RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3589
(604 letters)
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 137 bits (347), Expect = 4e-38
Identities = 44/57 (77%), Positives = 47/57 (82%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 425
TIG VG PNVGKSSL+NA++G K VSVS TPG TKHFQTIFL I LCDCPGLVFP
Sbjct: 84 TIGLVGYPNVGKSSLINALVGSKKVSVSSTPGKTKHFQTIFLEPGITLCDCPGLVFP 140
Score = 109 bits (275), Expect = 3e-28
Identities = 30/83 (36%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 187 TWRQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLG-KDMILVMNKIDLAPAPLV 245
WRQLWRV+E SD+++ I+D R P P L YV K+ +L++NK DL
Sbjct: 1 VWRQLWRVIERSDVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKADLVTEEQR 60
Query: 246 LAWKHYFQSKFPKLTILCFTSYP 268
AW YF+ + + F S
Sbjct: 61 KAWARYFKKEGIV---VLFFSAL 80
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 131 bits (331), Expect = 6e-34
Identities = 90/341 (26%), Positives = 135/341 (39%), Gaps = 85/341 (24%)
Query: 180 YFELNLETWRQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDL 239
+ + RQL VL+ D+++ ++D R P P L V K +LV+NK DL
Sbjct: 17 FPGHMKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIV---KEKPKLLVLNKADL 73
Query: 240 APAPLVLAWKHYFQSKFPKLTILCFTSYPTYNLRNNIENSNKKGLQVRRRRGKMKMAAEG 299
AP + WK YF ++G++ K + +G
Sbjct: 74 APKEVTKKWKKYF--------------------------KKEEGIKPIFVSAKSR---QG 104
Query: 300 AKKLLEACQTIVQGAVDLSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEV 359
KK+ +A + + E KI LKK
Sbjct: 105 GKKIRKALEKLS---------EEKIKR-----------------------LKKKGLLKR- 131
Query: 360 HEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDC 419
K + GV VG PNVGKS+L+N ++G+KV S PG TK Q I L D I L D
Sbjct: 132 --KIRVGV-----VGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYLLDT 184
Query: 420 PGLVFPSKVPKPLQVLMGSFPIAQLREPYSTVQYLAERMDLIKLLHIKH----------- 468
PG++ P L VL+ P ++++P +AER+ L LL +H
Sbjct: 185 PGIIPPKFDDDEL-VLLKLAPKGEIKDPVLPADEVAERL-LGGLLIDEHYGEKLNITRYE 242
Query: 469 PDDDEYWCAMDICDGWAQKRSYMTAKTGRYDSYRAANELLR 509
+ + + A+KR ++ K G D RAA +L+
Sbjct: 243 SNPIHRTDPEEFLELIAKKRGWLLLKGGEPDLERAAETILK 283
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 92.3 bits (230), Expect = 9e-22
Identities = 58/228 (25%), Positives = 91/228 (39%), Gaps = 63/228 (27%)
Query: 199 DIILIIIDIRYP----CLMFPPTLYDYV-TGTLGKDMILVMNKIDLAPAPLVLAWKHYFQ 253
D+IL ++D R P C P + V K ++LV+NKIDL P V W Y +
Sbjct: 1 DVILEVLDARDPLGCRC----PQVERAVLVLGPNKKLVLVLNKIDLVPKENVEKWLKYLR 56
Query: 254 SKFPKLTILCFTSYPTYNLRNNIENSNKKGLQVRRRRGKMKMAAEGAKKLLEACQTIVQG 313
+ +PT + + + K + ++ + L G
Sbjct: 57 N-----------EFPTVAFKASTQQQKKNLSRKSKKVKASDDLLSSSACL---------G 96
Query: 314 AVDLSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVLTIGCV 373
A L + L LK NY ++ K+ +T+G V
Sbjct: 97 ADAL----------LKL-------------------LK----NYARNKGIKTS-ITVGVV 122
Query: 374 GQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 421
G PNVGKSS++N++ + +V TPG TK Q + L +++L D PG
Sbjct: 123 GYPNVGKSSVINSLKRSRACNVGATPGVTKSMQEVHLDKHVKLLDSPG 170
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 75.4 bits (186), Expect = 1e-16
Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDN--IRLCDCPGLVFPS 426
+ VG+PNVGKS+L+NA+ G KV VS PG T+ L I L D PGL+ +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGA 60
Query: 427 KVPKPLQVLMGSFPIAQLRE 446
+ V + + +RE
Sbjct: 61 --SEGKGVEGFNRFLEAIRE 78
Score = 35.3 bits (82), Expect = 0.016
Identities = 11/55 (20%), Positives = 25/55 (45%)
Query: 182 ELNLETWRQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNK 236
+E + + + +D+IL+++D + + + K +ILV+NK
Sbjct: 63 GKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 72.5 bits (179), Expect = 5e-14
Identities = 79/350 (22%), Positives = 124/350 (35%), Gaps = 107/350 (30%)
Query: 189 RQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLAW 248
R++ L++ D+++ ++D R P P + + K +L++NK DLA + W
Sbjct: 16 REIKENLKLVDVVIEVLDARIPLSSENPMIDKIIGN---KPRLLILNKSDLADPEVTKKW 72
Query: 249 KHYFQSKFPKLTILCFTSYPTYNLRNNIENSNKKGLQVRRRRGKMKMAAEGAKKLLEACQ 308
YF+ + + L + KKG +G KK+L+A +
Sbjct: 73 IEYFEEQ--GIKALAINA--------------KKG--------------QGVKKILKAAK 102
Query: 309 TIVQGAVDLSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVL 368
+++ E E K I +
Sbjct: 103 KLLK--------------------EKNERRKAKGMRPRAIR-----------------AM 125
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKV 428
IG PNVGKS+L+N + G+K+ PG TK Q I L + L D PG + K+
Sbjct: 126 IIGI---PNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGKGLELLDTPG-ILWPKL 181
Query: 429 PKPLQVL-----------------MGSFPIAQLREPYSTVQYLAERMDLIKLLHIKHPDD 471
L + F + L + Y L ER L +L P+D
Sbjct: 182 EDQEVGLKLALTGAIKDEALDLEEVAIFALEYLSKHYPER--LKERYKLDEL-----PED 234
Query: 472 DEYWCAMDICDGWAQKRSYMTAKTGRYDSYRAANELL---RMATEGRICL 518
++ A+KR K G D RA+ LL R G+I L
Sbjct: 235 ILEL--LEA---IARKRG-ALRKGGEIDYERASELLLNEFRNGKLGKITL 278
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 68.6 bits (168), Expect = 9e-14
Identities = 36/108 (33%), Positives = 51/108 (47%), Gaps = 2/108 (1%)
Query: 315 VDLSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVLTIGCVG 374
V + +AE L G ++LK T ++ KYK G + +G VG
Sbjct: 41 VPKEVLRKWVAELSELYGTKTFFISATNGQG-ILKLKAEITKQKLKLKYKKG-IRVGVVG 98
Query: 375 QPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGL 422
PNVGKSS +NA++ + + V PG TK Q + L I L D PG+
Sbjct: 99 LPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
Score = 35.1 bits (81), Expect = 0.038
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 199 DIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLAWKHY-FQSKFP 257
D+++ ++D R P P + + K +I+V+NK DL P ++ W +
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLIN-EKNKKLIMVLNKADLVPKEVLRKWVAELSELYGT 59
Query: 258 K 258
K
Sbjct: 60 K 60
>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 = 66.4 bits (163), Expect = 9e-13
Identities = 34/110 (30%), Positives = 50/110 (45%), Gaps = 18/110 (16%)
Query: 373 VGQPNVGKSSLMNAIMGRK-VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKP 431
G+ NVGKSSL+NA+ RK + S+TPG T+ + D RL D PG + +KV K
Sbjct: 5 AGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGY-AKVSKE 63
Query: 432 LQVLMGSFPIAQLREPYSTVQYLAERMDLIKLLH---IKHP---DDDEYW 475
++ G +YL R +L ++ +H D E
Sbjct: 64 VREKWGKL----------IEEYLENRENLKGVVLLIDARHGPTPIDLEML 103
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 64.0 bits (157), Expect = 5e-12
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 19/75 (25%)
Query: 363 YKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKH----------FQTIFLTD 412
+KSG + I +G+PNVGKS+L+NA++G+K+ VS P T++ Q IF+
Sbjct: 1 FKSGFVAI--IGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFV-- 56
Query: 413 NIRLCDCPGLVFPSK 427
D PG+ P K
Sbjct: 57 -----DTPGIHKPKK 66
Score = 33.2 bits (77), Expect = 0.19
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 16/77 (20%)
Query: 192 WRVLEMSDIILIIIDIRYPCLMFPPTLYD-YVTGTLGKD---MILVMNKIDLAPAPLVLA 247
W L+ D++L ++D D ++ L K +ILV+NKIDL L
Sbjct: 77 WSALKDVDLVLFVVDASEW-----IGEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLL 131
Query: 248 W-------KHYFQSKFP 257
H F FP
Sbjct: 132 PLLEKLKELHPFAEIFP 148
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 65.2 bits (160), Expect = 1e-11
Identities = 58/243 (23%), Positives = 97/243 (39%), Gaps = 85/243 (34%)
Query: 189 RQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLAW 248
R++ L++ D+++ ++D R P P + + K ++V+NK DLA + W
Sbjct: 13 REIKEKLKLVDVVIEVLDARIPLSSRNPMIDEIRGN---KPRLIVLNKADLADPAVTKQW 69
Query: 249 -KHYFQSKFPKLTILCFTSYPTYNLRNNIENSNKKGLQVRRRRGKMKMAAEGAKKLLEAC 307
K++ + L I + KKG +G KK+++A
Sbjct: 70 LKYFEEKGIKALAI-----------------NAKKG--------------KGVKKIIKAA 98
Query: 308 QTIVQGAVDLSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKS-G 366
+ +++ E +EK K+ G
Sbjct: 99 KKLLK---------------------------------------------EKNEKLKAKG 113
Query: 367 VLTIG----CVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGL 422
+L VG PNVGKS+L+N + G+KV V PG TK Q I L+D + L D PG+
Sbjct: 114 LLNRPIRAMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKLSDGLELLDTPGI 173
Query: 423 VFP 425
++P
Sbjct: 174 LWP 176
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 62.3 bits (152), Expect = 1e-11
Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 421
+++G +G PNVGKSS++N + +KV V+ PG TK +Q I L I L DCPG
Sbjct: 103 ISVGFIGYPNVGKSSVINTLRSKKVCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
Score = 44.6 bits (106), Expect = 2e-05
Identities = 29/112 (25%), Positives = 50/112 (44%), Gaps = 22/112 (19%)
Query: 190 QLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKD-----MILVMNKIDLAPAPL 244
+L++V++ SD+I+ ++D R P T +V L K+ +I V+NK DL P +
Sbjct: 1 ELYKVIDSSDVIIQVLDARDP----MGTRCKHVEKYLRKEKPHKHLIFVLNKCDLVPTWV 56
Query: 245 VLAWKHYFQSKFPKLTILCFTSYPTYNLRNNIENSNKKG--LQVRRRRGKMK 294
W ++P L F +I N KG + + R+ K+
Sbjct: 57 TKRWVKVLSKEYP---TLAF--------HASITNPFGKGALINLLRQFAKLH 97
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 62.2 bits (152), Expect = 3e-11
Identities = 25/49 (51%), Positives = 31/49 (63%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 421
VG PNVGKS+L+N + G+KV V PG T+ Q I + NI L D PG
Sbjct: 121 VGIPNVGKSTLINRLRGKKVAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
Score = 41.4 bits (98), Expect = 3e-04
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 4/101 (3%)
Query: 195 LEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLAWKHYFQS 254
L++ D+++ + D R P P L D + G K ++V+NK DLA W YF+S
Sbjct: 17 LKLVDVVIEVRDARIPLSSRNPDL-DKILGN--KPRLIVLNKADLADPAKTKKWLKYFKS 73
Query: 255 K-FPKLTILCFTSYPTYNLRNNIENSNKKGLQVRRRRGKMK 294
+ P L + L + K+ +++ + +
Sbjct: 74 QGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPR 114
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 61.4 bits (150), Expect = 2e-10
Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 5/70 (7%)
Query: 361 EKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKH-FQTIFLTDN--IRLC 417
K+KSG + I +G+PNVGKS+L+NA++G+K+ VS P T++ + I TDN I
Sbjct: 2 MKFKSGFVAI--IGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFV 59
Query: 418 DCPGLVFPSK 427
D PG+ P
Sbjct: 60 DTPGIHKPKH 69
>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 = 58.9 bits (143), Expect = 3e-10
Identities = 25/56 (44%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRT---PGHTKHFQTIFLTDNIRLCDCPG 421
+G VG P VGKSS++NA+ GR S S PG+TK Q + + I L D PG
Sbjct: 101 IVGVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
Score = 47.7 bits (114), Expect = 2e-06
Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 188 WRQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLA 247
