RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005389
(699 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 = 388 bits (999), Expect = e-131
Identities = 169/278 (60%), Positives = 213/278 (76%), Gaps = 10/278 (3%)
Query: 45 IELPQVAVVGSQSSGKSSVLEALVGRDFLPRGNDICTRRPLVLQLLQTKT------DEEY 98
I+LPQ+ VVG QSSGKSSVLEALVGRDFLPRG+ ICTRRPL LQL ++ + EE+
Sbjct: 1 IDLPQIVVVGDQSSGKSSVLEALVGRDFLPRGSGICTRRPLELQLRRSPSESDEDEKEEW 60
Query: 99 GEFLHLPGKRFYDFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIFSPHVLDITLVDLPGI 158
GEFLHL K F DF E+R EI+ +TD+ AG NKG+S + IRL+I SP V ++TLVDLPG+
Sbjct: 61 GEFLHLKSKEFTDFEELREEIEKETDRVAGENKGISPEPIRLEIESPDVPNLTLVDLPGL 120
Query: 159 TKVPVGEQPADIEARIRTMIMSYIKQPSCLILAVTPANSDLANSDALQIAGIADPDGYRT 218
KVPVG+QP DIE +IR+M+ SYI P +ILAV PAN DLANS+AL++A DP+G RT
Sbjct: 121 IKVPVGDQPEDIEEQIRSMVKSYISNPRSIILAVVPANVDLANSEALKLAREVDPEGERT 180
Query: 219 IGIITKLDIMDRGTDARNLLL---GKVIPLRLGYVGVVNRSQEDIMFNRSIKDALVAEEK 275
IG++TKLD+MD GTDA ++LL GKVIPL+LGYVGVVNRSQ+DI +SI++AL AEE+
Sbjct: 181 IGVLTKLDLMDPGTDAEDILLLLQGKVIPLKLGYVGVVNRSQKDIDSGKSIEEALEAEEE 240
Query: 276 FFRSRPVYN-GLADRCGVPQLAKKLNQILVQHIKAILP 312
FF + P Y A R G P L K+L+++L +HI+ 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 = 382 bits (983), Expect = e-128
Identities = 142/292 (48%), Positives = 205/292 (70%), Gaps = 1/292 (0%)
Query: 234 ARNLLLGKVIPLRLGYVGVVNRSQEDIMFNRSIKDALVAEEKFFRSRPVYNGLADRCGVP 293
A ++L KV PL+LGYVGVVNRSQ+DI +SIK+AL E FF + P Y LA+RCG P
Sbjct: 1 AVDILENKVYPLKLGYVGVVNRSQQDINDKKSIKEALEDERAFFENHPHYRTLAERCGTP 60
Query: 294 QLAKKLNQILVQHIKAILPGLKSRISSALVSVAKEHASYGE-ITESKAGQGALLLNILSK 352
LAKKLNQ LV HI+ LP LKS+I+ L KE YG+ E A +GA LL++++
Sbjct: 61 YLAKKLNQELVNHIRKSLPDLKSQINKKLQETEKELERYGDDPPEDPAEKGAFLLDLITA 120
Query: 353 YSEAFSSMVEGKNEEMSTSELSGGARIHYIFQSIFVKSLEEVDPCEDLTDDDIRTAIQNA 412
+++ F ++++G+ +++ST+ELSGGARI YIF F K L+ +DP E L+D++IRTAI+N
Sbjct: 121 FNQDFKNLIDGEEDDLSTNELSGGARIRYIFHEWFPKLLKSIDPFEKLSDEEIRTAIRNY 180
Query: 413 TGPKSALFVPDVPFEVLIRRQIARLLDPSLQCARFIYDELMKISHHCLVNELQRFPVLRK 472
G + LFVP+ FE+L+++QI RL +P+L+C +Y+EL +I EL RFP L++
Sbjct: 181 RGRRLPLFVPEKAFELLVKKQIKRLEEPALKCVDLVYEELRRIFLKIASKELSRFPNLKE 240
