RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9995
(595 letters)
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 171 bits (434), Expect = 2e-48
Identities = 92/327 (28%), Positives = 137/327 (41%), Gaps = 57/327 (17%)
Query: 158 NLDFWRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTR 217
RQL V++ DV+V++VDAR+PL R +LER VKE K +++LNKADL +
Sbjct: 21 MKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIVKE----KPKLLVLNKADLAPK 76
Query: 218 KQRCYWTKYFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEE 277
+ W KYF F +
Sbjct: 77 EVTKKWKKYFKKEEGIKPIFVSAK-----------------------------------S 101
Query: 278 EDDGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSS 337
G+K+ + K+ EE I K + + +G+VGYPNVGKS+
Sbjct: 102 RQGGKKIRKALEKLS--------EEKIKRLKKKG------LLKRKIRVGVVGYPNVGKST 147
Query: 338 TINALLNAKKVSVSATPGKTKHFQTLFVDDELLLCDCPGLVMPSFVFSKADMILNGILPI 397
IN LL K S PG TK Q + +DD + L D PG++ P F + +L + P
Sbjct: 148 LINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIPPKFDDDEL--VLLKLAPK 205
Query: 398 DQMRDHVPAVNMLCTLVPRHVLEN-IYGIMITQPDEGEDPNRPPFSEELCNAYGYNRGFM 456
+++D V + + + +L + YG + +P EE RG++
Sbjct: 206 GEIKDPVLPADEVAERLLGGLLIDEHYGEKLNITRYESNPIHRTDPEEFLELIAKKRGWL 265
Query: 457 -TSNGQPDNPRSARYILKDFVNGHLLY 482
G+PD R+A ILKD NG L +
Sbjct: 266 LLKGGEPDLERAAETILKDIRNGKLGW 292
>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 = 152 bits (386), Expect = 8e-44
Identities = 56/81 (69%), Positives = 64/81 (79%)
Query: 161 FWRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQR 220
WRQLWRVIERSDV+VQIVDARNPL FRC DLE+YVKEV P K N++LLNKADL+T +QR
Sbjct: 1 VWRQLWRVIERSDVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKADLVTEEQR 60
Query: 221 CYWTKYFNSVNVAVAFFSATN 241
W +YF + V FFSA N
Sbjct: 61 KAWARYFKKEGIVVLFFSALN 81
Score = 133 bits (336), Expect = 1e-36
Identities = 44/57 (77%), Positives = 51/57 (89%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFVDDELLLCDCPGLVMP 380
TIGLVGYPNVGKSS INAL+ +KKVSVS+TPGKTKHFQT+F++ + LCDCPGLV P
Sbjct: 84 TIGLVGYPNVGKSSLINALVGSKKVSVSSTPGKTKHFQTIFLEPGITLCDCPGLVFP 140
>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 = 116 bits (292), Expect = 3e-30
Identities = 65/205 (31%), Positives = 106/205 (51%), Gaps = 36/205 (17%)
Query: 173 DVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRCYWTKYFNSVNV 232
DVI++++DAR+PL RC +ER V + P+K+ +++LNK DL+ ++ W KY +
Sbjct: 1 DVILEVLDARDPLGCRCPQVERAVLVLGPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFP 60
Query: 233 AVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIK 292
VAF ++T +++ S +S+ S++ +
Sbjct: 61 TVAFKASTQ----------------QQKKNLSRKSKKVKASDD---------------LL 89
Query: 293 SSPKLLNREELISLFKSF-HDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVS 351
SS L + L+ L K++ + I +T+G+VGYPNVGKSS IN+L ++ +V
Sbjct: 90 SSSACLGADALLKLLKNYARNKGIKTS----ITVGVVGYPNVGKSSVINSLKRSRACNVG 145
Query: 352 ATPGKTKHFQTLFVDDELLLCDCPG 376
ATPG TK Q + +D + L D PG
Sbjct: 146 ATPGVTKSMQEVHLDKHVKLLDSPG 170
>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 = 114 bits (287), Expect = 8e-30
Identities = 58/206 (28%), Positives = 84/206 (40%), Gaps = 61/206 (29%)
Query: 173 DVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRCYWTKY-FNSVN 231
DV+V++VDAR+PL R D+E + E +K+ +++LNKADL+ ++ W
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLINE--KNKKLIMVLNKADLVPKEVLRKWVAELSELYG 58
Query: 232 VAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKI 291
F SATN
Sbjct: 59 TKTFFISATNG------------------------------------------------- 69
Query: 292 KSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVS 351
+L + I+ K + +G+VG PNVGKSS INALLN K+ V
Sbjct: 70 ---QGILKLKAEITKQKLKLKYKKG------IRVGVVGLPNVGKSSFINALLNKFKLKVG 120
Query: 352 ATPGKTKHFQTLFVDDELLLCDCPGL 377
+ PG TK Q + +D E+ L D PG+
Sbjct: 121 SIPGTTKLQQDVKLDKEIYLYDTPGI 146
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 93.7 bits (234), Expect = 3e-21
Identities = 72/329 (21%), Positives = 122/329 (37%), Gaps = 82/329 (24%)
Query: 163 RQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRCY 222
R++ ++ DV+++++DAR PL +++ + K +++LNK+DL +
Sbjct: 16 REIKENLKLVDVVIEVLDARIPLSSENPMIDKIIGN----KPRLLILNKSDLADPEVTKK 71
Query: 223 WTKYFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQ 282
W +YF E+ G
Sbjct: 72 WIEYF--------------------------------------------------EEQGI 81
Query: 283 KVLENDLKIKSSPKLLNREELISLFKSFHDVNIPR-MNPD---VMTIGLVGYPNVGKSST 338
K L + K K + + L K ++ + M P M IG+ PNVGKS+
Sbjct: 82 KALAINAKKGQGVKKIL-KAAKKLLKEKNERRKAKGMRPRAIRAMIIGI---PNVGKSTL 137
Query: 339 INALLNAKKVSVSATPGKTKHFQTLFVDDELLLCDCPGLVMPSFVFSKA-------DMIL 391
IN L K PG TK Q + + L L D PG++ P + I
Sbjct: 138 INRLAGKKIAKTGNRPGVTKAQQWIKLGKGLELLDTPGILWPKLEDQEVGLKLALTGAIK 197
Query: 392 NGILPIDQMRDHVPAVNMLCTLVPRHVLENIYGIMITQPDEGEDPNRPPFSEELCNAYGY 451
+ L ++++ + A+ L P L+ Y + P++ EL A
Sbjct: 198 DEALDLEEVA--IFALEYLSKHYP-ERLKERYKLDEL-PEDI---------LELLEAIAR 244
Query: 452 NRGFMTSNGQPDNPRSARYILKDFVNGHL 480
RG + G+ D R++ +L +F NG L
Sbjct: 245 KRGALRKGGEIDYERASELLLNEFRNGKL 273
>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 = 91.0 bits (227), Expect = 2e-20
Identities = 77/320 (24%), Positives = 120/320 (37%), Gaps = 84/320 (26%)
Query: 173 DVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRCYWTKYFNSVNV 232
DV+++++DAR PL R ++ +K +I+LNKADL W KYF
Sbjct: 23 DVVIEVLDARIPLSSRNPMIDEIRG----NKPRLIVLNKADLADPAVTKQWLKYF----- 73
Query: 233 AVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIK 292
E+ G K L + K
Sbjct: 74 ---------------------------------------------EEKGIKALAINAK-- 86
Query: 293 SSPKLLNR--EELISLFKSFHDVNIPR-MNPDVMTIGLVGYPNVGKSSTINALLNAKKVS 349
K + + + L K ++ + + + +VG PNVGKS+ IN L K
Sbjct: 87 -KGKGVKKIIKAAKKLLKEKNEKLKAKGLLNRPIRAMIVGIPNVGKSTLINRLAGKKVAK 145
Query: 350 VSATPGKTKHFQTLFVDDELLLCDCPGLVMPSFVFSKA-------DMILNGILPIDQMRD 402
V PG TK Q + + D L L D PG++ P F + I + L ++ +
Sbjct: 146 VGNRPGVTKGQQWIKLSDGLELLDTPGILWPKFEDQEVGLKLAATGAIKDEALDLEDV-- 203
Query: 403 HVPAVNMLCTLVPRH--VLENIYGIMITQPDEGEDPNRPPFSEELCNAYGYNRGFMTSNG 460
A+ +L L+ + +L+ Y + + ED EL A RG + G
Sbjct: 204 ---ALFLLEYLLEHYPELLKERYKL----DELPEDI------VELLEAIAKKRGCLLKGG 250
Query: 461 QPDNPRSARYILKDFVNGHL 480
+ D R+A +L DF G L
Sbjct: 251 ELDLDRAAEILLNDFRKGKL 270
>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 = 82.2 bits (204), Expect = 2e-18
Identities = 52/204 (25%), Positives = 77/204 (37%), Gaps = 55/204 (26%)
Query: 173 DVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRCYWTKYFNSVNV 232
DV++++ DAR PL R DL+ ++ +K +I+LNKADL + W KYF
Sbjct: 21 DVVIEVRDARIPLSSRNPDLD----KILGNKPRLIVLNKADLADPAKTKKWLKYF----- 71
Query: 233 AVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIK 292
+ G+ VL + K