R + R+++ +D++L ++D R P L L LGK +I+V+NK DL P ++
Sbjct: 2 KRLVRRIIKEADVVLEVVDARDPELTRSRKLERMAL-ELGKKLIIVLNKADLVPREVLEK 60
Query: 248 WKHYFQS 254
WK F+S
Sbjct: 61 WKEVFES 67
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 59.2 bits (144), Expect = 4e-10
Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 15/104 (14%)
Query: 373 VGQPNVGKSSLMNAIMGRK-VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKP 431
G+ NVGKSSL+NA+ +K + S+TPG T+ + D +RL D PG + +KVPK
Sbjct: 30 AGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPGYGY-AKVPKE 88
Query: 432 LQVLMGSFPIAQLREPYSTVQYLAERMDL---IKLLHIKHPDDD 472
++ +YL +R +L + L+ +HP D
Sbjct: 89 VKEKWKKL----------IEEYLEKRANLKGVVLLIDARHPPKD 122
>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 = 57.5 bits (140), Expect = 1e-09
Identities = 38/110 (34%), Positives = 54/110 (49%), Gaps = 23/110 (20%)
Query: 373 VGQPNVGKSSLMNAIMGRK-VVSVSRTPGHTKHFQTI---FLTDNIRLCDCPGLVFPSKV 428
G+ NVGKSSL+NA+ RK + S+TPG T Q I + D RL D PG + +KV
Sbjct: 24 AGRSNVGKSSLINALTNRKKLARTSKTPGRT---QLINFFEVNDGFRLVDLPGYGY-AKV 79
Query: 429 PKPLQVLMGSFPIAQLREPYSTVQYLAERMDL---IKLLHIKHP--DDDE 473
K + I +YL +R +L + L+ I+HP + D
Sbjct: 80 SKEEKEKWQKL-IE---------EYLEKRENLKGVVLLMDIRHPLKELDL 119
>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 = 56.3 bits (136), Expect = 2e-09
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHT-----KHFQTIFLTDNIRLCDCPGLV 423
VG+ VGKSSL+NA++G +V VS PG T + + L D PGL
Sbjct: 3 VGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLD 58
Score = 37.4 bits (87), Expect = 0.006
Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 2/92 (2%)
Query: 185 LETWRQLWRVLEMSDIILIIIDI-RYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAP 243
L +L +D+IL+++D L G +ILV NKIDL
Sbjct: 63 LGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEER 122
Query: 244 LVLAWKHYFQ-SKFPKLTILCFTSYPTYNLRN 274
V + +K + + ++ +
Sbjct: 123 EVEELLRLEELAKILGVPVFEVSAKTGEGVDE 154
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 57.4 bits (140), Expect = 5e-09
Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 19/72 (26%)
Query: 361 EKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPG----------HTKHFQTIFL 410
+KSG + I VG+PNVGKS+L+NA++G+K+ VS P Q IF+
Sbjct: 1 MGFKSGFVAI--VGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFV 58
Query: 411 TDNIRLCDCPGL 422
D PG+
Sbjct: 59 -------DTPGI 63
>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 = 54.9 bits (133), Expect = 7e-09
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQ----TIFLTDNIRLCDCPGL 422
G+PNVGKSSL+NA++G+ V VS PG T+ + + L D PGL
Sbjct: 3 FGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGL 56
Score = 39.5 bits (93), Expect = 0.001
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 192 WRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTL---GKDMILVMNKIDLAPAPLVLAW 248
+V + +D++L+++D P + G L GK ++LV+NKIDL P
Sbjct: 71 RQVADRADLVLLVVDSD-----LTPVEEEAKLGLLRERGKPVLLVLNKIDLVPESEEEEL 125
Query: 249 KHYFQSKF 256
+ +
Sbjct: 126 LRERKLEL 133
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 53.2 bits (129), Expect = 4e-08
Identities = 38/114 (33%), Positives = 54/114 (47%), Gaps = 31/114 (27%)
Query: 373 VGQPNVGKSSLMNAIMGRK-VVSVSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKV 428
G+ NVGKSSL+NA+ RK + S+TPG T Q I F + D +RL D PG + +KV
Sbjct: 30 AGRSNVGKSSLINALTNRKNLARTSKTPGRT---QLINFFEVNDKLRLVDLPGYGY-AKV 85
Query: 429 PKPL----QVLMGSFPIAQLREPYSTVQYLAERMDLIKLLH---IKHP--DDDE 473
K Q L+ +YL R +L ++ +HP + D
Sbjct: 86 SKEEKEKWQKLIE--------------EYLRTRENLKGVVLLIDSRHPLKELDL 125
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. 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. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 49.7 bits (120), Expect = 4e-07
Identities = 18/37 (48%), Positives = 25/37 (67%)
Query: 366 GVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
+ I +G+PNVGKSSL+NA++G + V VS G T
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTT 37
Score = 30.1 bits (69), Expect = 2.3
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 193 RVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVL--AWKH 250
+ +E +D++L+++D + + GK +I+V+NK DL ++
Sbjct: 80 KAIERADVVLLVLDASEGITEQDLRIAGLILEE-GKALIIVVNKWDLVEKDEKTMKEFEK 138
Query: 251 YFQSKFPKL 259
+ K P L
Sbjct: 139 ELRRKLPFL 147
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 51.6 bits (125), Expect = 7e-07
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 331 EYEDVEEEDEKVEVG-ETI--ELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAI 387
E + DEK+ E + EL+ + + E + G L + G+PNVGKSSL+NA+
Sbjct: 177 EEDIEFLSDEKILEKLEELIAELEALLASARQGEILREG-LKVVIAGRPNVGKSSLLNAL 235
Query: 388 MGRKVVSVSRTPGHT 402
+G + V+ G T
Sbjct: 236 LGEERAIVTDIAGTT 250
Score = 37.0 bits (87), Expect = 0.027
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 192 WRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAP 243
+E +D++L+++D P + + + K +I+V+NK DL
Sbjct: 289 REAIEEADLVLLVLDASEPLTEEDDEILEELKD---KPVIVVLNKADLTGEI 337
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 51.3 bits (124), Expect = 7e-07
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 358 EVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
E E+ + G + I +G+PNVGKS+L+NA++G + V VS G T
Sbjct: 163 EEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTT 207
Score = 42.0 bits (100), Expect = 8e-04
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHT--KHFQTIFLTD-NIRLCDCPGLVF 424
VG+PNVGKS+L N + G++ VS TPG T + + L D G+
Sbjct: 5 VGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEE 59
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 50.6 bits (122), Expect = 2e-06
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT--KHFQTIFLTD-NIRLCDCPGLVFP 425
+ VG+PNVGKS+L N + GR++ VS TPG T + + L D GL
Sbjct: 5 VVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDG 64
Query: 426 SKVPKPLQVLM 436
+ LQ L+
Sbjct: 65 DE--DELQELI 73
Score = 45.6 bits (109), Expect = 5e-05
Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 20/73 (27%)
Query: 330 LEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMG 389
LE +EE+E+ E + I+ I +G+PNVGKSSL+NAI+G
Sbjct: 161 LELLPPDEEEEEEEETDPIK--------------------IAIIGRPNVGKSSLINAILG 200
Query: 390 RKVVSVSRTPGHT 402
+ V VS G T
Sbjct: 201 EERVIVSDIAGTT 213
Score = 29.8 bits (68), Expect = 4.0
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 186 ETWRQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTL----GKDMILVMNKID 238
Q +E +D+IL ++D R T D + K +ILV+NKID
Sbjct: 72 LIREQALIAIEEADVILFVVDGREG-----ITPADEEIAKILRRSKKPVILVVNKID 123
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 50.0 bits (121), Expect = 2e-06
Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 358 EVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
E E + + I +G+PNVGKSSL+NA++G + V VS G T
Sbjct: 164 EEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTT 208
Score = 40.8 bits (97), Expect = 0.002
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK--HFQTIFLTD-NIRLCDCPGLVF 424
VG+PNVGKS+L N + G++ V+ TPG T+ + L D G+
Sbjct: 7 VGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEP 61
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 49.9 bits (120), Expect = 2e-06
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 36/162 (22%)
Query: 291 GKMKMA-AEGAKKLLEACQTI---------VQGAVD--LSSWERKIAE-EMHLEYE-DVE 336
GK+ + AE L++A +T +QGA+ ++ + E +E D
Sbjct: 120 GKLDLTQAEAIADLIDA-KTEQAARIALRQLQGALSQLINELREALLELLAQVEANIDFP 178
Query: 337 EEDEKVEVGETI---------ELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAI 387
EED + V E I EL ++ + + + G L + +G+PNVGKSSL+NA+
Sbjct: 179 EEDIEELVLEKIREKLEELIAELDELLATAKQGKILREG-LKVVIIGRPNVGKSSLLNAL 237
Query: 388 MGRKVVSVSRTPGHTK-------HFQTIFLTDNIRLCDCPGL 422
+GR V+ G T+ + I +RL D G+
Sbjct: 238 LGRDRAIVTDIAGTTRDVIEEDINLNGI----PVRLVDTAGI 275
Score = 39.9 bits (94), Expect = 0.003
Identities = 30/137 (21%), Positives = 52/137 (37%), Gaps = 15/137 (10%)
Query: 192 WRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLVLAWKHY 251
+ +E +D++L ++D P L + + K +I+V+NK DL +
Sbjct: 291 KKAIEEADLVLFVLDASQPLDKEDLALIELLP--KKKPIIVVLNKADLVSKIELE--SEK 346
Query: 252 FQSKFPKLTILCFTSYPTYNLRNNIEN------SNKKGLQVRRRRGKM-----KMAAEGA 300
+ ++I T LR I+ N++GL + R E A
Sbjct: 347 LANGDAIISISAKTGEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQLLEQAAEHLEDA 406
Query: 301 KKLLEACQTIVQGAVDL 317
+ LE Q + A DL
Sbjct: 407 LQQLELGQPLDLLAEDL 423
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 50.2 bits (120), Expect = 3e-06
Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 20/119 (16%)
Query: 295 MAAEGAKKL----------LEACQTIVQGAVDLSSWERKIAEEMHLEYEDVEEEDEKVEV 344
AA+G L L+ +V+ A++ +++ A LE +++E DE
Sbjct: 203 SAADGVTTLDNSDLDFDETLDLLIGLVEDAIEEQEYDQYAAN---LEGYELDEGDE---- 255
Query: 345 GETIELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK 403
+ +E E GV+ I VG+PNVGKS+L+N I+GR+ V TPG T+
Sbjct: 256 -DLLEGSGFVAGDEKAGPKAVGVVAI--VGRPNVGKSTLVNRILGRREAVVEDTPGVTR 311
Score = 35.9 bits (83), Expect = 0.062
Identities = 16/31 (51%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 365 SGVLTIGCVGQPNVGKSSLMNAIMG--RKVV 393
SG+ + VG+PNVGKSSL+N + R VV
Sbjct: 448 SGLRRVALVGRPNVGKSSLLNQLTHEERAVV 478
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 48.2 bits (115), Expect = 5e-06
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 370 IGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKH-FQTIFLTD--NIRLCDCPGL 422
+ +G+PNVGKS+L+N + G+K+ S T++ I T I D PG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGF 58
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 47.6 bits (114), Expect = 9e-06
Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 13/113 (11%)
Query: 317 LSSWERKIAEEMHLEYEDVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVLTIGCVGQP 376
+ W +K A+E+ L+ D+ V + + ++ + + K V +G
Sbjct: 112 IKEWMKKRAKELGLKPVDII----LVSAKKGNGIDELL-DKIKKARNKKDVYVVGVT--- 163
Query: 377 NVGKSSLMNAIMG-----RKVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVF 424
NVGKSSL+N ++ + V++ S PG T I L D L D PG++
Sbjct: 164 NVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGIIN 216
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 45.6 bits (109), Expect = 1e-05
Identities = 17/30 (56%), Positives = 20/30 (66%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
G+PNVGKSSL+NA+ GR VS G T
Sbjct: 9 AGKPNVGKSSLLNALAGRDRAIVSDIAGTT 38
Score = 33.6 bits (78), Expect = 0.11
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 192 WRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAP 243
+E +D++L+++D + + K +I+V+NK DL