Query: 473 RMDEVIGNFLREGLEPSETMIGHIIEMEMDYINTSHPNFIGGSKAVEIALQQ 524
+ EV+ + LRE LEP+E M+ +I+ME+ YINT+HP+FIGG +AV+ ++
Sbjct: 241 AIKEVVEDILREQLEPTEKMVRDLIDMELAYINTNHPDFIGGLQAVKKKEEE 292
>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 = 327 bits (839), Expect = e-108
Identities = 153/237 (64%), Positives = 192/237 (81%), Gaps = 2/237 (0%)
Query: 24 SVIPLVNKLQDIFAQLGSQSTIELPQVAVVGSQSSGKSSVLEALVGRDFLPRGNDICTRR 83
+IPLVNKLQD F+ LG ++LPQ+AVVG QS+GKSSVLE VGRDFLPRG+ I TRR
Sbjct: 3 ELIPLVNKLQDAFSALGQSCDLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRR 62
Query: 84 PLVLQLLQTKTDEEYGEFLHLPGKRFYDFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIF 143
PL+LQL+++KT EY EFLH GK+F DF E+R EI+A+TD+ G NKG+S I L+++
Sbjct: 63 PLILQLIKSKT--EYAEFLHCKGKKFTDFDEVRNEIEAETDRVTGTNKGISGIPINLRVY 120
Query: 144 SPHVLDITLVDLPGITKVPVGEQPADIEARIRTMIMSYIKQPSCLILAVTPANSDLANSD 203
SPHVL++TL+DLPGITKV VG+QP DIE +I+ MI +I + CLILAVTPAN+DLANSD
Sbjct: 121 SPHVLNLTLIDLPGITKVAVGDQPPDIEYQIKKMIKQFISREECLILAVTPANTDLANSD 180
Query: 204 ALQIAGIADPDGYRTIGIITKLDIMDRGTDARNLLLGKVIPLRLGYVGVVNRSQEDI 260
AL++A DP G RTIG+ITKLD+MD GTDAR++L K++PLR GY+GVVNRSQ+DI
Sbjct: 181 ALKLAKEVDPQGLRTIGVITKLDLMDEGTDARDILENKLLPLRRGYIGVVNRSQKDI 237
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 199 bits (507), Expect = 4e-60
Identities = 89/182 (48%), Positives = 115/182 (63%), Gaps = 20/182 (10%)
Query: 50 VAVVGSQSSGKSSVLEALVGRDFLPRGNDICTRRPLVLQL------LQTKTDEEYGEFLH 103
+AVVG QS+GKSSVL AL+GRD LPRG TRRPLVL+L + EY + L
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDGL- 59
Query: 104 LPGKRFYDFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIFSPHVLDITLVDLPGITKVPV 163
K+F DFSE+R EI+ +TDK +G KG+S + I L+I SP V +TLVD PG+ V V
Sbjct: 60 ---KKFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPGLDSVAV 116
Query: 164 GEQPADIEARIRTMIMSYIKQPSCLILAVTPANSDLANSDALQIAGIADPDGYRTIGIIT 223
G+Q + YIK P+ +ILAV AN DL+ S+AL +A DP+G RTIG++T
Sbjct: 117 GDQ---------DLTEEYIK-PADIILAVVDANHDLSTSEALFLAREVDPNGKRTIGVLT 166
Query: 224 KL 225
K
Sbjct: 167 KD 168
>gnl|CDD|223771 COG0699, COG0699, Predicted GTPases (dynamin-related) [General
function prediction only].