Sbjct: 72 ---------------------------------------------KSQGEPVLFVNAKNG 86
Query: 293 SSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVSA 352
K L ++ L K + + P + +VG PNVGKS+ IN L K V
Sbjct: 87 KGVKKL-LKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAKVGN 145
Query: 353 TPGKTKHFQTLFVDDELLLCDCPG 376
PG T+ Q + + + L D PG
Sbjct: 146 KPGVTRGQQWIRIGPNIELLDTPG 169
>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 = 76.6 bits (189), Expect = 8e-17
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFVDDE--LLLCDCPGLVMPS 381
+ LVG PNVGKS+ INAL AK VS PG T+ + ++L D PGL+ +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGA 60
Query: 382 FVFSKADMI 390
+
Sbjct: 61 SEGKGVEGF 69
Score = 34.6 bits (80), Expect = 0.029
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 149 GLVIT-PYEKNLDFWRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMI 207
GL+ K ++ + + I +D+I+ +VDA L E++ ++++ ++
Sbjct: 55 GLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPI-IL 113
Query: 208 LLNK 211
+LNK
Sbjct: 114 VLNK 117
>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 = 71.9 bits (177), Expect = 7e-15
Identities = 29/82 (35%), Positives = 53/82 (64%), Gaps = 8/82 (9%)
Query: 164 QLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADL----LTRKQ 219
+L++VI+ SDVI+Q++DAR+P+ RC+ +E+Y+++ PHK + +LNK DL +T++
Sbjct: 1 ELYKVIDSSDVIIQVLDARDPMGTRCKHVEKYLRKEKPHKHLIFVLNKCDLVPTWVTKR- 59
Query: 220 RCYWTKYFNSVNVAVAFFSATN 241
W K + +AF ++
Sbjct: 60 ---WVKVLSKEYPTLAFHASIT 78
Score = 61.9 bits (151), Expect = 2e-11
Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 300 REELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKH 359
+ LI+L + F ++ + +++G +GYPNVGKSS IN L + K V+ PG+TK
Sbjct: 83 KGALINLLRQFAKLHSDK---KQISVGFIGYPNVGKSSVINTLRSKKVCKVAPIPGETKV 139
Query: 360 FQTLFVDDELLLCDCPG 376
+Q + + + L DCPG
Sbjct: 140 WQYITLMKRIYLIDCPG 156
>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 = 65.0 bits (159), Expect = 2e-12
Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 2/79 (2%)
Query: 162 WRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQRC 221
R + R+I+ +DV++++VDAR+P L R LER E+ K+ +I+LNKADL+ R+
Sbjct: 2 KRLVRRIIKEADVVLEVVDARDPELTRSRKLERMALELG--KKLIIVLNKADLVPREVLE 59
Query: 222 YWTKYFNSVNVAVAFFSAT 240
W + F S + V + SA
Sbjct: 60 KWKEVFESEGLPVVYVSAR 78
Score = 55.0 bits (133), Expect = 5e-09
Identities = 26/56 (46%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGK---TKHFQTLFVDDELLLCDCPG 376
+G+VGYP VGKSS INAL S S PG TK Q + +D ++ L D PG
Sbjct: 101 IVGVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
>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 = 63.3 bits (155), Expect = 1e-11
Identities = 25/53 (47%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKHFQTLFVDDELLLCDCPG 376
+ G NVGKSS INAL N KK++ S TPG+T+ V D+ L D PG
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPG 54
>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 = 61.3 bits (150), Expect = 6e-11
Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 319 NPDVMTIGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKHFQTLFVDDELLLCDCPG 376
D I G NVGKSS INAL N KK++ S TPG+T+ V+D L D PG
Sbjct: 15 PDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFEVNDGFRLVDLPG 73
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 59.6 bits (145), Expect = 3e-10
Identities = 29/59 (49%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 319 NPDVMTIGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKHFQTLFVDDELLLCDCPG 376
D+ I G NVGKSS INAL N K ++ S TPG+T+ VDDEL L D PG
Sbjct: 21 EDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPG 79
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 58.2 bits (142), Expect = 9e-10
Identities = 27/56 (48%), Positives = 34/56 (60%), Gaps = 7/56 (12%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKH---FQTLFVDDELLLCDCPG 376
I G NVGKSS INAL N K ++ S TPG+T+ F+ V+D+L L D PG
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQLINFFE---VNDKLRLVDLPG 79
>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 = 52.1 bits (125), Expect = 7e-08
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 14/80 (17%)
Query: 326 GLVGYPNVGKSSTINALLNAKKVSVSATPGKT-----KHFQTLFVDDELLLCDCPGLV-- 378
+VG VGKSS +NALL + VS PG T + +L+L D PGL
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 379 -------MPSFVFSKADMIL 391
+ + AD+IL
Sbjct: 61 GGLGREELARLLLRGADLIL 80
Score = 34.7 bits (80), Expect = 0.057
Identities = 25/132 (18%), Positives = 50/132 (37%), Gaps = 15/132 (11%)
Query: 137 WRRELNLLQEEDGLVI--TP---YEKNLDFWRQLWRVIERSDVIVQIVDARNPLLFRCED 191
L + + LV+ TP L ++ +D+I+ +VD+ + +
Sbjct: 36 DVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEE-DA 94
Query: 192 LERYVKEVSPHKRNMIL-LNKADLLTRKQRCYWT---KYFNSVNVAVAFFSATNIYDDIP 247
++ + +IL NK DLL ++ + + V V SA
Sbjct: 95 KLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKT-----G 149
Query: 248 EGDEELEDEVVS 259
EG +EL ++++
Sbjct: 150 EGVDELFEKLIE 161
>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 = 51.5 bits (124), Expect = 9e-08
Identities = 27/81 (33%), Positives = 35/81 (43%), Gaps = 15/81 (18%)
Query: 326 GLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQ----TLFVDDELLLCDCPGLVMPS 381
+ G PNVGKSS +NALL VS PG T+ L ++L D PGL
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 382 F-----------VFSKADMIL 391
V +AD++L
Sbjct: 61 GLGRERVEEARQVADRADLVL 81
Score = 32.2 bits (74), Expect = 0.41
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQR 220
+V +R+D+++ +VD+ E+ + K +++LNK DL+ +
Sbjct: 71 RQVADRADLVLLVVDSDLT---PVEEEAKLGLLRERGKPVLLVLNKIDLVPESEE 122
>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 = 48.6 bits (117), Expect = 1e-06
Identities = 19/37 (51%), Positives = 25/37 (67%)
Query: 321 DVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT 357
D + I ++G PNVGKSS +NALL ++V VS G T
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTT 37
Score = 28.2 bits (64), Expect = 8.0
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 167 RVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQR 220
+ IER+DV++ ++DA + + + + E K +I++NK DL+ + ++
Sbjct: 80 KAIERADVVLLVLDASEGITEQDLRIAGLILE--EGKALIIVVNKWDLVEKDEK 131
>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 = 49.7 bits (120), Expect = 2e-06
Identities = 50/192 (26%), Positives = 71/192 (36%), Gaps = 63/192 (32%)
Query: 169 IERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILL-NKADLLTRKQRCY--WTK 225
IE +DVI+ +VD R L ED E K + + +IL+ NK D ++
Sbjct: 76 IEEADVILFVVDGREGLT--PEDEE-IAKWLRKSGKPVILVANKIDGKKEDAVAAEFYSL 132
Query: 226 YFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVL 285
F + ++ I D L D ++ E +E EEEEED
Sbjct: 133 GFGEP-IPISAEHGRGIGD--------LLDAILELLPEEEE-------EEEEEDGP---- 172