Sbjct: 77 REAIEEADLVLLVVDASEGLDEEDLEILELPAK---KPVIVVLNKSDLLSDA 125
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 45.6 bits (109), Expect = 5e-05
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
L IG G+ N GKSSL+NA+ G+ + VS PG T
Sbjct: 7 LHIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTT 41
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 45.4 bits (108), Expect = 8e-05
Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHT---KHFQTIFLTDNIRLCDCPG 421
LT+ VG PNVGK++L NA+ G V PG T K + + I + D PG
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGAN-QKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPG 59
Score = 29.2 bits (66), Expect = 7.2
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 226 LGKDMILVMNKIDLAP 241
LG MIL +N ID A
Sbjct: 107 LGIPMILALNMIDEAK 122
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 43.2 bits (103), Expect = 9e-05
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKV-------VSVSRTPGHTKHFQTIFLTDNIRLCDCP 420
+TI VG PNVGK++L NA+ G + V+V + G K+ I + D P
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGY-----EIEIVDLP 55
Query: 421 G 421
G
Sbjct: 56 G 56
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 44.4 bits (105), Expect = 9e-05
Identities = 28/66 (42%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 539 DEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
D I + T ++PY +P DDE V+ GEE E +EGEE+E EE EEESEE
Sbjct: 43 DAIELAEPETSDDPYGNPDPFGEDDEGR-IEVRISEDGEEEEVEEGEEDEEEEGEEESEE 101
Query: 599 DNITGV 604
G
Sbjct: 102 FEPLGD 107
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. 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. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 42.8 bits (102), Expect = 9e-05
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHT--KHFQTIFLTDN-IRLCDCPGLVFPSKVP 429
VG+PNVGKS+L N + GR+ VS TPG T + + L D G+
Sbjct: 3 VGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEP---DD 59
Query: 430 KPLQVLM 436
+ + +
Sbjct: 60 EGISKEI 66
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 44.6 bits (106), Expect = 1e-04
Identities = 17/31 (54%), Positives = 23/31 (74%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK 403
VG+PNVGKS+L+N I+GR+ V PG T+
Sbjct: 44 VGRPNVGKSTLVNRILGRREAVVEDVPGVTR 74
Score = 38.0 bits (89), Expect = 0.014
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHT 402
VG+PNVGKSSL+N + G + V G T
Sbjct: 217 VGKPNVGKSSLLNKLAGEERSVVDDVAGTT 246
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 44.0 bits (104), Expect = 2e-04
Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 20/105 (19%)
Query: 327 EMHLEYEDVEEEDEKVEVGETI-----ELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKS 381
E++++YE E++DE+ + + + ELK + +Y++ EK G + VG PNVGKS
Sbjct: 162 EVNIDYE--EDDDEQDSLNQLLLSIIAELKDILNSYKL-EKLDDGF-KLAIVGSPNVGKS 217
Query: 382 SLMNAIMGRKVVSVSRTPGHTK-----------HFQTIFLTDNIR 415
SL+NA++ + VS G T+ + T IR
Sbjct: 218 SLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIR 262
Score = 32.8 bits (75), Expect = 0.50
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 195 LEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAPLV 245
++ +D+++ ++D P L L + K ILV+NKIDL L
Sbjct: 280 IKQADLVIYVLDASQP-LTKDDFLIIDLN-KSKKPFILVLNKIDLKINSLE 328
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 42.3 bits (100), Expect = 2e-04
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 16/78 (20%)
Query: 358 EVHEKYKSG--VLTIGCVGQPNVGKSSLMNAIMGRK-----------VVSVSRTPGHTKH 404
E+ + K V +G NVGKS+L+NA++ ++VS PG T
Sbjct: 117 EIKKLAKYRGDVYVVGA---TNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLG 173
Query: 405 FQTIFLTDNIRLCDCPGL 422
I L + +L D PG+
Sbjct: 174 LIKIPLGEGKKLYDTPGI 191
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 41.8 bits (99), Expect = 3e-04
Identities = 26/64 (40%), Positives = 36/64 (56%), Gaps = 8/64 (12%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK---HFQTIFLTDNIRLCDCPGLVFPSKVP 429
VG+ NVGKS+L+ + G+K V V + PG T+ H+ + L D PG F S VP
Sbjct: 15 VGRSNVGKSTLVRELTGKK-VRVGKRPGVTRKPNHYD----WGDFILTDLPGFGFMSGVP 69
Query: 430 KPLQ 433
K +Q
Sbjct: 70 KEVQ 73
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 42.9 bits (102), Expect = 3e-04
Identities = 39/119 (32%), Positives = 56/119 (47%), Gaps = 27/119 (22%)
Query: 317 LSSWERKIAEEMHLEYEDV-----EEEDEKVEVGETIELKKVDTNYEVHEKYKSG--VLT 369
+ +W R+ A+E+ L DV ++ E+ E IE KY+ G V
Sbjct: 118 VKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLEAIE------------KYREGRDVYV 165
Query: 370 IGCVGQPNVGKSSLMNAIM----GRK-VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLV 423
+G NVGKS+L+N I+ G K V++ SR PG T I L D L D PG++
Sbjct: 166 VGVT---NVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLYDTPGII 221
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 40.1 bits (95), Expect = 7e-04
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 373 VGQPNVGKSSLMNAIMGRKV-------VSVSRTPGHTKHFQTIFLTDNIRLCDCPG 421
VG PNVGK++L NA+ G + V+V + G K I + D PG
Sbjct: 3 VGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKL-----GGKEIEIVDLPG 53
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 40.0 bits (94), Expect = 0.001
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 370 IGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQT 407
I VG PNVGKS+L+N ++G K+ PG T+++ T
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVT 41
Score = 29.6 bits (67), Expect = 2.9
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 189 RQLWRVLEMSDIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDL 239
R + L + DI+++++D+ + + G +ILV NKIDL
Sbjct: 73 RAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAES--GVPIILVGNKIDL 121
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 40.9 bits (96), Expect = 0.001
Identities = 30/136 (22%), Positives = 41/136 (30%), Gaps = 26/136 (19%)
Query: 373 VGQPNVGKSSLMNAIMGR------KVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPS 426
GQ VGKSSL+NA+ + S HT +F + D PG
Sbjct: 126 AGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGGLIADTPGFNEFG 185
Query: 427 KVPKPLQVLMGSFPIAQLREPYSTVQYLAERMDLIKLLHIKHPDDDEYWCAMDICDGWAQ 486
L L QL + + + LH P CA + Q
Sbjct: 186 -----LWHL----EPEQLTQGFVEFRDYLGLCKFRDCLHQSEPG-----CA--VRQAVEQ 229
Query: 487 KRSYMTAKTGRYDSYR 502
RY++Y
Sbjct: 230 GEISEW----RYENYL 241
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 41.9 bits (98), Expect = 0.001
Identities = 18/38 (47%), Positives = 22/38 (57%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
D + + EE EE+E EEEE EEEEEE EE+
Sbjct: 853 DGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 40.0 bits (93), Expect = 0.004
Identities = 18/24 (75%), Positives = 20/24 (83%)
Query: 577 EETEEDEGEEEESEEEEEESEEDN 600
EE EE+E EEEE EEEEEE EE+N
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 39.2 bits (91), Expect = 0.007
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 564 EAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
++G + + + + EE EE+E EEEE EEEEEE E+
Sbjct: 857 GSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 34.2 bits (78), Expect = 0.24
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 561 SDDEAEGKNVKRKHKGEET----EEDEGEEEESEEEEEESEED 599
++++ E K ++ G + +E EEEE EEEEEE EE+
Sbjct: 839 AENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEE 881
Score = 33.4 bits (76), Expect = 0.36
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 6/35 (17%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEE 595
S++E E + + EE EE+E EEEE EEEE E
Sbjct: 863 SEEEEE------EEEEEEEEEEEEEEEEEEEEENE 891
Score = 30.3 bits (68), Expect = 4.1
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 12/50 (24%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEG------------EEEESEEEEEESEED 599
DE + + +++GE ++++G EEEE EEEEEE EE+
Sbjct: 829 KDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEE 878
Score = 29.2 bits (65), Expect = 7.5
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
D E E + + + + EE EE+E EEEE E EE S E
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEE-EEEEEENEEPLSLE 897
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 41.2 bits (97), Expect = 0.001
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 14/62 (22%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMG--RKV-----VSVSRTPGHTKHFQTIFLTDN-IRLCDC 419
LTIG +G PN GK++L N + G ++V V+V R G F T TD+ + L D
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEG---QFST---TDHQVTLVDL 57
Query: 420 PG 421
PG
Sbjct: 58 PG 59
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 38.9 bits (91), Expect = 0.002
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 371 GCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK-----HFQTIFLTDNIRLCDCPGLV 423
G VG PNVGKS+L++A+ K V ++ P T F+ D I++ D PGL+
Sbjct: 1 GLVGLPNVGKSTLLSALTSAK-VEIASYPFTTLEPNVGVFEFGDGVD-IQIIDLPGLL 56
>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 = 39.0 bits (92), Expect = 0.003
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 349 ELKKVDTNYEVHEK--YKSGVLTIGCVGQPNVGKSSLMNAIMGRKV 392
EL+KV E+ +SGV T+ VG N GKS+L NA+ G V
Sbjct: 21 ELEKVKKQRELQRARRKRSGVPTVALVGYTNAGKSTLFNALTGADV 66
Score = 29.3 bits (67), Expect = 4.4
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 227 GKDMILVMNKIDLAPAP 243
+ILV+NKIDL
Sbjct: 153 DIPIILVLNKIDLLDDE 169
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 39.7 bits (93), Expect = 0.004
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 374 GQPNVGKSSLMNAIMGRKVVSVSRTPGHT---KHFQTIFLTDNIRLCDCPG 421
G PNVGKS+L NA+ G +V PG T K + F ++I + D PG
Sbjct: 1 GNPNVGKSTLFNALTG-ANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPG 50
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 38.9 bits (90), Expect = 0.005
Identities = 19/43 (44%), Positives = 27/43 (62%)
Query: 557 LVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
L ++ + G K+ K +E++EDE EEEE EEEE E EE+
Sbjct: 113 LAALQLPKKAGNAGKKATKEDESDEDEEEEEEEEEEEAEVEEN 155
Score = 32.4 bits (73), Expect = 0.56
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 579 TEEDEGEEEESEEEEEESEEDNI 601
T+EDE +E+E EEEEEE EE +
Sbjct: 130 TKEDESDEDEEEEEEEEEEEAEV 152
Score = 32.4 bits (73), Expect = 0.60
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 565 AEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
GK ++ + +E EE+E EEEE E E EE+E+
Sbjct: 124 NAGKKATKEDESDEDEEEEEEEEEEEAEVEENEQ 157
Score = 30.0 bits (67), Expect = 3.6
Identities = 16/38 (42%), Positives = 19/38 (50%)
Query: 565 AEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNIT 602
A K K E+ EE+E EEEE E EE + N T
Sbjct: 125 AGKKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGT 162