Length = 546
Score = 161 bits (409), Expect = 2e-42
Identities = 131/594 (22%), Positives = 229/594 (38%), Gaps = 100/594 (16%)
Query: 96 EEYGEFLHLPGKRFYDFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIFSPHVLDITLVDL 155
E EF H P RF DFS +R E + +T K+ G N G+++ I LKI + +L +T VDL
Sbjct: 1 TEEFEFTHAPIFRFLDFSRVRSEKEKETLKDDGRNSGITEVIIELKIAAERLLQLTDVDL 60
Query: 156 PGITKVPVGEQPADIEARIRTMIMSYIKQPSCLILAVTPANSDLANSDALQIAGIADPDG 215
PG+ KVP+ +P DI + + I+ + LIL N+D ++++ AD
Sbjct: 61 PGLRKVPLSLEPEDIAQEDELLDLGKIEIENALILLGIAPNADEEAELSIEVIREADR-- 118
Query: 216 YRTIGIITKLDIMDRGTDARNLLLGKVIPLRLGYVGVVNRSQEDIMFNRSIKDALVAEEK 275
+ TK++ ++ GT+ + L G V VV+ + DI ++ +ALV E +
Sbjct: 119 -----VPTKINFLNGGTNL-------TLILGNGDVLVVDALETDIQLLKTALEALVKELE 166
Query: 276 FFRSRPVYNGLADRCGVPQLAKKLNQILVQHIKAILPGLKSRISSALVSVAKEHASYGEI 335
+F P+ +P L K L++IL H+ +LP L V + E
Sbjct: 167 YFAEHPLLEDNEKLVLLPYLKKLLSKILELHL-RLLPKYDK-----LQDVIQLSQDLFE- 219
Query: 336 TESKAGQGALLLNILSKYSEAFSSMVEGKNEEMSTSELSGGARIHYIFQSIFVKSLEEVD 395
+L ++ + SEL GARI
Sbjct: 220 --------NEVLAVIQTLLKRL-------------SELVRGARIRLNIILF--------S 250
Query: 396 PCEDLTDDDIRTAIQNATGPKSALFVPDVPFEVLIRRQIARLLDPSLQCARFIYDELMKI 455
E+++D + + G + +L + L+ I + Q R + EL++I
Sbjct: 251 DLEEVSDSPVLLKELASKGERPSLLSGLTLLDTLVETPIGQFDTQINQLLRKLISELVRI 310
Query: 456 SHHCLVNELQ-RFPVLRKRMDEVIGNFLREGLEPSETMIGHIIEMEMDYINTSHPNFIGG 514
L + FP L + ++EV+ + E+ + II++E YINT HP F+
Sbjct: 311 LLKELESASSSPFPKLSEALEEVVNQLKNKVDSGLESGLLAIIDIEERYINTKHPLFLSL 370
Query: 515 SKAVEIALQQIKSSKVPLPITRHKDGVEPDKAPSSERSLKSRAILARQVNGIMADQGVRP 574
+A I L ++ + L + + R + +N ++++
Sbjct: 371 RQAAAI-LSKVLDNLEALLRSLDDSRL--------------RELSDMGLNSLLSNNLEEH 415
Query: 575 TVEVEKVAPAGNTSGSSWGISSIFGGSDNRVPAGKESVTNKPFSEPVQNVEHAFAMIHLR 634
+ + S + + F K E ++ +
Sbjct: 416 LLG---------SDFSLYKFLNEFLE------LKKLDALLATLGEALRRLTGL------- 453
Query: 635 EPPTILRPSESHSEQENVEIAVTKLLLRSYYDIVRKNIEDSIPKAVMHFLVNPE 688
E++ +E + K LL S I+ + I DS+ KA+ L N
Sbjct: 454 -----------LPERKTLEKQLIKSLLES-LLILAQKIRDSVLKAIFELLKNKR 495
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 60.2 bits (147), Expect = 2e-11
Identities = 20/34 (58%), Positives = 27/34 (79%)
Query: 653 EIAVTKLLLRSYYDIVRKNIEDSIPKAVMHFLVN 686
E+ + LL+SY++IVRK I D IPKA+M+FLVN
Sbjct: 3 EVEEIRRLLKSYFNIVRKRIADQIPKAIMYFLVN 36
>gnl|CDD|128597 smart00302, GED, Dynamin GTPase effector domain.