Query: 286 ENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNA 345
IK I ++G PNVGKS+ +NALL
Sbjct: 173 -----IK--------------------------------IAIIGRPNVGKSTLVNALLGE 195
Query: 346 KKVSVSATPGKT 357
++V VS G T
Sbjct: 196 ERVIVSDIAGTT 207
Score = 40.5 bits (96), Expect = 0.002
Identities = 28/98 (28%), Positives = 39/98 (39%), Gaps = 21/98 (21%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT--KHFQTLFVDD-ELLLCDCPGLVMP 380
+ +VG PNVGKS+ N L + VS TPG T + + E +L D G+
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEED 60
Query: 381 SFVFSK------------ADMIL------NGILPIDQM 400
K AD+IL G+ P D+
Sbjct: 61 DDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEE 98
>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 = 46.1 bits (110), Expect = 1e-05
Identities = 30/96 (31%), Positives = 42/96 (43%), Gaps = 19/96 (19%)
Query: 293 SSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLN-------- 344
S+ K EELI K + DV +VG NVGKS+ INALL
Sbjct: 104 SAKKGWGVEELIEEIKKLA-----KYRGDVY---VVGATNVGKSTLINALLKSNGGKVQA 155
Query: 345 ---AKKVSVSATPGKTKHFQTLFVDDELLLCDCPGL 377
++++VS PG T + + + L D PG+
Sbjct: 156 QALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTPGI 191
Score = 29.2 bits (66), Expect = 4.8
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 160 DFWRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRK 218
DF L ++ + ++V +VD + L + K +++ NK DLL +
Sbjct: 22 DFLEILSTLLNDNALVVHVVDIFDFPGSLIPGLAELIGA----KPVILVGNKIDLLPKD 76
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 47.2 bits (113), Expect = 2e-05
Identities = 52/200 (26%), Positives = 77/200 (38%), Gaps = 64/200 (32%)
Query: 162 WRQLWRVIERSDVIVQIVDARNPLLFRCEDLERYV-KEVSPHKRNMIL-LNKADLLTRKQ 219
Q IE +DVI+ +VD R + + + K + K+ +IL +NK D L ++
Sbjct: 74 REQALIAIEEADVILFVVDGREGIT----PADEEIAKILRRSKKPVILVVNKIDNLKAEE 129
Query: 220 RCY--WTKYFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEE 277
Y ++ F V + SA + G +L D V+ E EEEE
Sbjct: 130 LAYEFYSLGFGEP-VPI---SAEH-----GRGIGDLLDAVL---------ELLPPDEEEE 171
Query: 278 EDDGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSS 337
E++ IK I ++G PNVGKSS
Sbjct: 172 EEEETDP------IK--------------------------------IAIIGRPNVGKSS 193
Query: 338 TINALLNAKKVSVSATPGKT 357
INA+L ++V VS G T
Sbjct: 194 LINAILGEERVIVSDIAGTT 213
Score = 40.6 bits (96), Expect = 0.002
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT 357
+ +VG PNVGKS+ N L + VS TPG T
Sbjct: 5 VVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVT 38
Score = 31.8 bits (73), Expect = 1.1
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 167 RVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNM-ILLNKADLLTRKQ 219
+ IER+DV++ ++DA + E R + R + I++NK DL+ +
Sbjct: 256 KAIERADVVLLVIDATEGI---SEQDLRIAGLIEEAGRGIVIVVNKWDLVEEDE 306
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 46.2 bits (111), Expect = 3e-05
Identities = 51/204 (25%), Positives = 71/204 (34%), Gaps = 88/204 (43%)
Query: 169 IERSDVIVQIVDARNPLLFRCEDLERYV-KEVSPHKRNMILL-NKADLLTRKQRCYWTKY 226
IE +DVI+ +VD R L + + K + + +IL+ NK D + Y
Sbjct: 78 IEEADVILFVVDGRAGLT----PADEEIAKILRKSNKPVILVVNKVDGPDEEADAY---- 129
Query: 227 FNSVNVAVAFF----------SA---TNIYDDIPEGDEELEDEVVSEESESDESEWEDIS 273
F+ SA I D L D ++ E E +E
Sbjct: 130 --------EFYSLGLGEPYPISAEHGRGIGD--------LLDAILEELPEEEE------- 166
Query: 274 EEEEEDDGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNV 333
E+EED+ IK I ++G PNV
Sbjct: 167 -EDEEDEP---------IK--------------------------------IAIIGRPNV 184
Query: 334 GKSSTINALLNAKKVSVSATPGKT 357
GKSS INALL ++V VS G T
Sbjct: 185 GKSSLINALLGEERVIVSDIAGTT 208
Score = 40.8 bits (97), Expect = 0.002
Identities = 28/98 (28%), Positives = 40/98 (40%), Gaps = 21/98 (21%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK--HFQTLFVDD-ELLLCDCPGLVMP 380
+ +VG PNVGKS+ N L + V+ TPG T+ + E +L D G+
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPD 62
Query: 381 SFVFSK------------ADMIL------NGILPIDQM 400
F K AD+IL G+ P D+
Sbjct: 63 DDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEE 100
Score = 30.8 bits (71), Expect = 2.3
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 16/61 (26%)
Query: 167 RVIERSDVIVQIVDARNPLLFRCEDLE----RYVKEVSPHKRN---MILLNKADLLTRKQ 219
+ IER+DV++ ++DA + + + + +I++NK DL+ K
Sbjct: 251 KAIERADVVLLVIDATEGI----TEQDLRIAGLA-----LEAGRALVIVVNKWDLVDEKT 301
Query: 220 R 220
Sbjct: 302 M 302
>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 = 43.6 bits (104), Expect = 5e-05
Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 16/100 (16%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMIL-LNKADLLTRKQRC--- 221
W ++ D+++ +VDA + E E ++ + K +IL LNK DL+ K+
Sbjct: 77 WSALKDVDLVLFVVDASEWI---GEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPL 133
Query: 222 --YWTKYFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVS 259
+ + SA E +EL + +V
Sbjct: 134 LEKLKELHP--FAEIFPISALKG-----ENVDELLEYIVE 166
Score = 43.6 bits (104), Expect = 6e-05
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 19/67 (28%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKH----------FQTLFVDDELLLCD 373
+ ++G PNVGKS+ +NAL+ +K+S VS P T++ Q +FV D
Sbjct: 6 VAIIGRPNVGKSTLLNALVG-QKISIVSPKPQTTRNRIRGIYTDDDAQIIFV-------D 57
Query: 374 CPGLVMP 380
PG+ P
Sbjct: 58 TPGIHKP 64
>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 = 43.6 bits (104), Expect = 6e-05
Identities = 14/25 (56%), Positives = 20/25 (80%), Gaps = 1/25 (4%)
Query: 325 IGLVGYPNVGKSSTINALLNAK-KV 348
+GLVG PN GKS+ ++A+ NAK K+
Sbjct: 3 VGLVGLPNAGKSTLLSAISNAKPKI 27
Score = 32.4 bits (75), Expect = 0.37
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 13/56 (23%)
Query: 169 IERSDVIVQIVDA---RNPLLFRCEDLERYVKEVSPHKRNM------ILLNKADLL 215
IER+ V++ ++D +P+ ED E E+ + + ++LNK DLL
Sbjct: 76 IERTRVLLHVIDLSGEDDPV----EDYETIRNELEAYNPGLAEKPRIVVLNKIDLL 127
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 45.1 bits (108), Expect = 8e-05
Identities = 27/87 (31%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 271 DISEEEEEDDGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGY 330
D EE+ E + + L+ +L EL +L S I R + + + + G
Sbjct: 174 DFPEEDIEFLSDEKILEKLE-----EL--IAELEALLASARQGEILR---EGLKVVIAGR 223
Query: 331 PNVGKSSTINALLNAKKVSVSATPGKT 357
PNVGKSS +NALL ++ V+ G T
Sbjct: 224 PNVGKSSLLNALLGEERAIVTDIAGTT 250
Score = 34.3 bits (80), Expect = 0.17
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLT 216
IE +D+++ ++DA PL ED E E K +++LNKADL
Sbjct: 289 REAIEEADLVLLVLDASEPLT--EEDDEIL--EELKDKPVIVVLNKADLTG 335
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 44.5 bits (106), Expect = 1e-04
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 10/87 (11%)