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 38.8 bits (91), Expect = 0.006
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 364 KSGVLTIGCVGQPNVGKSSLMNAIMGRKV 392
KSG T+ VG P+VGKS+L+N + K
Sbjct: 60 KSGDATVALVGFPSVGKSTLLNKLTNTKS 88
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 38.2 bits (89), Expect = 0.008
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPG----HTKHFQTIFLTDNIRLCDCPGL 422
+ + +G GKSSL+NA+ +V VS+ T+ + +N+ L D PGL
Sbjct: 40 VNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDG-ENLVLWDTPGL 97
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 38.3 bits (90), Expect = 0.009
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 368 LTIGCVGQPNVGKSSLMNAI 387
L IG VG PNVGKS+L NA+
Sbjct: 3 LKIGIVGLPNVGKSTLFNAL 22
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 38.1 bits (89), Expect = 0.009
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 560 VSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
V DE + + + K + EE E+D E E+ +EE+E+ EE+
Sbjct: 272 VGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEE 311
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 38.1 bits (90), Expect = 0.011
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 368 LTIGCVGQPNVGKSSLMNAI 387
L G VG PNVGKS+L NA+
Sbjct: 3 LKCGIVGLPNVGKSTLFNAL 22
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 37.3 bits (87), Expect = 0.013
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDN---IRLCDCPGLV 423
LTI +G+ VGKSS +N+I G + VSVS T + + T + + + D PGL+
Sbjct: 32 LTILVLGKTGVGKSSTINSIFGERKVSVSAFQSETLRPREVSRTVDGFKLNIIDTPGLL 90
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 36.6 bits (86), Expect = 0.014
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
+G VG PN GKS+L++AI
Sbjct: 3 VGLVGLPNAGKSTLLSAI 20
Score = 32.4 bits (75), Expect = 0.30
Identities = 9/38 (23%), Positives = 13/38 (34%)
Query: 226 LGKDMILVMNKIDLAPAPLVLAWKHYFQSKFPKLTILC 263
K I+V+NKIDL A + +
Sbjct: 113 AEKPRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFP 150
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 37.4 bits (88), Expect = 0.017
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 349 ELKKVDTNYEVHEK--YKSGVLTIGCVGQPNVGKSSLMNAIMGRKV 392
EL+KV+ E + ++ V T+ VG N GKS+L NA+ G V
Sbjct: 169 ELEKVEKQRERQRRRRKRADVPTVALVGYTNAGKSTLFNALTGADV 214
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 34.6 bits (80), Expect = 0.023
Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNITG 603
EE+E EEEE EEEEEESEE+ + G
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESEEEAMAG 99
Score = 31.9 bits (73), Expect = 0.21
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNITG 603
E+E EEEE EEEEEE E+
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEESEEEAMA 98
Score = 28.9 bits (65), Expect = 2.5
Identities = 14/23 (60%), Positives = 15/23 (65%)
Query: 575 KGEETEEDEGEEEESEEEEEESE 597
E EE+E EEEE EEEE E E
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEE 95
>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 = 35.6 bits (83), Expect = 0.030
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIF---LTDNIRLCDCPGL 422
+ VG+ + GKS+L+NA++G +V+ T T+ L + L D PGL
Sbjct: 1 FLLAVVGEFSAGKSTLLNALLGEEVLPTG--VTPTTAVITVLRYGLLKGVVLVDTPGL 56
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The CAF-1
or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression in
addition to DNA-based checkpoints.
Length = 76
Score = 33.3 bits (77), Expect = 0.037
Identities = 13/20 (65%), Positives = 18/20 (90%)
Query: 580 EEDEGEEEESEEEEEESEED 599
EE+EGE+ ESE+EE+E E+D
Sbjct: 50 EEEEGEDLESEDEEDEEEDD 69
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including YchF,
possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis suggest
that YchF may be part of a nucleoprotein complex and may
function as a GTP-dependent translational factor.
Length = 274
Score = 35.9 bits (84), Expect = 0.047
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
IG VG PNVGKS+L NA+
Sbjct: 1 IGIVGLPNVGKSTLFNAL 18
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 36.0 bits (83), Expect = 0.047
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 355 TNYEVHE---KYKS---GVLTIGCVGQPNVGKSSLMNAIMGRKVVSVS 396
T ++ E K K LTI +G+ VGKSS +N+I+G ++ +VS
Sbjct: 20 TQTKLLELLGKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGERIATVS 67
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 34.8 bits (81), Expect = 0.049
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKV 392
T+ G PNVGKSSL+N + K
Sbjct: 2 TLVIAGYPNVGKSSLVNKLTRAKP 25
Score = 30.6 bits (70), Expect = 1.3
Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 199 DIILIIIDIRYPCLMFPP----TLYDYVTGTLGKDMILVMNKIDLA-PAPLVLAWKHYFQ 253
+L ID C + +L+ + K +I+V+NKIDL L K +
Sbjct: 81 AAVLFFIDPSETC-GYSIEEQLSLFKEIKPLFNKPVIVVLNKIDLLTEEDLSEIEKELEK 139
Query: 254 SKFPKLTILCFTSYPTYNLRNNIEN 278
+ I T L+N
Sbjct: 140 EGEEVIKISTLTEEGVDELKNKACE 164
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 36.1 bits (84), Expect = 0.050
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
IG VG+PNVGKS+ NA
Sbjct: 1 IGLVGKPNVGKSTFFNAA 18
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 36.1 bits (84), Expect = 0.054
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 349 ELKKVDTNYEVHEK--YKSGVLTIGCVGQPNVGKSSLMNAIMGRKV 392
EL+ V+ E K +SG+ + VG N GKS+L NA+ G V
Sbjct: 172 ELENVEKAREPRRKKRSRSGIPLVALVGYTNAGKSTLFNALTGADV 217
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 33.8 bits (78), Expect = 0.055
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNITG 603
E++ EEEE EEE+EESEE+ G
Sbjct: 74 AAAAEEKKEEEEEEEEKEESEEEAAAG 100
Score = 31.8 bits (73), Expect = 0.24
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 575 KGEETEEDEGEEEESEEEEEESEE 598
EE +E+E EEEE EE EEE+
Sbjct: 76 AAEEKKEEEEEEEEKEESEEEAAA 99
Score = 29.9 bits (68), Expect = 0.97
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 575 KGEETEEDEGEEEESEEEEEES 596
E +++E EEEE +EE EE
Sbjct: 75 AAAEEKKEEEEEEEEKEESEEE 96
Score = 28.8 bits (65), Expect = 3.0
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNI 601
+E +EEE EEEE+E E+
Sbjct: 72 AAAAAAEEKKEEEEEEEEKEESEEEA 97
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 35.5 bits (82), Expect = 0.075
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 558 VSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEE 594
V D+E E + ++K + E+T + E E +E EE+EE
Sbjct: 33 KEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEE 69
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 33.1 bits (76), Expect = 0.097
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 575 KGEETEEDEGEEEESEEEEEESEED 599
G E + E EE E+EEE EE
Sbjct: 75 AGAEAAAEADEAEEEEKEEEAEEES 99
Score = 30.1 bits (68), Expect = 1.0
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNITG 603
++ EEE+ EE EEES++D + G
Sbjct: 80 AAEADEAEEEEKEEEAEEESDDDMLFG 106
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 34.8 bits (81), Expect = 0.098
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 560 VSDDEA---EGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
++D +A E K V E+E EEEE EEEEE SEE+
Sbjct: 278 LADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEE 320
Score = 31.8 bits (73), Expect = 1.1
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNI 601
+ +E EEEE EEEEEE E+
Sbjct: 297 QAAAAEEEEEEEEEEEEEEPSEEEA 321
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 34.6 bits (80), Expect = 0.12
Identities = 34/143 (23%), Positives = 50/143 (34%), Gaps = 39/143 (27%)
Query: 373 VGQPNVGKSSLMNAIMG---RKVVSVSRTPGHTKHFQT----IFLTDNIRLCDCPGLVFP 425
+GQ VGKS+L+NA++ +K +S G +H T L + D PG
Sbjct: 170 LGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDTPG---- 225
Query: 426 SKVPKPLQVLMGSFPIAQLREPYSTVQYLAERMDLIKL------LHIKHPDDDEYWCAMD 479
S +A L EP VQ E +L + H P CA
Sbjct: 226 ----------FRSLGLAHL-EPEDLVQAFPEFAELARQCKFRDCTHTHEPG-----CA-- 267
Query: 480 ICDGWAQKRSYMTAKTGRYDSYR 502
+ + RY++Y
Sbjct: 268 VKAAVEEG----EIAPERYENYL 286
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 34.7 bits (79), Expect = 0.12
Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 340 EKVEVGETIELKKVDTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTP 399
E G T +L ++ + K+ +++ +G+PN GKS+L+N I+G K+ V+
Sbjct: 28 EDASTGSTSKLP-LEVKFGKMSNQKT--VSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKV 84
Query: 400 GHTKHFQTIFLT---DNIRLCDCPGLVFP 425
T+ T +T + L D PG+ P
Sbjct: 85 QTTRSIITGIITLKDTQVILYDTPGIFEP 113
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 35.4 bits (81), Expect = 0.12
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITG 603
+E ++ +EDE +++E ++EEEE EE+ I G
Sbjct: 141 AEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKG 182
Score = 29.6 bits (66), Expect = 5.6
Identities = 9/42 (21%), Positives = 23/42 (54%)
Query: 558 VSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+ AE R + + ++++ +E++ +EE++E EE+
Sbjct: 134 RRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEE 175
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 34.7 bits (80), Expect = 0.13
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 569 NVKRKHKGEETEEDEGEEEESEEEEEESEE 598
N ++K + EE E++E EEEE E EE E EE
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
Score = 32.3 bits (74), Expect = 0.81
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
++ EE+E E+EE EEEEEE EE
Sbjct: 346 QKDEEEEQEDEEEEEEEEEPEEP 368
Score = 31.2 bits (71), Expect = 1.5
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 570 VKRKHKGEETEEDEGEEEESEEEEEESEE 598
V + K EE E+++ EEEE EEE EE E
Sbjct: 342 VNPEQKDEEEEQEDEEEEEEEEEPEEPEP 370
Score = 30.8 bits (70), Expect = 2.5
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 566 EGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITG 603
+G+ + ++ EE++ +EEE EEEEE E + G
Sbjct: 336 QGRCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEEG 373
>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family. This
family includes the HABP4 family of hyaluronan-binding
proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.
HABP4 has been observed to bind hyaluronan (a
glucosaminoglycan), but it is not known whether this is
its primary role in vivo. It has also been observed to
bind RNA, but with a lower affinity than that for
hyaluronan. PAI-1 mRNA-binding protein specifically
binds the mRNA of type-1 plasminogen activator inhibitor
(PAI-1), and is thought to be involved in regulation of
mRNA stability. However, in both cases, the sequence
motifs predicted to be important for ligand binding are
not conserved throughout the family, so it is not known
whether members of this family share a common function.