Length = 92
Score = 54.2 bits (131), Expect = 3e-09
Identities = 17/38 (44%), Positives = 26/38 (68%)
Query: 649 QENVEIAVTKLLLRSYYDIVRKNIEDSIPKAVMHFLVN 686
E+ E+ K L++SY+ IV K + D +PKA+M+ LVN
Sbjct: 1 YEDSELEEIKSLVKSYFTIVSKTLADQVPKAIMYLLVN 38
>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 = 41.4 bits (98), Expect = 5e-04
Identities = 18/39 (46%), Positives = 25/39 (64%)
Query: 50 VAVVGSQSSGKSSVLEALVGRDFLPRGNDICTRRPLVLQ 88
+AVVG S+GKS++L AL+G + LP G T VL+
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVLR 41
>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 = 40.5 bits (95), Expect = 7e-04
Identities = 35/211 (16%), Positives = 61/211 (28%), Gaps = 60/211 (28%)
Query: 51 AVVGSQSSGKSSVLEALVGRDFLPRGNDICTRRPLVLQLLQTKTDEEYGEFLHLPGKRFY 110
VVG GKSS+L AL+G + + T D + GK
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDV-----------PGTTRDPDVYVKELDKGKV-- 47
Query: 111 DFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIFSPHVLDITLVDLPGITKVPVGEQPADI 170
+ LVD PG+ +
Sbjct: 48 --------------------------------------KLVLVDTPGLDE----FGGLGR 65
Query: 171 EARIRTMIMSYIKQPSCLILAVTPANSDLANSDALQIAGIADPDGYRTIGIITKLDIMDR 230
E R ++ ++L V + + L I +G I + K+D+++
Sbjct: 66 EELAR----LLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEE 121
Query: 231 GTDARNLLLGKV-IPLRLGYVGVVNRSQEDI 260
L L ++ L + V ++ E +
Sbjct: 122 REVEELLRLEELAKILGVPVFEVSAKTGEGV 152
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 36.7 bits (85), Expect = 0.048
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 7/84 (8%)
Query: 8 NTTAAQSQPSAVPLGGS-VIPLVNKLQDIFAQLGS-----QSTIELPQV-AVVGSQSSGK 60
+ P +VP + + L +I + + L V A+VG+ +GK
Sbjct: 23 QLQLLEKMPLSVPGDDAPQLALPWSQPNIAERHAMLNNELRKISRLEMVLAIVGTMKAGK 82
Query: 61 SSVLEALVGRDFLPRGNDICTRRP 84
S+ + A+VG + LP N T P
Sbjct: 83 STTINAIVGTEVLPNRNRPMTALP 106
>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 = 35.3 bits (82), Expect = 0.053
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 52 VVGSQSSGKSSVLEALVGRDFLPRGN 77
V+G++ SGKS++L+A +GR F
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAY 34
>gnl|CDD|218027 pfam04324, Fer2_BFD, BFD-like [2Fe-2S] binding domain. The two Fe
ions are each coordinated by two conserved cysteine
residues. This domain occurs alone in small proteins
such as Bacterioferritin-associated ferredoxin (BFD).
The function of BFD is not known, but it may may be a
general redox and/or regulatory component involved in
the iron storage or mobilisation functions of
bacterioferritin in bacteria. This domain is also found
in nitrate reductase proteins in association with
Nitrite and sulphite reductase 4Fe-4S domain
(pfam01077), Nitrite/Sulfite reductase ferredoxin-like
half domain (pfam03460) and Pyridine
nucleotide-disulphide oxidoreductase (pfam00070). It is
also found in NifU nitrogen fixation proteins, in
association with NifU-like N terminal domain (pfam01592)
and NifU-like domain (pfam01106).
Length = 55
Score = 31.5 bits (72), Expect = 0.12
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 397 CEDLTDDDIRTAIQNATGPKSA 418
C +T+ +IR AI ATG K+
Sbjct: 6 CNGVTEGEIRDAIAEATGAKTL 27
>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 = 32.8 bits (75), Expect = 0.15
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 50 VAVVGSQSSGKSSVLEALVGRDFLP 74
V V+G + SGKSS+L LVG +F P
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPP 26
>gnl|CDD|226567 COG4081, COG4081, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 148
Score = 31.3 bits (71), Expect = 0.73
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 7/90 (7%)
Query: 199 LANSDALQIAGIADPDGYRTIGIITKLDIMDRGTDARNLLLGKV-----IPLRLGYVGVV 253
A AL++ +ADP+ Y + ++ + LL V + + V
Sbjct: 38 AATEAALKLLEVADPEKYYVDETVDLEKYLEDPIEGGILLAAFVHNDAGLQYAVTLKAVS 97
Query: 254 NRSQEDIMFNRSIKDALVAEEKFFRSRPVY 283
N I+F R +D L EE F V
Sbjct: 98 NPDTYAIVFGREAEDRL--EETGFLDAEVI 125
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.4 bits (72), Expect = 0.86
Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 30/92 (32%)
Query: 50 VAVVGSQSSGKSSVLEAL----------VGRDFLPRGNDICTRRPLVLQLLQTKTDEEYG 99
+ + G S+GK+++LEAL GR+++
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVVPEYGREYIEEQLAD-------------------- 41
Query: 100 EFLHLPGKRFYDFSEIRREIQAQTDKEAGGNK 131
LP F+E+ E Q + + A N
Sbjct: 42 GGDALPWADLLAFAELMLEAQLEQEAAAQANG 73
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 32.5 bits (75), Expect = 0.96
Identities = 14/30 (46%), Positives = 23/30 (76%), Gaps = 3/30 (10%)
Query: 49 QVAVVGSQSSGKSSVLEALVGRDFLP-RGN 77
++A+VG +GK+S+L AL+G FLP +G+
Sbjct: 378 RIALVGPSGAGKTSLLNALLG--FLPYQGS 405
>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 = 31.7 bits (73), Expect = 0.98
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 50 VAVVGSQSSGKSSVLEALVG 69
VA+VG SGKSS+L AL+G
Sbjct: 34 VAIVGPVGSGKSSLLSALLG 53
>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 = 1.3
Identities = 21/113 (18%), Positives = 39/113 (34%), Gaps = 11/113 (9%)
Query: 32 LQDIFAQLGSQSTIELPQVAVVGSQSSGKSSVLEALV-GRDFLPRGNDICTR-------- 82
L+ + L + P V + G +GK+S+L L+ G D R
Sbjct: 9 LERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQ 68
Query: 83 --RPLVLQLLQTKTDEEYGEFLHLPGKRFYDFSEIRREIQAQTDKEAGGNKGV 133
R L+ QLL+ E L + E +++ ++ + +
Sbjct: 69 ALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPL 121
>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 = 30.4 bits (69), Expect = 1.6
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 50 VAVVGSQSSGKSSVLEALVGR 70
V VVG GKSS++ AL GR
Sbjct: 102 VGVVGYPKVGKSSIINALKGR 122
>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 = 1.8
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 50 VAVVGSQSSGKSSVLEALVGR 70
V+V GSQSSGKS +L L G
Sbjct: 10 VSVFGSQSSGKSFLLNHLFGT 30
>gnl|CDD|238376 cd00735, bacteriophage_T4-like_lysozyme, Bacteriophage T4-like
lysozymes hydrolyse the beta-1,4-glycosidic bond between
N-acetylmuramic acid (MurNAc) and N-acetylglucosamine
(GlcNAc) in peptidoglycan heteropolymers of prokaryotic
cell walls. Members include a variety of bacteriophages
(T4, RB49, RB69, Aeh1) as well as Dictyostelium. .
Length = 164
Score = 30.5 bits (69), Expect = 1.9
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 212 DPDGYRTIGI---ITKLDIMDRGTDARNLLLGKVIPLRLGYVGVVNRSQEDIMFNRSIKD 268
D +GY TIGI IT+ D A N L K I R GV+ + + +F + +
Sbjct: 19 DTEGYPTIGIGHLITRKKTKDLN--AINSELSKQIG-REVTNGVITSEEVEALFEKDLAK 75
Query: 269 ALVAEEKFFRSRPVYNGL 286
A + PVY L
Sbjct: 76 AQRDIMSNPKLSPVYKKL 93
>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 = 30.5 bits (70), Expect = 1.9
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 46 ELPQVAVVGSQSSGKSSVLEALVGRD 71
+P VA+VG ++GKS++ AL G D
Sbjct: 40 GVPTVALVGYTNAGKSTLFNALTGAD 65
>gnl|CDD|240177 cd05156, ChoK_euk, Choline Kinase (ChoK) in eukaryotes. The ChoK
subfamily is part of a larger superfamily that includes
the catalytic domains of other kinases, such as the
typical serine/threonine/tyrosine protein kinases (PKs),
RIO kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). It is composed of
bacterial and eukaryotic choline kinases, as well as
eukaryotic ethanolamine kinase. ChoK catalyzes the
transfer of the gamma-phosphoryl group from ATP (or CTP)
to its substrate, choline, producing phosphorylcholine
(PCho), a precursor to the biosynthesis of two major
membrane phospholipids, phosphatidylcholine (PC) and
sphingomyelin (SM). Although choline is the preferred
substrate, ChoK also shows substantial activity towards
ethanolamine and its N-methylated derivatives. ChoK
plays an important role in cell signaling pathways and
the regulation of cell growth. Along with PCho, it is
involved in malignant transformation through Ras
oncogenes in various human cancers such as breast, lung,
colon, prostate, neuroblastoma, and hepatic lymphoma. In
mammalian cells, there are three ChoK isoforms (A-1,
A-2, and B) which are active in homo or heterodimeric
forms.