Query: 271 DISEEEEEDDGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGY 330
D EE+ E+ + + L+ EL L + I R + + + ++G
Sbjct: 176 DFPEEDIEELVLEKIREKLE-------ELIAELDELLATAKQGKILR---EGLKVVIIGR 225
Query: 331 PNVGKSSTINALLNAKKVSVSATPGKT 357
PNVGKSS +NALL + V+ G T
Sbjct: 226 PNVGKSSLLNALLGRDRAIVTDIAGTT 252
Score = 29.1 bits (66), Expect = 7.6
Identities = 20/54 (37%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMIL-LNKADLLTRK 218
+ IE +D+++ ++DA PL EDL E+ P K+ +I+ LNKADL+++
Sbjct: 291 KKAIEEADLVLFVLDASQPLD--KEDLALI--ELLPKKKPIIVVLNKADLVSKI 340
>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 = 44.4 bits (105), Expect = 1e-04
Identities = 30/85 (35%), Positives = 38/85 (44%), Gaps = 15/85 (17%)
Query: 276 EEEDDGQKVLENDLK--IKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNV 333
EE+DD Q L L I +LN +L L F + +VG PNV
Sbjct: 168 EEDDDEQDSLNQLLLSIIAELKDILNSYKLEKLDDGF-------------KLAIVGSPNV 214
Query: 334 GKSSTINALLNAKKVSVSATPGKTK 358
GKSS +NALL + VS G T+
Sbjct: 215 GKSSLLNALLKQDRAIVSDIKGTTR 239
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 42.8 bits (102), Expect = 3e-04
Identities = 15/26 (57%), Positives = 20/26 (76%), Gaps = 3/26 (11%)
Query: 321 DVMTIGLVGYPNVGKSSTINALLNAK 346
DV GLVG+PNVGKS+ ++ + NAK
Sbjct: 160 DV---GLVGFPNVGKSTLLSVVSNAK 182
Score = 34.3 bits (80), Expect = 0.17
Identities = 37/144 (25%), Positives = 59/144 (40%), Gaps = 32/144 (22%)
Query: 167 RVIERSDVIVQIVDA-----RNPLLFRCEDLERYVKEVSPH-----KRNMIL-LNKADLL 215
R IER+ VIV ++D R+P+ ED E+ KE+ + +R I+ NK DL
Sbjct: 232 RHIERTRVIVHVIDMSGSEGRDPI----EDYEKINKELKLYNPRLLERPQIVVANKMDLP 287
Query: 216 TRKQRCYWTKYFNSVNVAVAFFSA-------------TNIYDDIPEGDEELEDEVVSEES 262
++ ++ + V SA + ++ PE LE+E V EE
Sbjct: 288 EAEEN--LEEFKEKLGPKVFPISALTGQGLDELLYAVAELLEETPE--FPLEEEEVEEEV 343
Query: 263 ESDESEWEDISEEEEEDDGQKVLE 286
E E ++DG V+
Sbjct: 344 YYKFEEEEKDFTITRDEDGVFVVS 367
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 42.6 bits (101), Expect = 4e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKH-FQTLFVDDE--LLLCDCPGLVMP 380
+ ++G PNVGKS+ +NAL+ K VS P T++ + + D ++ D PG+ P
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIHKP 67
>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 = 42.4 bits (101), Expect = 4e-04
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 17/64 (26%)
Query: 325 IGLVGYPNVGKSSTINALLNAK-KVSVSATPGKTKHFQTLF-------VDD--ELLLCDC 374
+GLVG PN GKS+ I+A+ AK K++ F TL VDD ++ D
Sbjct: 160 VGLVGLPNAGKSTLISAVSAAKPKIA-------DYPFTTLVPNLGVVRVDDGRSFVIADI 212
Query: 375 PGLV 378
PGL+
Sbjct: 213 PGLI 216
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 42.5 bits (101), Expect = 4e-04
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 17/63 (26%)
Query: 325 IGLVGYPNVGKSSTINALLNAK-KVSVSATPGKTKHFQTL---------FVDDELLLCDC 374
+GLVG PN GKS+ ++A+ AK K++ F TL + ++ D
Sbjct: 162 VGLVGLPNAGKSTLLSAVSAAKPKIA-------DYPFTTLVPNLGVVRVDGGESFVVADI 214
Query: 375 PGL 377
PGL
Sbjct: 215 PGL 217
>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 = 41.3 bits (98), Expect = 4e-04
Identities = 23/56 (41%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT---KHFQTLFVDDELLLCDCPG 376
TI LVG PNVGK++ NAL A + V PG T K + E+ + D PG
Sbjct: 2 TIALVGNPNVGKTTLFNALTGA-RQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPG 56
Score = 29.4 bits (67), Expect = 4.0
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 170 ERSDVIVQIVDARNP---LLFRCEDLERYVKEVSPHKRNMIL-LNKADLLTRK 218
E+ DVI+ +VDA N L + LE +++ LN D +K
Sbjct: 77 EKPDVIINVVDATNLERNLYLTLQLLEL--------GIPVVVALNMMDEAEKK 121
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 42.1 bits (99), Expect = 5e-04
Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 280 DGQKVLENDLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVGYPNVGKSSTI 339
+ L N LK L E ++ + +N + L+G GKSS I
Sbjct: 2 NNSDSLNNVLKGLLGLPSLLSERILEQLRMLQLTEKEPVN-----VLLMGATGAGKSSLI 56
Query: 340 NALL--NAKKVS-VSATPGKTKHFQTLFVDDELLLCDCPGL 377
NAL K+VS V T + + + L+L D PGL
Sbjct: 57 NALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97
>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 = 39.8 bits (94), Expect = 0.001
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT 357
+ + + G PNVGKSS +NAL + VS G T
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTT 38
Score = 35.2 bits (82), Expect = 0.041
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQR 220
IE +D+++ +VDA L EDLE E+ K +++LNK+DLL+ +
Sbjct: 77 REAIEEADLVLLVVDASEGLD--EEDLEIL--ELPAKKPVIVVLNKSDLLSDAEG 127
>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 = 39.5 bits (93), Expect = 0.001
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK-----HFQTLFVDDELLLCDCPGL 377
T+ + GYPNVGKSS +N L A K V+ P TK HF ++ +++ D PG+
Sbjct: 2 TLVIAGYPNVGKSSLVNKLTRA-KPEVAPYPFTTKSLFVGHFDYKYLRWQVI--DTPGI 57
>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 = 40.4 bits (95), Expect = 0.001
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKH-FQTLFVDDE--LLLCDCPGL 377
+ ++G PNVGKS+ +N L K S T++ + ++ D PG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGF 58
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 41.5 bits (98), Expect = 0.001
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKT---KHFQTLFVDDELLLCDCPG 376
T+ LVG PNVGK++ NAL A V PG T K + + E+ + D PG
Sbjct: 5 TVALVGNPNVGKTTLFNALTGA-NQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPG 59
Score = 30.3 bits (69), Expect = 3.3
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 18/56 (32%)
Query: 170 ERSDVIVQIVDARNPLLFRCEDLERYV------KEVSPHKRNMIL-LNKADLLTRK 218
+ D+IV +VDA N LER + E+ MIL LN D ++
Sbjct: 80 GKPDLIVNVVDATN--------LERNLYLTLQLLEL---GIPMILALNMIDEAKKR 124
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 40.7 bits (96), Expect = 0.001
Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 8/69 (11%)
Query: 314 NIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK-----HFQTLFVDDE 368
+P ++PD+ TI + GYPNVGKSS + L A K V+ P TK HF+
Sbjct: 160 KLPAIDPDLPTIVVAGYPNVGKSSLVRKLTTA-KPEVAPYPFTTKGIHVGHFE--RGYLR 216
Query: 369 LLLCDCPGL 377
+ + D PGL
Sbjct: 217 IQVIDTPGL 225
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 40.8 bits (97), Expect = 0.001
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 12/53 (22%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVS-VSATPGKTKH----------FQTLFVD 366
+ +VG PNVGKS+ +NAL+ K+S VS P T+H Q +FVD
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRHRIRGIVTEDDAQIIFVD 59
Score = 33.1 bits (77), Expect = 0.39
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNMIL-LNKADLLTRKQR 220
W ++ D+++ +VDA + E ++++ K +IL LNK DL+ K+
Sbjct: 79 WSSLKDVDLVLFVVDADEKI---GPGDEFILEKLKKVKTPVILVLNKIDLVKDKEE 131
>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 = 39.7 bits (94), Expect = 0.002