Length = 106
Score = 32.4 bits (74), Expect = 0.15
Identities = 17/43 (39%), Positives = 20/43 (46%)
Query: 556 PLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
L +E E V+ K EE EG EE E EEEE +E
Sbjct: 36 ELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78
Score = 27.4 bits (61), Expect = 8.0
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 559 SVSDDEAEGK-------NVKRKHKGEETEEDEGEEEESEEEEEESEED 599
SV D+ AE + + EE+ +E EEEE E EED
Sbjct: 29 SVKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEED 76
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 34.4 bits (79), Expect = 0.15
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
D+E + ++ + E E++E EE E EEEEE+ +E
Sbjct: 249 DEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285
Score = 31.7 bits (72), Expect = 1.0
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 9/59 (15%)
Query: 555 HPLVSVSDDEAEGKNVKRKHK---------GEETEEDEGEEEESEEEEEESEEDNITGV 604
+ DD +G +VK K G+ EE E +E+E EEE EE EE+
Sbjct: 227 SDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 34.0 bits (78), Expect = 0.16
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 554 KHPLVSVSDDEAEGKNV---KRKHKGEETEEDEGEEEESEEEEEESEEDN 600
K L + +++ + K K+ + E + DE +E++ EEEEEE EED
Sbjct: 138 KVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDE 187
Score = 32.0 bits (73), Expect = 0.63
Identities = 11/40 (27%), Positives = 27/40 (67%)
Query: 560 VSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+ + EAE + + + EE EE+E E+E+ ++++++ ++D
Sbjct: 160 LKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDDD 199
Score = 31.3 bits (71), Expect = 1.0
Identities = 11/37 (29%), Positives = 26/37 (70%)
Query: 564 EAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
E E ++V + + +E EE+E EEE+ + ++++ ++D+
Sbjct: 162 ELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDD 198
Score = 30.5 bits (69), Expect = 1.7
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 555 HPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+S E + K ++ + EE E+DE EEEE EEE+E+ ++D
Sbjct: 148 DIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDD 192
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 34.7 bits (80), Expect = 0.17
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 546 ARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
+ KE + L + S E E N +R + EE EE+E EE+E E +E +D
Sbjct: 362 TKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDE 416
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 33.0 bits (76), Expect = 0.17
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 189 RQLWRVLEMS----DIILIIIDIRYPCLMFPPTLYDYVTGTLGKDMILVMNKIDLAPAP 243
R+ + L ++ D+I ++ D P +FPP K +I ++ KIDLA
Sbjct: 51 RRFYSALIVTAADADVIALVQDATEPWSVFPP----GFASMFNKPVIGIITKIDLAKDE 105
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 34.4 bits (80), Expect = 0.18
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 368 LTIGCVGQPNVGKSSLMNA 386
+TIG VG+PNVGKS+ NA
Sbjct: 2 ITIGLVGKPNVGKSTFFNA 20
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM). This
family consists of several Plasmodium falciparum SPAM
(secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the alanine
heptad-repeat domain. Heptad repeats in which the a and
d position contain hydrophobic residues generate
amphipathic alpha-helices which give rise to helical
bundles or coiled-coil structures in proteins. SPAM is
an example of a P. falciparum antigen in which a
repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 33.3 bits (76), Expect = 0.20
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
++ E + + + + EE E+ E EEE E+EEEE E++
Sbjct: 48 QEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEE 86
Score = 29.1 bits (65), Expect = 4.3
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 566 EGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNI 601
E ++VK + + ++ EE+E +EEE EE E+ +E+ I
Sbjct: 39 ENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEI 74
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 32.1 bits (73), Expect = 0.20
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 575 KGEETEEDEGEEEESEEEEEESEEDNITG 603
EE E++ EE++ EEE+EE EE+ + G
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEEEEEEALAG 101
Score = 29.0 bits (65), Expect = 2.5
Identities = 14/24 (58%), Positives = 19/24 (79%)
Query: 573 KHKGEETEEDEGEEEESEEEEEES 596
+ K EE EE++ +EEE EEEEEE+
Sbjct: 75 EEKAEEKEEEKKKEEEKEEEEEEA 98
Score = 27.8 bits (62), Expect = 6.8
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 577 EETEEDEGEEEESEEEEEESEE 598
EE E+EE +++EEE EE
Sbjct: 72 AAAEEKAEEKEEEKKKEEEKEE 93
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 34.2 bits (79), Expect = 0.20
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 368 LTIGCVGQPNVGKSSLMNAI 387
L +G VG PNVGKS+ NA+
Sbjct: 22 LKMGIVGLPNVGKSTTFNAL 41
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 33.4 bits (76), Expect = 0.22
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 364 KSGVLTIGCVGQPNVGKSSLMNAIMGRKVV 393
I +G VGK++L+N ++G +
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVGDEFP 31
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 33.9 bits (79), Expect = 0.23
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
+G VG PN GKS+L++A+
Sbjct: 160 VGLVGLPNAGKSTLISAV 177
Score = 29.3 bits (67), Expect = 6.2
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 226 LGKDMILVMNKIDLAPAPLVLAWKHYFQSKFPK 258
K I+V+NKIDL + + K
Sbjct: 272 AEKPRIVVLNKIDLLDEEELEELLKELKEALGK 304
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 33.9 bits (78), Expect = 0.27
Identities = 16/26 (61%), Positives = 18/26 (69%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNIT 602
E EE+E EEE EEEEEE EE+ T
Sbjct: 304 EPEEEEEEEEEVPEEEEEEEEEEERT 329
Score = 31.5 bits (72), Expect = 1.6
Identities = 15/23 (65%), Positives = 17/23 (73%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
E EE+E EEEE EEEEE EE+
Sbjct: 303 PEPEEEEEEEEEVPEEEEEEEEE 325
Score = 29.6 bits (67), Expect = 5.3
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
E+E EEEE EEEE EE+
Sbjct: 302 PPEPEEEEEEEEEVPEEEEEEEE 324
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 33.5 bits (77), Expect = 0.28
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
+ E + K +G E+++D+ EEEE E EE+E +D
Sbjct: 77 KWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDE 115
Score = 33.5 bits (77), Expect = 0.29
Identities = 17/41 (41%), Positives = 22/41 (53%)
Query: 558 VSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
S S+DE E +K K + EE E+EE EEEE+E
Sbjct: 129 SSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEA 169
Score = 30.4 bits (69), Expect = 2.7
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 564 EAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
E + ++K + E+ E + +++E EE E E +ED
Sbjct: 76 EKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDED 111
Score = 29.2 bits (66), Expect = 5.3
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 560 VSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
SD E E + + K +E ++E EE+ EE EE E +
Sbjct: 129 SSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEA 169
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 32.6 bits (75), Expect = 0.28
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 572 RKHKGEETEEDEGEEEESEEEEEESEEDNIT 602
RK G + +E E EEEE E EE EE+ I
Sbjct: 91 RKLLGLDKKEKEEEEEEEVEVEELDEEEQID 121
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 32.2 bits (73), Expect = 0.30
Identities = 12/54 (22%), Positives = 21/54 (38%)
Query: 545 QARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
+A + + +D E + + + DE + E E +EEE EE
Sbjct: 75 EAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEE 128
Score = 29.1 bits (65), Expect = 2.6
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 560 VSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
+D+ E + E D EE EEE+EE+E
Sbjct: 93 AADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.4 bits (77), Expect = 0.30
Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTK-----HFQTIFLTDNIRLCDCPGL 422
TI G PNVGKSSL+ + K V+ P TK HF I++ D PGL
Sbjct: 170 TIVVAGYPNVGKSSLVRKLTTAK-PEVAPYPFTTKGIHVGHF--ERGYLRIQVIDTPGL 225
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 33.0 bits (76), Expect = 0.34
Identities = 26/66 (39%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKV-VSVSRTPGHTKHFQTIFLTDN---IRLCDCPGLV 423
L I VG+ GKS+ N+I+GRK S R G TK Q + T + I + D PGL
Sbjct: 1 LRIVLVGKTGNGKSATGNSILGRKAFESKLRAQGVTKTCQLVSRTWDGRIINVIDTPGL- 59
Query: 424 FPSKVP 429
F V
Sbjct: 60 FDLSVS 65
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 33.3 bits (77), Expect = 0.35
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
+G VG PN GKS+L++A+
Sbjct: 162 VGLVGLPNAGKSTLLSAV 179
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 32.9 bits (76), Expect = 0.43
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 373 VGQPNVGKSSLMNAIMG 389
VGQ VGKSSL+NA++
Sbjct: 211 VGQSGVGKSSLINALLP 227
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 31.9 bits (73), Expect = 0.46
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNITGV 604
++ EEDE EE++ E+++E+ E+ + V
Sbjct: 114 SDDDEEDEEEEDDEEDDDEDESEEEESPV 142
Score = 31.5 bits (72), Expect = 0.54
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
E+ +D+ E+EE E++EE+ +ED
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDED 133
Score = 30.8 bits (70), Expect = 0.90
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNI 601
EE E D+ EE+E EE++EE ++++
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDE 134
Score = 30.8 bits (70), Expect = 0.94
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
E +E + +EE+ EEE++E ++D
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDD 131
Score = 30.8 bits (70), Expect = 1.00
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 9/42 (21%)
Query: 557 LVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
LV+ +DE++ +E +E+E ++EE ++E+E EE
Sbjct: 106 LVASEEDESDD---------DEEDEEEEDDEEDDDEDESEEE 138
Score = 30.8 bits (70), Expect = 1.0
Identities = 9/25 (36%), Positives = 21/25 (84%)
Query: 575 KGEETEEDEGEEEESEEEEEESEED 599
+ +E+++DE +EEE ++EE++ E++
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDE 134
Score = 30.0 bits (68), Expect = 1.6
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
E +++E EEEE +EE+++ +E
Sbjct: 112 DESDDDEEDEEEEDDEEDDDEDES 135
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 30.3 bits (69), Expect = 0.51
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 580 EEDEGEEEESEEEEEESEED 599
EE++ EEEEEE ++D
Sbjct: 63 AAAAEEEKKEEEEEEEEDDD 82
Score = 29.5 bits (67), Expect = 1.0
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 580 EEDEGEEEESEEEEEESEED 599
EEE+ EEEEEE E+D
Sbjct: 62 AAAAAEEEKKEEEEEEEEDD 81
Score = 28.7 bits (65), Expect = 2.4
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
EEE +EEEEE EED
Sbjct: 57 AAAAAAAAAAEEEKKEEEEEEEED 80
Score = 28.4 bits (64), Expect = 2.5
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 576 GEETEEDEGEEEESEEEEEE 595
E+E +EEE EEEE++
Sbjct: 62 AAAAAEEEKKEEEEEEEEDD 81
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 31.8 bits (73), Expect = 0.51
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 370 IGCVGQPNVGKSSLMNAIMGRKV 392
I VG + GKSS++NA++GR +
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDI 23
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 31.8 bits (73), Expect = 0.52
Identities = 29/143 (20%), Positives = 42/143 (29%), Gaps = 39/143 (27%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGH-------TKHFQTIFLTDNIRLCDCPGLVFP 425
GQ VGKS+L+NA++ + T H + L L D PG
Sbjct: 41 AGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLIDTPG---- 96
Query: 426 SKVPKPLQVLMGSFPIAQLREPYSTVQYLAERMDLIKL------LHIKHPDDDEYWCAMD 479
+ L +P +Y E +L LH P CA+
Sbjct: 97 ----------FRELGLWHL-DPEELAEYFPEFRELAGQCKFRDCLHTNEPG-----CAVK 140
Query: 480 ICDGWAQKRSYMTAKTGRYDSYR 502
RY++Y
Sbjct: 141 --AAVENG----EISEERYENYL 157
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 32.1 bits (74), Expect = 0.55
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 369 TIGCVGQPNVGKSSLMNAIMG 389
+ VG P+VGKS+L++ +
Sbjct: 2 RVALVGFPSVGKSTLLSKLTN 22
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 33.0 bits (76), Expect = 0.59
Identities = 17/69 (24%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 533 EKHPDIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEE--TEEDEGEEEESE 590
E PD D+ + ++E + V D+E + +++ + + + EE++ E+E+S+
Sbjct: 305 EFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSD 364
Query: 591 EEEEESEED 599
+E++E EE+
Sbjct: 365 DEDDEEEEE 373
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 30.8 bits (70), Expect = 0.63
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
+ +EE+ EEEEEES++D
Sbjct: 74 AAAAAAEAKKEEKKEEEEEESDDD 97
Score = 28.4 bits (64), Expect = 3.8
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 581 EDEGEEEESEEEEEESEEDNI 601
E ++EE +EEEEE +D++
Sbjct: 78 AAEAKKEEKKEEEEEESDDDM 98
>gnl|CDD|147523 pfam05384, DegS, Sensor protein DegS. This is small family of
Bacillus DegS proteins. The DegS-DegU two-component
regulatory system of Bacillus subtilis controls various
processes that characterize the transition from the
exponential to the stationary growth phase, including
the induction of extracellular degradative enzymes,
expression of late competence genes and down-regulation
of the sigma D regulon. The family also contains one
sequence from Thermoanaerobacter tengcongensis which is
described as a sensory transduction histidine kinase.
