 577 WGFPIIFGGKVQAGESPA 594
W FP GGKV+ GE+P
Sbjct: 30 WEFP---GGKVEPGETPE 44
>gnl|CDD|223456 COG0379, NadA, Quinolinate synthase [Coenzyme metabolism].
Length = 324
Score = 29.5 bits (67), Expect = 6.1
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 168 DQPTDIEARIRKMIMAYIRQENCIILA---VSPANSDLA--TSDALQMAREA 214
+ D++ I+++ ++ N +ILA P D+A D+L++AREA
Sbjct: 18 MEDADLKEEIKRLK----KERNAVILAHNYQRPEIQDIADFVGDSLELAREA 65
>gnl|CDD|227406 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 29.5 bits (66), Expect = 6.7
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 7/52 (13%)
Query: 269 MQDALAYEKNFFHDHPVYNG-------LSDRCGIPQLAKKLNQILEQHIRMV 313
M DA Y + NG LS + K++NQI H ++
Sbjct: 1 MSDANPYSLRIYEMIETLNGVTFMNKILSINKNLSVYEKEINQIDNLHKDLL 52
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 29.3 bits (65), Expect = 6.9
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 49 AVVGSQSSGKSSVLEAL 65
++G SGKS++L+AL
Sbjct: 3 VIIGPNGSGKSNLLKAL 19
>gnl|CDD|183571 PRK12522, PRK12522, RNA polymerase sigma factor; Provisional.
Length = 173
Score = 28.7 bits (64), Expect = 7.4
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 625 EMTEQEAVEILVTKLLLQSYYDVVRKN------VQDLVPKSIMHFLVNHAKRNLHNTFIQ 678
+++ E + +T + ++++YD RK + DL K + N+ FIQ
Sbjct: 47 QLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHKEDGGEIEFADDVNISEEFIQ 106
Query: 679 KLYRENHVEELLQEHDE 695
K+ E + E++Q +E
Sbjct: 107 KVEAEM-IREVIQLLNE 122
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.5 bits (67), Expect = 7.5
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 41 SKISLPQVAVVGSQSSGKSSVLEALVGRD 69
S+ +P VA+VG ++GKS++ AL G D
Sbjct: 188 SRSGIPLVALVGYTNAGKSTLFNALTGAD 216
>gnl|CDD|218139 pfam04545, Sigma70_r4, Sigma-70, region 4. Region 4 of sigma-70
like sigma-factors are involved in binding to the -35
promoter element via a helix-turn-helix motif. Due to
the way Pfam works, the threshold has been set
artificially high to prevent overlaps with other
helix-turn-helix families. Therefore there are many
false negatives.
Length = 50
Score = 26.2 bits (59), Expect = 7.6
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 537 GEKGTLSEIGQRFGLTSQGRHSQ 559
GE TL EIG+R G+ S+ R Q
Sbjct: 18 GEGLTLEEIGERLGI-SRERVRQ 39
>gnl|CDD|115392 pfam06730, FAM92, FAM92 protein. This family of proteins has a
role in embryogenesis. During embryogenesis it is
essential for ectoderm and axial mesoderm development.
It may regulate cell proliferation and apoptosis.
Length = 219
Score = 28.8 bits (64), Expect = 8.1
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 463 AVTELQRFPV----LRRHLDDVMGKFIRDSVRPAERMIDSLIEIEM 504
A TELQR + RHL++ +G F + ++ +++I I IEM
Sbjct: 147 AETELQRAKMDAQRTSRHLEETIGNFEQQKLKDIKQIISEFITIEM 192
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 29.5 bits (67), Expect = 8.3
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 48 VAVVGSQSSGKSSVLEALVGRDFLPRGCDICTRR 81
+ +VG SGKS++ AL+G LP G I +
Sbjct: 38 LGIVGESGSGKSTLALALMG--LLPEGGRITSGE 69
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 8.9
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 47 QVAVVGSQSSGKSSVLEALVGRDF 70
++ V+G GK+++L LVG +F
Sbjct: 7 KIVVLGDGGVGKTTLLNRLVGDEF 30
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
0.317 0.134 0.377
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,873,152
Number of extensions: 3679316
Number of successful extensions: 3998
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3979
Number of HSP's successfully gapped: 81
Length of query: 728
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 624
Effective length of database: 6,324,786
Effective search space: 3946666464
Effective search space used: 3946666464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.0 bits)