Identities = 15/29 (51%), Positives = 17/29 (58%)
Query: 317 RMNPDVMTIGLVGYPNVGKSSTINALLNA 345
R V T+ LVGY N GKS+ NAL A
Sbjct: 36 RKRSGVPTVALVGYTNAGKSTLFNALTGA 64
Score = 28.6 bits (65), Expect = 7.5
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 10/88 (11%)
Query: 172 SDVIVQIVDARNPL-LFRCEDLERYVKEVSPHKRNMIL-LNKADLLTRKQRCYWTKYFNS 229
+D+++ +VDA +P + E +E +KE+ +IL LNK DLL ++ + +
Sbjct: 121 ADLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLLDDEEL---EERLRA 177
Query: 230 VNVAVAFFSATNIYDDIPEGDEELEDEV 257
F SA EG + L++ +
Sbjct: 178 GRPDAVFISAKT-----GEGLDLLKEAI 200
>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 = 40.6 bits (96), Expect = 0.002
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKKVS-VSATPGKT 357
IG+ G N GKSS INAL + ++ VS PG T
Sbjct: 8 HIGIFGRRNAGKSSLINALTG-QDIAIVSDVPGTT 41
Score = 29.0 bits (66), Expect = 6.9
Identities = 22/110 (20%), Positives = 47/110 (42%), Gaps = 19/110 (17%)
Query: 167 RVIERSDVIVQIVDARNPLLFRCEDLERYVKEVSPHKRNM---ILLNKADLLTRKQRCYW 223
V++++D+ + +VDA E ++E+ +R + +++NK DL
Sbjct: 81 EVLDKTDLALLVVDAGVGPG---EYELELIEELK--ERKIPYIVVINKIDLGEESAE--L 133
Query: 224 TKYFNSVNVAVAFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDIS 273
K + F SA EG +EL++ ++ E ++E+ +
Sbjct: 134 EKLEKKFGLPPIFVSALTG-----EGIDELKEAIIELLPE----DFEEPT 174
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 40.3 bits (95), Expect = 0.002
Identities = 13/18 (72%), Positives = 16/18 (88%)
Query: 325 IGLVGYPNVGKSSTINAL 342
+G+VG PNVGKS+T NAL
Sbjct: 24 MGIVGLPNVGKSTTFNAL 41
>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 = 38.9 bits (91), Expect = 0.002
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFV 365
+ I +VG PNVGKS+ +N LL K PG T+++ T +
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVI 44
>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 = 38.2 bits (90), Expect = 0.003
Identities = 29/95 (30%), Positives = 39/95 (41%), Gaps = 21/95 (22%)
Query: 327 LVGYPNVGKSSTINALLNAKKVSVSATPGKT--KHFQTLFVDD-ELLLCDCPGLVMPSFV 383
+VG PNVGKS+ N L + VS TPG T + + E +L D G+
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPDDEG 61
Query: 384 FSK------------ADMIL------NGILPIDQM 400
SK AD+IL G+ P D+
Sbjct: 62 ISKEIREQAEIAIEEADVILFVVDGREGLTPADEE 96
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 39.7 bits (94), Expect = 0.003
Identities = 14/26 (53%), Positives = 20/26 (76%), Gaps = 1/26 (3%)
Query: 325 IGLVGYPNVGKSSTINALLNAK-KVS 349
+GLVG PN GKS+ I+A+ AK K++
Sbjct: 161 VGLVGLPNAGKSTLISAVSAAKPKIA 186
>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 = 39.8 bits (94), Expect = 0.003
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 321 DVMTIGLVGYPNVGKSSTINALLNA 345
DV T+ LVGY N GKS+ NAL A
Sbjct: 188 DVPTVALVGYTNAGKSTLFNALTGA 212
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 39.7 bits (94), Expect = 0.003
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAK 346
+ G+VG PNVGKS+ NAL A
Sbjct: 3 LKCGIVGLPNVGKSTLFNALTKAG 26
>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 = 39.9 bits (93), Expect = 0.004
Identities = 17/43 (39%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 244 DDIPEGDEELEDEVVSEESESD-ESEWEDISEEEEEDDGQKVL 285
DD+ E D++ ++ E+SES+ ES+ ED E+E+EDD +
Sbjct: 653 DDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANE 695
Score = 33.3 bits (76), Expect = 0.42
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQ 282
EG+EE ED++ + + DE E + SE E E DG+
Sbjct: 646 EGEEEDEDDLEETDDDEDECEAIEDSESESESDGE 680
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 39.2 bits (92), Expect = 0.006
Identities = 24/109 (22%), Positives = 43/109 (39%), Gaps = 35/109 (32%)
Query: 250 DEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLNREELISLFKS 309
++ E E+ ++ + +DES+WE E+ E +
Sbjct: 1 YDDDEAEMRADGTWADESDWELDDEDLAELEAA--------------------------- 33
Query: 310 FHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK 358
+P + +VG PNVGKS+ +N +L ++ V PG T+
Sbjct: 34 -EGGPLP-------VVAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTR 74
Score = 37.3 bits (87), Expect = 0.024
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFVD--DEL 369
+ LVG PNVGKSS +N L ++ V G T VD D L
Sbjct: 214 VALVGKPNVGKSSLLNKLAGEERSVVDDVAGTT-------VDPVDSL 253
>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 = 38.3 bits (90), Expect = 0.006
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 324 TIGLVGYPNVGKSSTINALLNAK 346
+ LVG+P+VGKS+ ++ L N K
Sbjct: 2 RVALVGFPSVGKSTLLSKLTNTK 24
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 38.7 bits (91), Expect = 0.006
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 323 MTIGLVGYPNVGKSSTINALLNA 345
+ IG+VG PNVGKS+ NAL A
Sbjct: 3 LKIGIVGLPNVGKSTLFNALTKA 25
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 38.8 bits (91), Expect = 0.007
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 324 TIGLVGYPNVGKSSTINALLNAK 346
T+ LVG+P+VGKS+ +N L N K
Sbjct: 65 TVALVGFPSVGKSTLLNKLTNTK 87
>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 = 38.8 bits (91), Expect = 0.007
Identities = 22/56 (39%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 328 VGYPNVGKSSTINALLN-----AKKVSVSATPGKTKHFQTLFVDDELLLCDCPGLV 378
VG NVGKSS IN LL ++ S PG T + +DD L D PG++
Sbjct: 160 VGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGII 215
>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 = 37.4 bits (87), Expect = 0.008
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 326 GLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFVDD----ELLLCDCPGLV 378
GLVG PNVGKS+ ++AL +A KV +++ P T + ++ + D PGL+
Sbjct: 1 GLVGLPNVGKSTLLSALTSA-KVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLL 56
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 38.2 bits (89), Expect = 0.014
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 322 VMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK 358
V + +VG PNVGKS+ +N +L ++ V TPG T+
Sbjct: 275 VGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTR 311
Score = 35.2 bits (81), Expect = 0.12
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK 358
+ LVG PNVGKSS +N L + ++ V+ G T+
Sbjct: 453 VALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTR 486
>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 = 0.015
Identities = 29/75 (38%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTL--FVDD-ELLLCDCPGLVM 379
+TI ++G VGKSSTIN++ +KVSVSA +T + + VD +L + D PGL+
Sbjct: 32 LTILVLGKTGVGKSSTINSIFGERKVSVSAFQSETLRPREVSRTVDGFKLNIIDTPGLL- 90
Query: 380 PSFVFSKADMILNGI 394
S IL+ I
Sbjct: 91 ESQDQRVNRKILSII 105
>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 = 36.3 bits (85), Expect = 0.017