Length = 159
Score = 31.4 bits (72), Expect = 0.69
Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 324 IAEEMHLEYEDVEEEDE--KVEVGETIELKKVDTNYEVHEKY 363
IAE+ EYE +E+E E K EV E I K+VD E E+
Sbjct: 21 IAEQARQEYERLEQELEEVKEEVSEVI--KEVDK-LEKQERR 59
>gnl|CDD|216269 pfam01056, Myc_N, Myc amino-terminal region. The myc family
belongs to the basic helix-loop-helix leucine zipper
class of transcription factors, see pfam00010. Myc forms
a heterodimer with Max, and this complex regulates cell
growth through direct activation of genes involved in
cell replication. Mutations in the C-terminal 20
residues of this domain cause unique changes in the
induction of apoptosis, transformation, and G2 arrest.
Length = 329
Score = 32.2 bits (73), Expect = 0.73
Identities = 16/27 (59%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNIT 602
G ++E +E EEEE EEEEEE E D +T
Sbjct: 223 GSDSESEEDEEEEEEEEEEE-EIDVVT 248
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 32.7 bits (74), Expect = 0.73
Identities = 11/39 (28%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEE-EEEESEE 598
+D++ E +E+E D +EE+ E+ +E ES+
Sbjct: 952 TDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKA 990
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 32.4 bits (74), Expect = 0.77
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
D++ E + +H+ EE E+ E E +S E+
Sbjct: 373 DEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSS 410
Score = 29.7 bits (67), Expect = 5.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 577 EETEEDEGEEEESEEEEEESEEDN 600
+E EE+E +E EEEE E E+
Sbjct: 373 DEDEEEEQRSDEHEEEEGEDSEEE 396
Score = 29.3 bits (66), Expect = 6.4
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
+ +EDE EE+ S+E EEE ED
Sbjct: 370 VDEDEDEEEEQRSDEHEEEEGED 392
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 32.0 bits (74), Expect = 0.91
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
+G VG PNVGKS+L++ +
Sbjct: 161 VGLVGFPNVGKSTLLSVV 178
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 32.2 bits (73), Expect = 0.91
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 368 LTIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDN---IRLCDCPGL 422
L I +G+ VGKS+ +N+I G S T Q I IR+ D PGL
Sbjct: 119 LNILVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVKIRVIDTPGL 176
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 31.6 bits (72), Expect = 0.92
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITG 603
D E E + + +++ E+ E + E+E+EE+ E + E IT
Sbjct: 82 GDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITN 124
Score = 30.9 bits (70), Expect = 1.6
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEE----EEEESEEDNITGV 604
+ ++ E K K E EE+E E+EES + E EE E N+
Sbjct: 74 NSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKE 121
>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family.
This family contains a number of defence peptides
secreted from the skin of amphibians, including the
opiate-like dermorphins and deltorphins, and the
antimicrobial dermoseptins and temporins. The alignment
for this family includes the signal peptide.
Length = 46
Score = 28.5 bits (64), Expect = 0.93
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 577 EETEEDEGEEEESEEEEEESEE 598
EE EDE E E+ EE EE+SE
Sbjct: 23 EEKREDEEENEDEEEGEEQSEV 44
Score = 25.8 bits (57), Expect = 9.4
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 580 EEDEGEEEESEEEEEESEED 599
EE++ E+EE E+EEE EE
Sbjct: 22 EEEKREDEEENEDEEEGEEQ 41
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 30.1 bits (67), Expect = 0.95
Identities = 8/25 (32%), Positives = 20/25 (80%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNI 601
+E E+D+ E+EE ++E+++ ++D +
Sbjct: 17 DEEEDDDDEDEEDDDEDDDEDDDEV 41
Score = 29.0 bits (64), Expect = 2.3
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 575 KGEETEEDEGEEEESEEEEEESEED 599
+GEE + + +EEE +++E+E ++D
Sbjct: 7 EGEEDSDSDSDEEEDDDDEDEEDDD 31
Score = 29.0 bits (64), Expect = 2.4
Identities = 8/25 (32%), Positives = 19/25 (76%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDN 600
E+++ D EEE+ ++E+EE ++++
Sbjct: 9 EEDSDSDSDEEEDDDDEDEEDDDED 33
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 32.2 bits (73), Expect = 0.95
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 539 DEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
+ + I K + K + + E E ++ EET++DE E E E+ E ESE
Sbjct: 623 EGLQLILDVLKADENKSRHQQLFEGEEEDEDDL-----EETDDDEDECEAIEDSESESES 677
Query: 599 DNITG 603
D G
Sbjct: 678 DGEDG 682
Score = 31.0 bits (70), Expect = 2.0
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 550 EEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESE 597
EE + L DDE E + ++ E E +GE+ E +E+E+++E
Sbjct: 648 EEEDEDDLEETDDDEDECEAIE---DSESESESDGEDGEEDEQEDDAE 692
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 31.6 bits (73), Expect = 1.0
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 370 IGCVGQPNVGKSSLMNAI 387
+G VG PN GKS+L++A+
Sbjct: 161 VGLVGLPNAGKSTLISAV 178
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 30.8 bits (71), Expect = 1.3
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 373 VGQPNVGKSSLMNAIMG---RKVVSVSRTPGHTKHFQT------IFLTDNIRLCDCPG 421
VGQ VGKS+L+NA++ +S G +H T L + D PG
Sbjct: 91 VGQSGVGKSTLLNALLPELVLATGEISEKLGRGRH--TTTHRELFPLPGGGLIIDTPG 146
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 31.0 bits (71), Expect = 1.3
Identities = 5/27 (18%), Positives = 18/27 (66%)
Query: 574 HKGEETEEDEGEEEESEEEEEESEEDN 600
E +E++ E+++ ++E+E+ +++
Sbjct: 43 AIESELDEEDLEDDDDDDEDEDEDDEE 69
Score = 29.8 bits (68), Expect = 3.1
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 577 EETEEDEGEEEESEEEEEESEEDN 600
EE ED+ +++E E+E++E E D
Sbjct: 50 EEDLEDDDDDDEDEDEDDEEEADL 73
Score = 29.5 bits (67), Expect = 4.4
Identities = 8/40 (20%), Positives = 21/40 (52%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNI 601
A ++ + E+ E+D+ ++E+ +E++EE +
Sbjct: 36 AAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGP 75
Score = 29.1 bits (66), Expect = 4.8
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
E+ ++D+ +E+E +EEE + D
Sbjct: 54 EDDDDDDEDEDEDDEEEADLGPD 76
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 31.2 bits (70), Expect = 1.5
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 551 EPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
+P + L+S + + + K EE EE+E EEE +EE + +++
Sbjct: 196 KPKQEQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
Length = 258
Score = 30.9 bits (71), Expect = 1.5
Identities = 16/34 (47%), Positives = 19/34 (55%)
Query: 565 AEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
EG+ + EE EE+ EEEE EEEEE E
Sbjct: 222 LEGRQGRLAEAAEEEEEEAEEEEEEEEEEEAEEA 255
>gnl|CDD|227931 COG5644, COG5644, Uncharacterized conserved protein [Function
unknown].
Length = 869
Score = 31.6 bits (71), Expect = 1.6
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 537 DIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEES 596
D+D +L K E S ++D A K + + + E EE +SE E E S
Sbjct: 126 DLDTLLDNDQPEKNE-------SGNNDHATDKENLLESDASSSNDSESEESDSESEIESS 178
Query: 597 EED 599
+ D
Sbjct: 179 DSD 181
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 30.0 bits (68), Expect = 1.7
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 572 RKHKGEETEEDEGEEEESEEEEEESEEDNITGV 604
++ EE++ EE+ E+ E+ E+D G
Sbjct: 73 KEALKLLEEENDDEEDAETEDTEDVEDDEWEGF 105
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.4 bits (72), Expect = 1.7
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 563 DEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
E + K K K EE EE++ ++EE +EEEEE E+
Sbjct: 428 KEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464
Score = 29.9 bits (68), Expect = 4.2
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 560 VSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+ + + K+K + EE E+++ EEE+ EEEEE EE
Sbjct: 427 KKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEK 466
Score = 29.9 bits (68), Expect = 4.7
Identities = 19/55 (34%), Positives = 29/55 (52%)
Query: 545 QARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+A K E K + + + + + K ++ EE E EEEE+EEE+EE EE
Sbjct: 418 KAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEK 472
Score = 29.5 bits (67), Expect = 5.4
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 537 DIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEES 596
+EI ++ ++ K V E + + K++ K + + EEEE EE+E++
Sbjct: 395 TEEEIEFL--TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKE 452
Query: 597 EEDN 600
EE
Sbjct: 453 EEKE 456
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 31.2 bits (70), Expect = 1.8
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
+ + E HK E + E E +EE++E+EE
Sbjct: 295 EQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEE 331
>gnl|CDD|132796 cd06886, PX_SNX27, The phosphoinositide binding Phox Homology
domain of Sorting Nexin 27. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX27 contains an N-terminal
PDZ domain followed by a PX domain and a Ras-Associated
(RA) domain. It binds G protein-gated potassium (Kir3)
channels, which play a role in neuronal excitability
control, through its PDZ domain. SNX27 downregulates
Kir3 channels by promoting their movement in the
endosome, reducing surface expression and increasing
degradation. SNX27 also associates with
5-hydroxytryptamine type 4 receptor (5-HT4R), cytohesin
associated scaffolding protein (CASP), and
diacylglycerol kinase zeta, and may play a role in their
intracellular trafficking and endocytic recycling. The
SNX27 PX domain preferentially binds to
phosphatidylinositol-3-phosphate (PI3P) and is important
for targeting to the early endosome.
Length = 106
Score = 29.3 bits (66), Expect = 1.8
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 135 PELDFPKRP-EWNFNMSIDQLDRR 157
P+ FPK P +W F++S QLD R
Sbjct: 53 PDFQFPKLPGKWPFSLSEQQLDAR 76
>gnl|CDD|148100 pfam06288, DUF1040, Protein of unknown function (DUF1040). This
family consists of several bacterial YihD proteins of
unknown function.