Length = 302
Score = 30.7 bits (70), Expect = 2.4
Identities = 40/207 (19%), Positives = 70/207 (33%), Gaps = 58/207 (28%)
Query: 316 SRISSAL------VSVAKEHASYGEITESKAGQGALLLNILSKYSEAFSSMV-EGKN-EE 367
S+IS L VS+ E A E + +LL + + E E
Sbjct: 4 SKISGGLTNAVYKVSLPDEDALSDEPRK-------VLLRVYGQSVELLIDRERELVVFAR 56
Query: 368 MSTSELSGGARIHYIFQSIFVKSLEEVDPCEDLTDDDIRTAIQNATGPKSALFVPDVPFE 427
+S L G +++ IF + +EE P LT +++R PD
Sbjct: 57 LSERNL--GPKLYGIFPNG---RIEEFIPSRTLTTEELR--------------DPD---- 93
Query: 428 VLIRRQIARLLDPSLQCARFIYDELMKISHHCLVNELQRFPVLRKRMDE-------VIGN 480
I +IAR + ++ ++ +S E P + K + + VI
Sbjct: 94 --ISAEIARRM-------AKLHSIVVPLSPE----ERDLTPAIWKLLKQWLDLAETVIEI 140
Query: 481 FLREGLEPSETMIGHIIEMEMDYINTS 507
+ + E + +E E Y+
Sbjct: 141 VDSDSEKLLEVELSLFLEDEAKYLRFL 167
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 30.6 bits (69), Expect = 3.4
Identities = 28/89 (31%), Positives = 42/89 (47%), Gaps = 13/89 (14%)
Query: 425 PFEVLIRRQIARLLDPSLQCARFIYDELMKISHHCLVNELQRFPVLRKRMDEVIGNFLRE 484
+V+I A L+ ARFI D L K +L RF + K+ +++IG+ L
Sbjct: 811 VQDVIIPYNCAEYF---LKVARFIDDLLEKFY------KLDRFYNV-KKKEDLIGH-LVI 859
Query: 485 GLEP--SETMIGHIIEMEMDYINTSHPNF 511
G+ P S M+G II + +HP F
Sbjct: 860 GMAPHTSAGMVGRIIGYSDALVGYAHPYF 888
>gnl|CDD|140213 PTZ00186, PTZ00186, heat shock 70 kDa precursor protein;
Provisional.
Length = 657
Score = 30.4 bits (68), Expect = 3.6
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 426 FEVLIRRQIARLLDPSLQCARFIYDELMKISHHCLVNELQRFPVLRKRMDEVIGNFLREG 485
FE + +R I R + P QC + EL +I+ LV + R P + + + + G
Sbjct: 325 FEGITQRLIERSIAPCKQCMKDAGVELKEINDVVLVGGMTRMPKVVEEVKKFFQKDPFRG 384
Query: 486 LEPSETM 492
+ P E +
Sbjct: 385 VNPDEAV 391
>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 = 3.7
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 46 ELPQVAVVGSQSSGKSSVLEALVGR 70
+ P++A G + GKSS++ AL R
Sbjct: 17 DGPEIAFAGRSNVGKSSLINALTNR 41
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 29.4 bits (67), Expect = 4.4
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 7/46 (15%)
Query: 149 DITLVDLP--GITKVPVGEQPADIEARIRTMIMSYIKQPSCLILAV 192
LVDLP G KV + + +I Y++ L V
Sbjct: 46 KFRLVDLPGYGYAKVSKEVR-----EKWGKLIEEYLENRENLKGVV 86
>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 = 5.0
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 51 AVVGSQSSGKSSVLEALVGRD 71
A+ G + GKSS+L AL+G++
Sbjct: 1 AIFGRPNVGKSSLLNALLGQN 21
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.9 bits (68), Expect = 5.1
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 46 ELPQVAVVGSQSSGKSSVLEALVGRD 71
+P VA+VG ++GKS++ AL G D
Sbjct: 191 GIPLVALVGYTNAGKSTLFNALTGAD 216
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 29.8 bits (68), Expect = 5.6
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 473 RMDEVIGNFLREGLE 487
R +E+I NF++ GLE
Sbjct: 188 RKNEMINNFIKPGLE 202
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.5 bits (64), Expect = 5.7
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 48 PQVAVVGSQSSGKSSVLEALV 68
P V VVG + SGK++++ L+
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLL 21
>gnl|CDD|217138 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family
consists of tetraacyldisaccharide-1-P 4'-kinase also
known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyzes the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer (LPS).