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 327 LVGYPNVGKSSTINALLNAKKVSVSATPGKT 357
LVG PNVGK++ NAL A + V PG T
Sbjct: 2 LVGNPNVGKTTLFNALTGA-RQKVGNWPGVT 31
Score = 28.2 bits (64), Expect = 7.3
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 18/56 (32%)
Query: 170 ERSDVIVQIVDARNPLLFRCEDLER--Y----VKEVSPHKRNMIL-LNKADLLTRK 218
E D+IV +VDA N LER Y + E+ +++ LN D ++
Sbjct: 74 EEPDLIVNVVDATN--------LERNLYLTLQLLEL---GLPVVVALNMIDEAEKR 118
>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 = 37.2 bits (87), Expect = 0.021
Identities = 16/30 (53%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 325 IGLVGYPNVGKSSTINALLNAKKVSVSATP 354
IGLVG PNVGKS+ NA A V ++ P
Sbjct: 1 IGLVGKPNVGKSTFFNAATLA-DVEIANYP 29
>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 = 36.7 bits (86), Expect = 0.021
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 325 IGLVGYPNVGKSSTINALLNAK 346
IG+VG PNVGKS+ NAL +
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSN 22
>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 = 36.0 bits (84), Expect = 0.025
Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 166 WRVIERSDVIVQIVDARNPLLFRCEDLERYVKEVS-PHKRNM-ILLNKADLLTRKQRCYW 223
+ R+D ++ ++ A P + E ++KE+ + + +LNK DLL+ ++
Sbjct: 68 ESFLPRADAVIFVLSADQP--LTESERE-FLKEILKWSGKKIFFVLNKIDLLSEEELEEV 124
Query: 224 TKYFNSVNV 232
+Y
Sbjct: 125 LEYSREELG 133
Score = 32.1 bits (74), Expect = 0.43
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSATP 354
+ +VG + GKS+ +NALL + + TP
Sbjct: 1 FLLAVVGEFSAGKSTLLNALLGEEVLPTGVTP 32
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 36.8 bits (86), Expect = 0.032
Identities = 14/22 (63%), Positives = 18/22 (81%)
Query: 325 IGLVGYPNVGKSSTINALLNAK 346
+GLVG+P+ GKSS I+AL AK
Sbjct: 162 VGLVGFPSAGKSSLISALSAAK 183
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 36.3 bits (85), Expect = 0.034
Identities = 14/19 (73%), Positives = 16/19 (84%)
Query: 323 MTIGLVGYPNVGKSSTINA 341
+TIGLVG PNVGKS+ NA
Sbjct: 2 ITIGLVGKPNVGKSTFFNA 20
>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 = 36.1 bits (84), Expect = 0.055
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 12/80 (15%)
Query: 244 DDIPEGDEELED---EVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLL-- 298
+D + D++LE+ +V + E DE + + E++EE++ ++ + K S +
Sbjct: 333 EDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSELP 392
Query: 299 -------NREELISLFKSFH 311
+ EE + L K
Sbjct: 393 FTFPCPKSHEEFLELLKGVS 412
Score = 33.8 bits (78), Expect = 0.28
Identities = 11/51 (21%), Positives = 26/51 (50%)
Query: 238 SATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEND 288
++ +G ++ ++E ++ E +E + + EEE+E+D E+D
Sbjct: 318 QGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDD 368
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 36.1 bits (83), Expect = 0.057
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 4/77 (5%)
Query: 232 VAVAFFSATNIYDDIPEGDEELEDEVVSEES--ESDESEWEDISEEEEEDDGQKVLENDL 289
V F DD E E++ V E + + D+ + S EE
Sbjct: 274 VVTRTFPERTSDDDEDA--IETEEDDVDESAIEDDDDDSDWEDSVEESGRSSVDEKTMFQ 331
Query: 290 KIKSSPKLLNREELISL 306
++ S P L +R L++L
Sbjct: 332 RVDSKPNLTSRRSLLTL 348
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 35.1 bits (81), Expect = 0.067
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 245 DIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSP 295
D+ E DEE ED+VV E+ E + ED +E EE++ + + ++K+SP
Sbjct: 33 DLTE-DEEAEDDVVDEDEEDEAVVEEDENELTEEEE-----DEEGEVKASP 77
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 35.8 bits (83), Expect = 0.070
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 12/61 (19%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKK-------VSVSATPGKTKHFQTLFVDDELLLCDCP 375
+TIGL+G PN GK++ N L A++ V+V K F T D ++ L D P
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVER---KEGQFST--TDHQVTLVDLP 58
Query: 376 G 376
G
Sbjct: 59 G 59
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 35.3 bits (82), Expect = 0.074
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 321 DVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLF 364
+ + LVGY N GKS+ NAL A + F TL
Sbjct: 191 GIPLVALVGYTNAGKSTLFNALTGAD------VYVADQLFATLD 228
Score = 29.9 bits (68), Expect = 3.8
Identities = 32/145 (22%), Positives = 54/145 (37%), Gaps = 23/145 (15%)
Query: 172 SDVIVQIVDARNPLLFR-CEDLERYVKEVSPHKRNMIL-LNKADLLT--RKQRCYWTKYF 227
+D+++ +VDA +P + E +E + E+ + +IL LNK DLL
Sbjct: 272 ADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELERGSP 331
Query: 228 NSVNVAVAFFSATN----------IYDDIPEGDEELEDEVVSEESESDESEWEDISEEEE 277
N V F SA I + + E + S D E
Sbjct: 332 NPV-----FISAKTGEGLDLLRERIIELLSGLRTE-VTLELPYTDAGRLSWLHDNGIVLE 385
Query: 278 EDDGQKVLENDLKIKSSPKLLNREE 302
E+ G+ V +K ++ +L R +
Sbjct: 386 EEYGEDV---RIKAEAPERLAKRLQ 407
>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 = 35.5 bits (82), Expect = 0.080
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 329 GYPNVGKSSTINALLNAKKVSVSATPGKT---KHFQTLFVDDELLLCDCPG 376
G PNVGKS+ NAL A +V PG T K + F +++ + D PG
Sbjct: 1 GNPNVGKSTLFNALTGA-NQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPG 50
>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 = 35.0 bits (81), Expect = 0.086
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 250 DEELEDEVVSEESESDESEWEDISEEEEEDD 280
DEE E EV +E DE EW D+ ++E +
Sbjct: 99 DEEEEWEVEEDEDSDDEGEWIDVESDKEIES 129
Score = 34.2 bits (79), Expect = 0.14
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 13/75 (17%)
Query: 233 AVAFFSATNIYDDIP------------EGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
+ + D IP +E E + S++ + +E EWE +E+ +D+
Sbjct: 56 EKKGYGEEEVVDGIPGLELLEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDE 115
Query: 281 GQKV-LENDLKIKSS 294
G+ + +E+D +I+SS
Sbjct: 116 GEWIDVESDKEIESS 130
Score = 28.5 bits (64), Expect = 9.7
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSS 294
+ D+E E V + E + S+ ED EEE+++ +K E+ + S
Sbjct: 111 DSDDEGEWIDVESDKEIESSDSED--EEEKDEAAKKAKEDSDEELSE 155
>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 = 34.3 bits (79), Expect = 0.11
Identities = 21/61 (34%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 328 VGYPNVGKSSTINAL---LNAKKVSVSATPGKTKHFQT---LFVDDELLLCDCPGLVMPS 381
G VGKSS INAL + + +S+ G KH T LF L+ D PG
Sbjct: 126 AGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGGLIADTPGFNEFG 185
Query: 382 F 382
Sbjct: 186 L 186
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.8 bits (81), Expect = 0.12
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 325 IGLVGYPNVGKSSTINALLNAK-KV 348
+GL+G PN GKS+ I A+ AK KV
Sbjct: 162 VGLLGLPNAGKSTFIRAVSAAKPKV 186
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 34.6 bits (80), Expect = 0.15