Length = 86
Score = 28.9 bits (65), Expect = 1.9
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 529 QEYWEKHPDIDEILWIQARTKEEPYKHPLVSVSDD 563
Q YW+K PD+ I ++Q +E + PL ++DD
Sbjct: 14 QPYWQKDPDLSLIQFLQKLAQEAGFDGPLEDLTDD 48
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 29.7 bits (68), Expect = 2.1
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 354 DTNYEVHEKYKSGVLTIGCVGQPNVGKSSLMNAIMGRKV 392
D + ++ + IG VG+ GKS+L+ I G
Sbjct: 18 DISLTINPGDR-----IGLVGRNGAGKSTLLKLIAGELE 51
>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 = 30.2 bits (69), Expect = 2.2
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 362 KYKSGVLTIGCVGQPNVGKSSLMNAIMGRK 391
K K G LT +G GKS+L+NA+ GR+
Sbjct: 31 KAKPGELT-AIMGPSGAGKSTLLNALAGRR 59
>gnl|CDD|225626 COG3084, COG3084, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 88
Score = 28.7 bits (64), Expect = 2.5
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 529 QEYWEKHPDIDEILWIQARTKEEPYKHPLVSVSDD 563
Q W+K PD++ + ++Q KE + L ++DD
Sbjct: 14 QPAWQKEPDLNLLQFLQKLAKESGFDGELADLTDD 48
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 30.7 bits (69), Expect = 2.5
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
++E E + + + + EE E ++ EEEE E + SEE+
Sbjct: 447 EEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEE 485
Score = 30.7 bits (69), Expect = 3.0
Identities = 20/59 (33%), Positives = 29/59 (49%)
Query: 542 LWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
+ + E P S ++ E + + + + EE +E E EE E EEEEEE E DN
Sbjct: 422 SKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADN 480
>gnl|CDD|238425 cd00829, SCP-x_thiolase, Thiolase domain associated with sterol
carrier protein (SCP)-x isoform and related proteins;
SCP-2 has multiple roles in intracellular lipid
circulation and metabolism. The N-terminal presequence
in the SCP-x isoform represents a peroxisomal
3-ketacyl-Coa thiolase specific for branched-chain acyl
CoAs, which is proteolytically cleaved from the sterol
carrier protein.
Length = 375
Score = 30.3 bits (69), Expect = 2.7
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 13/46 (28%)
Query: 440 PIAQLREPYSTVQYLAERM--DLIKLLHIKHPDDDEYWCAMDICDG 483
P AQ R+P + L RM D ++LL C + DG
Sbjct: 173 PYAQFRKPITVEDVLNSRMIADPLRLLD----------CCP-VSDG 207
>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta;
Reviewed.
Length = 129
Score = 29.2 bits (66), Expect = 2.8
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 532 WEKHPDIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEE 591
W +IDE + +E+ K + D+ + + +D+ +EE+ +E
Sbjct: 70 WYPVDEIDEEI---IPLEEKFDKKKKKFMDGDDDIIDD-------DILPDDDFDEEDLDE 119
Query: 592 EEEESEED 599
E++E EED
Sbjct: 120 EDDEDEED 127
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 29.9 bits (68), Expect = 2.8
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 552 PYKHPLVSVSDDEAEGKNVKRKHKG--EETEEDEGEEEESEEEEEE 595
P K P ++EA ++ H+ E+ DE +EE EEE++
Sbjct: 14 PPKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDR 59
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 30.6 bits (70), Expect = 2.9
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 373 VGQPNVGKSSLMNAIMG 389
VG GK+SL+NA++G
Sbjct: 382 VGPSGAGKTSLLNALLG 398
>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and L12p.
Ribosomal proteins P1 and P2 are the eukaryotic proteins
that are functionally equivalent to bacterial L7/L12.
L12p is the archaeal homolog. Unlike other ribosomal
proteins, the archaeal L12p and eukaryotic P1 and P2 do
not share sequence similarity with their bacterial
counterparts. They are part of the ribosomal stalk
(called the L7/L12 stalk in bacteria), along with 28S
rRNA and the proteins L11 and P0 in eukaryotes (23S
rRNA, L11, and L10e in archaea). In bacterial ribosomes,
L7/L12 homodimers bind the extended C-terminal helix of
L10 to anchor the L7/L12 molecules to the ribosome.
Eukaryotic P1/P2 heterodimers and archaeal L12p
homodimers are believed to bind the L10 equivalent
proteins, eukaryotic P0 and archaeal L10e, in a similar
fashion. P1 and P2 (L12p, L7/L12) are the only proteins
in the ribosome to occur as multimers, always appearing
as sets of dimers. Recent data indicate that most
archaeal species contain six copies of L12p (three
homodimers), while eukaryotes have two copies each of P1
and P2 (two heterodimers). Bacteria may have four or six
copies (two or three homodimers), depending on the
species. As in bacteria, the stalk is crucial for
binding of initiation, elongation, and release factors
in eukaryotes and archaea.
Length = 105
Score = 28.8 bits (64), Expect = 2.9
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 580 EEDEGEEEESEEEEEESEED 599
E E EE EEEEEE +ED
Sbjct: 80 EPAEKAEEAKEEEEEEEDED 99
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 29.7 bits (67), Expect = 2.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 577 EETEEDEGEEEESEEEEEESEEDNI 601
+E +E E++ES +EEE D+
Sbjct: 13 DEELPEEDEDDESSDEEEVDLPDDE 37
Score = 29.3 bits (66), Expect = 4.4
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 576 GEETEEDEGEEEESEEEEEESEED 599
G E+E D+GEE+E EE+E +E
Sbjct: 2 GSESESDDGEEDEELPEEDEDDES 25
Score = 28.1 bits (63), Expect = 9.2
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 577 EETEEDEGEEEESEEEEEESEEDN 600
E+ E E +E++ +EEE + +
Sbjct: 12 EDEELPEEDEDDESSDEEEVDLPD 35
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the SitABCD
transporter of Shigella flexneri. Moreover other
uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 29.8 bits (68), Expect = 3.0
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 362 KYKSGVLTIGCVGQPN-VGKSSLMNAIMG 389
+ K G VG PN GKS+L+ AI+G
Sbjct: 21 EVKPGEFL-AIVG-PNGAGKSTLLKAILG 47
>gnl|CDD|223924 COG0855, Ppk, Polyphosphate kinase [Inorganic ion transport and
metabolism].
Length = 696
Score = 30.7 bits (70), Expect = 3.0
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 112 RAYETLVPVDQKDLEHNLDDYFLPEL-DFPKRPEWNFNMSIDQLDRRE-------QDYFR 163
R E L P+ L+ L + L D K E + S ++ R Q F
Sbjct: 624 RRVEVLFPILDPRLKQVLLEILEILLDDNVKAWELQPDGSSRRIVPRGNEEPVNAQQAFM 683
Query: 164 DYLSNIE 170
DYLS+ E
Sbjct: 684 DYLSSSE 690
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 30.3 bits (68), Expect = 3.1
Identities = 15/23 (65%), Positives = 15/23 (65%)
Query: 577 EETEEDEGEEEESEEEEEESEED 599
E EEDE EEE EE EEE E D
Sbjct: 6 ELEEEDESGEEEEEESEEEEETD 28
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 29.6 bits (67), Expect = 3.2
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 226 LGKDMILVMNKIDLAP 241
L K +I+V+NKIDL P
Sbjct: 119 LCKPLIVVLNKIDLIP 134
>gnl|CDD|226111 COG3583, COG3583, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 309
Score = 30.2 bits (68), Expect = 3.2
Identities = 12/56 (21%), Positives = 17/56 (30%), Gaps = 8/56 (14%)
Query: 544 IQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+ + E V V D KG+E EG+ E E E+
Sbjct: 210 SKTDKENEQVDFETVYVEDPSMN--------KGKEKVVQEGQPGTKEVTFEVVTEN 257
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 30.0 bits (67), Expect = 3.5
Identities = 15/51 (29%), Positives = 21/51 (41%)
Query: 550 EEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
E+P V D++ + + EE+E EE EEEE EE
Sbjct: 147 EKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVG 197
Score = 29.2 bits (65), Expect = 5.4
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+E++G+ + + EG E +EEEEEE+E
Sbjct: 182 LEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAEGS 219
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved in
conjugation with cellular fusion (mating) and invasive
growth. A high throughput localisation study has
localised RXT2 to the nucleus.
Length = 141
Score = 28.9 bits (65), Expect = 3.7
Identities = 9/47 (19%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 553 YKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
Y+ ++S + N + + + D+ +E++ ++EE ++E+D
Sbjct: 29 YERDVLS---RKRIKFNNPPRIDEDGGDIDDDDEDDEDDEEADAEDD 72
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 29.7 bits (67), Expect = 3.9
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 561 SDDEAEGKNVKR---KHKGEETEEDEGEEEESEEEEEESEEDNI 601
D E E + R K K E EE E EEEE EEE++ E+ I
Sbjct: 138 DDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAREEEI 181
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 30.2 bits (68), Expect = 4.0
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 577 EETEEDEGEEEESEEEEEESEE 598
EE EE+E EEEE+ E E EE
Sbjct: 404 EEEEEEEEEEEEAAEAEAPMEE 425
Score = 29.0 bits (65), Expect = 9.2
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 576 GEETEEDEGEEEESEEEEEESEEDNITGV 604
EE EE+E EEEE E E E+ + G
Sbjct: 402 AEEEEEEEEEEEEEAAEAEAPMEEPVPGF 430
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 28.4 bits (63), Expect = 4.2
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITGV 604
E + + + + E+ EE+EGE EE E EEEE E + TG
Sbjct: 43 GAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEE-ETEGATGK 85
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 30.0 bits (67), Expect = 4.2
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDN 600
+D + +N RK E EE EE++ EE++++ ++++
Sbjct: 29 NDTMKKENAIRKLGKEAEEEAMEEEDDDEEDDDDDDDED 67
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 30.0 bits (68), Expect = 4.3
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 536 PDIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVK----------RKHKGEETEEDEGE 585
E + K++ K + RK K + + ED+ +
Sbjct: 1311 KKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDD 1370
Query: 586 EEESEEEEEESEEDNI 601
E + E+E+ E+D
Sbjct: 1371 SEVDDSEDEDDEDDED 1386
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 29.9 bits (67), Expect = 4.4
Identities = 13/45 (28%), Positives = 20/45 (44%)
Query: 555 HPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
+SD A G + + + E E E +E+ EESEE+
Sbjct: 282 REEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEE 326
Score = 29.2 bits (65), Expect = 8.7
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 542 LWIQARTKEEPYKHPLVSVSDDEAEGKNVKRK----HKGEETEEDEGEEEESEEEEEESE 597
L + K P + +G + K E +ED+G+E + E+ + E
Sbjct: 180 LMMMKAAKNGPAAFGDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEE 239
Query: 598 ED 599
+
Sbjct: 240 KS 241
>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component. This
family is a region of the Myb-Related Cdc5p/Cef1
proteins, in fungi, and is part of the pre-mRNA splicing
factor complex.
Length = 363
Score = 29.6 bits (67), Expect = 4.5
Identities = 15/23 (65%), Positives = 15/23 (65%)
Query: 578 ETEEDEGEEEESEEEEEESEEDN 600
E E E EEEE EE EEE EED
Sbjct: 146 ELELPEEEEEEPEEMEEELEEDA 168
>gnl|CDD|182614 PRK10645, PRK10645, divalent-cation tolerance protein CutA;
Provisional.