The family contains a P-loop motif at the N terminus.
Length = 318
Score = 29.4 bits (67), Expect = 5.8
Identities = 11/55 (20%), Positives = 17/55 (30%)
Query: 161 VPVGEQPADIEARIRTMIMSYIKQPSCLILAVTPANSDLANSDALQIAGIADPDG 215
V + A ++ +PS + LA L AGI +P
Sbjct: 181 VILNGGEAADPEIAEAPVLRARLEPSAAVNLADGERRPLAGKRVLAFAGIGNPQR 235
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 29.3 bits (65), Expect = 5.9
Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 10/105 (9%)
Query: 51 AVVGSQSSGKSSVLEALVG-RDFLPRGNDICTRRPLVLQLLQTKTDEEYG--------EF 101
++G SGKS++L+AL L G + + ++LL DE E
Sbjct: 3 VIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKLLPFLLDENEIEIPLEFEIEE 62
Query: 102 LHLPGKRF-YDFSEIRREIQAQTDKEAGGNKGVSDKQIRLKIFSP 145
+ G R+ Y F + +I + E + + ++ R K
Sbjct: 63 FLIDGIRYRYGFELDKEDILEELLYEYRKGEELLFERERSKESFE 107
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 29.5 bits (66), Expect = 6.8
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 133 VSDKQIRLKIFSPHVLDITL---VDLPGITKVPVGEQPADIEARIRTMIMSYIKQ 184
D++ R +IF H + L VDL + ++ G ADIEA R M+ +++
Sbjct: 621 PPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRE 675
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 28.7 bits (65), Expect = 7.1
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 46 ELPQVAVVGSQSSGKSSVLEALVGRDFLPR 75
+LP++A G + GKSS++ AL + L R
Sbjct: 23 DLPEIAFAGRSNVGKSSLINALTNQKNLAR 52
>gnl|CDD|227783 COG5496, COG5496, Predicted thioesterase [General function
prediction only].
Length = 130
Score = 28.1 bits (63), Expect = 8.2
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 301 QILVQHIKAILPGLKSRISSALVSV 325
++LV+H+ A PGL I + L V
Sbjct: 62 EVLVRHLAATPPGLTVTIGARLEKV 86
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 8.8
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 49 QVAVVGSQSSGKSSVLEALVGRDFLPRGNDICTRRPLVLQLLQTKTDEEYGEFLHLPGKR 108
++ V+G GK+++L LVG +F P + L KT E Y + L
Sbjct: 7 KIVVLGDGGVGKTTLLNRLVGDEFPE------GYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 109 FYDFSEIRR 117
E R
Sbjct: 61 TAGQEEYRS 69
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 29.2 bits (66), Expect = 9.9
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 290 CGVPQLAKKLNQILVQHIKAILPGLKS-----RISSALVSVAKEHASYGEITESKAGQGA 344
+ L ++ NQ+L+ +LP LK S+ S A AS ++ +GQG
Sbjct: 197 AQLGDLYEEANQLLIDA--GVLPELKYAPGTKATSAGPRSQAPPAASGPSTDDAASGQGG 254
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 0.135 0.379
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: 35,800,796
Number of extensions: 3629407
Number of successful extensions: 3508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3497
Number of HSP's successfully gapped: 72
Length of query: 699
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 595
Effective length of database: 6,324,786
Effective search space: 3763247670
Effective search space used: 3763247670
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.6 bits)