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 243 YDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLNRE 301
D + D++ E + EES E + +D +++++D + + + RE
Sbjct: 121 RDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATR------ERSLERRRRRRE 173
>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 = 0.15
Identities = 13/46 (28%), Positives = 32/46 (69%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDL 289
+DI + +E+++DE ++ E +E + E+I E E+ +D ++++E++
Sbjct: 34 EDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEE 79
Score = 32.9 bits (75), Expect = 0.20
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLN 299
+D E +EE E+E+ E DE E + EEEEED+ V D++ K+ + N
Sbjct: 49 EDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFN 104
>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 = 34.5 bits (79), Expect = 0.16
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTL--FVDD-ELLLCDCPGLVM 379
+ I ++G VGKS+TIN++ K S A T Q + V ++ + D PGL
Sbjct: 119 LNILVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVKIRVIDTPGLKS 178
Query: 380 PSFVFSKADMILNGI 394
+ SK + IL+ +
Sbjct: 179 SASDQSKNEKILSSV 193
>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 = 34.5 bits (79), Expect = 0.17
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 247 PEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLK 290
E +EE E+E EE ES+E E ED EEEE + E +++
Sbjct: 445 VEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGS-EEEME 487
Score = 29.5 bits (66), Expect = 6.4
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 249 GDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEN 287
E E+E V EE E +E E E+ E EEE+ + E
Sbjct: 436 SQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEE 474
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 34.3 bits (78), Expect = 0.18
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 319 NPDVMTIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTKHFQTLFV---DDELLLCDCP 375
N +++ ++G PN GKS+ +N ++ K V+ T+ T + D +++L D P
Sbjct: 49 NQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTP 108
Query: 376 GLVMPSFVFSKA 387
G+ P KA
Sbjct: 109 GIFEPKGSLEKA 120
>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 = 33.2 bits (76), Expect = 0.25
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 250 DEELEDEVVSEESESDESEWEDISEEEEEDDG 281
D + EDE EE E +E E ED +++++DD
Sbjct: 167 DVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDD 198
Score = 30.9 bits (70), Expect = 1.7
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 244 DDIPEGDEELEDEVVS----EESESDESEWEDISEEEEEDD 280
+DI E LE ++ + E DE + E+ EEEEED+
Sbjct: 147 EDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDE 187
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 33.0 bits (76), Expect = 0.25
Identities = 23/61 (37%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 320 PDVM-TIGLVGYPNVGKSSTINALLNAKKVSVSATPGKTK---HFQTLFVDDELLLCDCP 375
PD I VG NVGKS+ + L KKV V PG T+ H+ + +L D P
Sbjct: 6 PDRKPEIVFVGRSNVGKSTLVRE-LTGKKVRVGKRPGVTRKPNHYDW----GDFILTDLP 60
Query: 376 G 376
G
Sbjct: 61 G 61
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 33.6 bits (78), Expect = 0.26
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 327 LVGYPNVGKSSTINAL---LNAKKVSVSATPGKTKH---FQTLF-VDDELLLCDCPGL 377
L G VGKS+ +NAL L K +S G+ KH L+ + LL D PG
Sbjct: 169 LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTHVELYDLPGGGLLIDTPGF 226
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 33.5 bits (77), Expect = 0.29
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 317 RMNPDVMTIGLVGYPNVGKSSTINALLNA 345
R+ DV T+ LVGY N GKS+ N + A
Sbjct: 192 RIKADVPTVSLVGYTNAGKSTLFNRITEA 220
>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 = 30.3 bits (69), Expect = 0.53
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 250 DEELEDEVVSEESESDESEWEDISEEEEEDD 280
D E E+E E+ ES++ E E+ ++++ D
Sbjct: 45 DAEWEEEEEGEDLESEDEEDEEEDDDDDMDG 75
Score = 26.8 bits (60), Expect = 7.4
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 243 YDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDG 281
YD E +EE E E + E E DE E +++++ DG
Sbjct: 42 YDSDAEWEEEEEGEDLESEDEEDEEE-----DDDDDMDG 75
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 31.6 bits (72), Expect = 0.54
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLK--------IKSSPKL 297
+ +EE E+E E + D E + S+E+++ + K K S PKL
Sbjct: 96 DEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPSKPKL 153
>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 = 30.5 bits (68), Expect = 0.65
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
EG+E+ + + EE + DE E +D +++E+DD
Sbjct: 7 EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDD 39
Score = 28.2 bits (62), Expect = 3.7
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 260 EESESDESEWEDISEEEEEDDGQKVLEND 288
E+S+SD E ED +E+EEDD + E+D
Sbjct: 10 EDSDSDSDEEEDDDDEDEEDDDEDDDEDD 38
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 32.3 bits (74), Expect = 0.72
Identities = 27/102 (26%), Positives = 41/102 (40%), Gaps = 22/102 (21%)
Query: 168 VIERSDV--IVQ---IVDARNPLLFRCEDLERY-----VKEVSPHKRNMILLNKADLLTR 217
V+ R V Q +V +P F L+RY + P +I+LNK DLL
Sbjct: 71 VLIRPPVANNDQAIIVVSLVDPD-FNTNLLDRYLVLAEAGGIEP----VIVLNKIDLLDD 125
Query: 218 KQRCYWTK--YFNSVNVAVAFFSATNIYDDIPEGDEELEDEV 257
++ + + V F SA N +G EEL + +
Sbjct: 126 EEAAVKELLREYEDIGYPVLFVSAKN-----GDGLEELAELL 162
Score = 31.5 bits (72), Expect = 1.3
Identities = 30/114 (26%), Positives = 42/114 (36%), Gaps = 23/114 (20%)
Query: 273 SEEEEEDDGQKVLEN---DLKIKSSPKLLNREELISLFKSFHDVNIPRMNPDVMTIGLVG 329
EE + + E+ + S+ EEL L L+G
Sbjct: 125 DEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELLAGK-------------ITVLLG 171
Query: 330 YPNVGKSSTINALL---NAKKVSVSATPGKTKHFQT---LF-VDDELLLCDCPG 376
VGKS+ INALL N K +S G+ +H T LF + + D PG
Sbjct: 172 QSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDTPG 225
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 32.4 bits (74), Expect = 0.73
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 14/80 (17%)
Query: 245 DIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDG----QKVLE--------NDLKI- 291
++P+ +EE E E EE E + E++ EEEE+++ +KV E N K
Sbjct: 34 EVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPI 93
Query: 292 -KSSPKLLNREELISLFKSF 310
+PK + +EE + +KS
Sbjct: 94 WTRNPKDVTKEEYAAFYKSL 113
>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2. This
domain family is found in eukaryotes, and is typically
between 138 and 153 amino acids in length. The family is
found in association with pfam00493. Mini-chromosome
maintenance (MCM) proteins are essential for DNA
replication. These proteins use ATPase activity to
perform this function.