Length = 112
Score = 28.2 bits (63), Expect = 4.6
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 295 MAAEGAKKLLEACQTIVQGAVDLSSWERKIAEE 327
+AA+ + L AC T++ GA L WE K+ +E
Sbjct: 27 LAAKVLAEKLAACVTLLPGATSLYYWEGKLEQE 59
>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP
synthase is a thiamine diphosphate-dependent enzyme
related to transketolase and the pyruvate dehydrogenase
E1-beta subunit. By an acyloin condensation of pyruvate
with glyceraldehyde 3-phosphate, it produces
1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
diphosphate (TPP), pyridoxal phosphate, and the
isoprenoid building block isopentenyl diphosphate (IPP)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridoxine, Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 617
Score = 29.7 bits (67), Expect = 4.6
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 23/103 (22%)
Query: 37 PEHQLAPKMEGKNIIVQVSKKKFADPDDEDTTESAAATIQAI---NKQPIMGGAKSNPNR 93
++A + K I V +F P DE+ AA+ + + + IMGGA S
Sbjct: 509 EALEVAESLNEKGIEATVVDARFVKPLDEELILEIAASHEKLVTVEENAIMGGAGSA--- 565
Query: 94 YVLQFHKESPAELKERKKRAYETLVPVDQKDLEHNLDDYFLPE 136
VL+F L ++ K LVPV + + D+F+P
Sbjct: 566 -VLEF-------LMDQNK-----LVPVKRLGIP----DFFIPH 591
>gnl|CDD|220112 pfam09110, HAND, HAND. The HAND domain adopts a secondary
structure consisting of four alpha helices, three of
which (H2, H3, H4) form an L-like configuration. Helix
H2 runs antiparallel to helices H3 and H4, packing
closely against helix H4, whilst helix H1 reposes in the
concave surface formed by these three helices and runs
perpendicular to them. The domain confers DNA and
nucleosome binding properties to the protein.
Length = 109
Score = 28.0 bits (63), Expect = 5.0
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 540 EILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
E L+ + + YK PL V D + E + + + E E+ + E +EEEEEE +
Sbjct: 49 EQLYYKKKIG---YKVPLDDVGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQR 104
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 29.3 bits (67), Expect = 5.2
Identities = 7/15 (46%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 376 PN-VGKSSLMNAIMG 389
N GK++L+ IMG
Sbjct: 34 RNGAGKTTLLKTIMG 48
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.5 bits (67), Expect = 5.3
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 363 YKSGVLTIGCVGQPNVGKSSLMNAIMGRKVVSVSR 397
+ SG T+ +G VGKS+L+NA++G +V
Sbjct: 191 WLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGA 225
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 29.7 bits (68), Expect = 5.3
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 14/62 (22%)
Query: 537 DIDEILWIQARTKEEPYKHPLVSVSDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEES 596
IDE WI + + P SV+ + + +EDE E+EE EE EEE
Sbjct: 449 PIDEF-WISYLEEFD--GKPFKSVARGDLD-----------LGKEDEEEKEEKEEAEEEF 494
Query: 597 EE 598
+
Sbjct: 495 KP 496
>gnl|CDD|233931 TIGR02565, cas_Csy2, CRISPR type I-F/YPEST-associated protein Csy2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family, typified by YPO2464 of Yersinia pestis, is a
CRISPR-associated (Cas) family strictly associated with
the Ypest subtype of CRISPR/Cas locus. This family is
designated Csy2, for CRISPR/Cas Subtype Ypest protein 2
[Mobile and extrachromosomal element functions, Other].
Length = 296
Score = 29.4 bits (66), Expect = 5.8
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 4/80 (5%)
Query: 50 IIVQVSKKKFADPDDEDTTESAAATIQAINKQPIMGGAKSNP-NRYVLQFHKESPAELKE 108
+++ VS A P D+ Q + +Q + GG R +Q E+ E +
Sbjct: 101 LVIGVSGSDIA-PTDDALQALLEHLKQLLKQQRLAGGTVIEFIERVQVQTLPEN--EDEA 157
Query: 109 RKKRAYETLVPVDQKDLEHN 128
+R +D++DL
Sbjct: 158 ATRRLLPGFALLDRQDLLAE 177
>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT. This family
consists of several bacterial cobalamin biosynthesis
(CobT) proteins. CobT is involved in the transformation
of precorrin-3 into cobyrinic acid.
Length = 282
Score = 29.4 bits (66), Expect = 5.8
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
S D + N E+ ++D+GEEEES + SE+
Sbjct: 218 SADSED--NEDEDDPKEDEDDDQGEEEESGSSDSLSED 253
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 29.4 bits (66), Expect = 6.0
Identities = 9/39 (23%), Positives = 20/39 (51%)
Query: 561 SDDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEED 599
E+ K+ + + + E+ + E E+ ++EEE + D
Sbjct: 162 EAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSD 200
>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 = 28.7 bits (65), Expect = 6.1
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 373 VGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHF 405
+G GKS+L+ A +GR + +P +
Sbjct: 10 LGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRY 42
>gnl|CDD|224414 COG1497, COG1497, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 29.3 bits (66), Expect = 6.2
Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 18/95 (18%)
Query: 274 NNIENSNKKGLQVRRRRGKMKMAAEGAKKLLEACQTIVQGAVDLSSWERKIAEEMHLEYE 333
+I+ K+GL + RG+ ++ +GA+ LLE ++ E
Sbjct: 44 EHIKELVKEGLIEKEGRGEYEITKKGAEWLLEQ------------------LSDLRRFSE 85
Query: 334 DVEEEDEKVEVGETIELKKVDTNYEVHEKYKSGVL 368
+VE + V V I + + V+ + K G L
Sbjct: 86 EVELVLDYVMVWTAIAKEDIKEGDTVYLRMKDGYL 120
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 28.5 bits (64), Expect = 6.8
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 22/75 (29%)
Query: 369 TIGCVGQPNVGKSSLMNAIMGRKVVSVSRTPGHTKHFQTIFLTDNIRLC----------- 417
T+ VG N GK++L++A+ G V+ T G T T D +C
Sbjct: 1 TLLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTP---TKLRLDKYEVCIFDLGGGANFR 57
Query: 418 --------DCPGLVF 424
+ GLVF
Sbjct: 58 GIWVNYYAEAHGLVF 72
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 29.3 bits (67), Expect = 6.9
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 320 WERKIAEEMHLEYEDVE 336
W R++ E+ EY DVE
Sbjct: 201 W-REVVTEVAKEYPDVE 216
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.4 bits (67), Expect = 7.0
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 373 VGQPNVGKSSLMNAI---MGRKVVSVS 396
VG P VGK+SL +I +GRK V +S
Sbjct: 356 VGPPGVGKTSLGKSIAKALGRKFVRIS 382
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 28.6 bits (65), Expect = 7.3
Identities = 7/15 (46%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 376 PN-VGKSSLMNAIMG 389
N GK++L+ IMG
Sbjct: 37 RNGAGKTTLLKTIMG 51
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 28.9 bits (65), Expect = 7.6
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 323 KIAEEMHLEYEDVEEEDEKVEV---GETIELKKVDTNYEVHEKYKSGVLTIGCVGQPNVG 379
+++ E+ E +++ VE T+ +K D NYE + K GVL+ G P
Sbjct: 80 RVSPEL---LEALKDRFADVEYNEAARTLAIK--DPNYEPKKGGKVGVLSAGTSDLPVAE 134
Query: 380 KSSLMNAIMGRKVVSV 395
++++ +G +V V
Sbjct: 135 EAAVTAEELGVEVQKV 150
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 29.0 bits (65), Expect = 8.2
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 562 DDEAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITGV 604
DD+ + + E DE EE+E+E + E EE +
Sbjct: 238 DDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAA 280
>gnl|CDD|219051 pfam06479, Ribonuc_2-5A, Ribonuclease 2-5A. This domain is a
endoribonuclease. Specifically it cleaves an intron from
Hac1 mRNA in humans, which causes it to be much more
efficiently translated.
Length = 127
Score = 27.9 bits (63), Expect = 8.3
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 250 HYFQSKFPKLTILCFT 265
YF +FP L I +T
Sbjct: 97 QYFTERFPDLLIHVYT 112
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 28.6 bits (65), Expect = 8.4
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 373 VGQPNVGKSSLMNAI 387
GQ VGKS+L+NA+
Sbjct: 170 AGQSGVGKSTLLNAL 184
>gnl|CDD|223473 COG0396, sufC, Cysteine desulfurase activator ATPase
[Posttranslational modification, protein turnover,
chaperones].
Length = 251
Score = 28.7 bits (65), Expect = 8.5
Identities = 24/69 (34%), Positives = 30/69 (43%), Gaps = 21/69 (30%)
Query: 327 EMHLEYEDVEEEDEKVEVGETIE-LKKVDTNY---EVHEKYKSGVLTIGCVGQPN-VGKS 381
M LE +D+ VEV E LK V+ EVH + +G PN GKS
Sbjct: 1 MMMLEIKDL-----HVEVEGKKEILKGVNLTVKEGEVH------AI-MG----PNGSGKS 44
Query: 382 SLMNAIMGR 390
+L IMG
Sbjct: 45 TLAYTIMGH 53
>gnl|CDD|233770 TIGR02188, Ac_CoA_lig_AcsA, acetate--CoA ligase. This model
describes acetate-CoA ligase (EC 6.2.1.1), also called
acetyl-CoA synthetase and acetyl-activating enzyme. It
catalyzes the reaction ATP + acetate + CoA = AMP +
diphosphate + acetyl-CoA and belongs to the family of
AMP-binding enzymes described by pfam00501.
Length = 625
Score = 29.1 bits (66), Expect = 8.7
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 470 DDDEYWCAMDICDGWAQKRSYM 491
D D +WC D+ GW SY+
Sbjct: 277 DGDIFWCTADV--GWITGHSYI 296
>gnl|CDD|218379 pfam05009, EBV-NA3, Epstein-Barr virus nuclear antigen 3 (EBNA-3).
This family contains EBNA-3A, -3B, and -3C which are
latent infection nuclear proteins important for
Epstein-Barr virus (EBV)-induced B-cell immortalisation
and the immune response to EBV infection.
Length = 254
Score = 28.6 bits (64), Expect = 8.9
Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 12/68 (17%)
Query: 543 WIQARTKEEPYKHPLVSVSDDEA---------EGKNVKRKHKGEETEEDEGEEEESEEEE 593
W+ A E PY L S A + + T E E E+SE
Sbjct: 170 WLSAHPNEVPYHRGLTSQDITAAFLRGQALGLSALRTPGEPDDDATVETSSESEDSE--- 226
Query: 594 EESEEDNI 601
ES+++ +
Sbjct: 227 SESDDEEL 234
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.7 bits (62), Expect = 9.1
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 370 IGCVGQPNVGKSSLMNAIMGRKVVSVSRTPG---HTKHFQTIFLTDNIRLCDCPG 421
+ VG + GK++L+ ++ + H H Q D PG
Sbjct: 3 VLVVGPKDSGKTTLIRKLL-NYLKRRGYRVAVVKHLDHGQGEI--------DKPG 48
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 28.7 bits (64), Expect = 9.7
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 578 ETEEDEGEEEESEEEEEESEE 598
TEE EE E E E +ES
Sbjct: 343 VTEESTDEESEDEVEIDESVI 363
Score = 28.7 bits (64), Expect = 9.9
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 564 EAEGKNVKRKHKGEETEEDEGEEEESEEEEEESEEDNITGV 604
E + V+ K E E +E E+E E +E I V
Sbjct: 326 EDIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEEV 366
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for centrosome
separation and maintenance of spindle bi-polarity. TPX2
is a microtubule-associated protein that mediates the
binding of the C-terminal domain of Xklp2 to
microtubules. It is phosphorylated during mitosis in a
microtubule-dependent way.
Length = 57
Score = 26.2 bits (58), Expect = 9.9
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 568 KNVKRKHKGEETEEDEGEEEESEEEEEESEE 598
K ++ K K E E++E E + EEEEE ++
Sbjct: 15 KKLEEKEKALEAEKEEAEARQKEEEEEAIKQ 45
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
0.315 0.133 0.396
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,267,099
Number of extensions: 3109479
Number of successful extensions: 8533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7263
Number of HSP's successfully gapped: 462
Length of query: 604
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 502
Effective length of database: 6,413,494
Effective search space: 3219573988
Effective search space used: 3219573988
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 (27.5 bits)