Length = 145
Score = 31.1 bits (71), Expect = 0.79
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 244 DDIPEGDEELEDEV-VSEESESDESEWEDISEEEEEDDGQKVLEND 288
+D P+ +EELED++ +E +E + ED+ + E D + E D
Sbjct: 1 EDEPDEEEELEDDIDDLDEEAEEEEDGEDLFGDNMERDYRANPELD 46
>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 = 30.8 bits (70), Expect = 0.91
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
E +++ ED + + ++ EWE E D
Sbjct: 81 EENDDEEDAETEDTEDVEDDEWEGFPEPTVTDY 113
>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 = 31.4 bits (72), Expect = 0.98
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 250 DEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKI 291
+ ESE DE + ED +++E++D E DL
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGP 75
Score = 31.0 bits (71), Expect = 1.2
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
D + SE E D + +D E+E+EDD
Sbjct: 31 DPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDD 67
Score = 29.5 bits (67), Expect = 4.3
Identities = 6/43 (13%), Positives = 19/43 (44%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLE 286
E E+++ ++ + ++ + +D E + D ++ E
Sbjct: 40 TAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEEARE 82
>gnl|CDD|220605 pfam10156, Med17, Subunit 17 of Mediator complex. This Mediator
complex subunit was formerly known as Srb4 in yeasts or
Trap80 in Drosophila and human. The Med17 subunit is
located within the head domain and is essential for cell
viability to the extent that a mutant strain of
cerevisiae lacking it shows all RNA polymerase
II-dependent transcription ceasing at non-permissive
temperatures.
Length = 454
Score = 31.9 bits (73), Expect = 1.0
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 245 DIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLNREELI 304
D+ E E L +E+ E ++ D SE D E++EEDD EN ++ PK R+E++
Sbjct: 48 DLTE--ESLREEIAKEAAKIDFSEESDEEEDDEEDDNDDSEENKDTVEEFPKA--RDEVL 103
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 31.7 bits (72), Expect = 1.2
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 243 YDDIPEGDEE----LEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDL 289
DD P+ +E+ E+ S+ESE DE+E D EE E D + E+
Sbjct: 237 DDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSE 287
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 30.6 bits (70), Expect = 1.2
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 327 LVGYPNVGKSSTINAL---LNAKKVSVSATPGKTKH---FQTLF-VDDELLLCDCPG 376
L G VGKS+ +NAL L+ + +S G+ +H LF + LL D PG
Sbjct: 40 LAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLIDTPG 96
>gnl|CDD|221323 pfam11931, DUF3449, Domain of unknown function (DUF3449). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 181 to 207 amino acids in length. This domain
has two conserved sequence motifs: PIP and CEICG. The
domain carries a zinc-finger domain of the C2H2-type.
Length = 187
Score = 31.1 bits (71), Expect = 1.2
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 254 EDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLK 290
E+E + ES E ED S+++ +DD ++ + N L
Sbjct: 33 EEERQASADESSEDASEDGSDDDSDDDEEEPIYNPLN 69
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 31.5 bits (72), Expect = 1.2
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 15/69 (21%)
Query: 333 VGKSSTINALLNAKKVSVSATPGK-------TKHFQTLFVDDEL----LLCDCPGLVMPS 381
VGKSS IN L+ ++ V GK T+H + LF EL LL D PG P
Sbjct: 183 VGKSSLINRLIPDVELRVGKVSGKLGRGRHTTRHVE-LF---ELPNGGLLADTPGFNQPD 238
Query: 382 FVFSKADMI 390
S ++
Sbjct: 239 LDCSPRELA 247
>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta;
Reviewed.
Length = 129
Score = 30.0 bits (68), Expect = 1.3
Identities = 9/33 (27%), Positives = 23/33 (69%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
+GD+++ D+ + + + DE + ++ +E+EED+
Sbjct: 96 DGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDE 128
Score = 30.0 bits (68), Expect = 1.6
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 247 PEGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
+ + +D + + D+ + ED+ EE++ED+
Sbjct: 92 KKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDE 125
Score = 28.8 bits (65), Expect = 4.1
Identities = 7/33 (21%), Positives = 21/33 (63%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
D+ ++D+++ ++ +E E+ E+EE+++
Sbjct: 97 GDDDIIDDDILPDDDFDEEDLDEEDDEDEEDEE 129
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems.
Length = 148
Score = 30.4 bits (69), Expect = 1.3
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 5/33 (15%)
Query: 325 IGLVGYPNVGKSSTINALLNA-----KKVSVSA 352
IG+ G P GKS+ I+AL+ A K+V+V A
Sbjct: 2 IGITGVPGAGKSTLIDALITALRARGKRVAVLA 34
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.5 bits (71), Expect = 1.5
Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 249 GDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVL 285
GD E E+E EE E +E E E+ EEEEE++ ++ L
Sbjct: 861 GDSEEEEE---EEEEEEEEEEEEEEEEEEEEENEEPL 894
Score = 29.6 bits (66), Expect = 6.6
Identities = 10/42 (23%), Positives = 24/42 (57%)
Query: 242 IYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQK 283
+ + ++ ++ S+ +S+E E E+ EEEEE++ ++
Sbjct: 841 NQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEE 882
Score = 29.2 bits (65), Expect = 8.2
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEE 278
+ +EE E+E EE E +E E E+ EE EE
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 30.5 bits (69), Expect = 1.7
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 241 NIYDDIPEGDEELEDEVVSEESES----DESEWEDISEEEEEDDGQKVLENDLKIKSSPK 296
N+ +D + +E E++ EE ++ E + SEE E +++ + + K+K K
Sbjct: 12 NMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENK 71
Query: 297 LLNRE 301
L E
Sbjct: 72 KLENE 76
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 30.6 bits (69), Expect = 1.9
Identities = 13/30 (43%), Positives = 22/30 (73%)
Query: 323 MTIGLVGYPNVGKSSTINALLNAKKVSVSA 352
+TI ++G VGKSST+N+++ + +VSA
Sbjct: 39 LTILVMGKGGVGKSSTVNSIIGERIATVSA 68
>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 = 30.7 bits (69), Expect = 1.9
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 252 ELEDEVVSEESESDESEWEDISEEEEE 278
ELE+E S E E +ESE E+ ++ E++
Sbjct: 6 ELEEEDESGEEEEEESEEEEETDSEDD 32
>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 = 30.0 bits (68), Expect = 1.9
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDIS 273
+D + DEE E+E EE + ++ E+ S
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEEES 140
Score = 29.2 bits (66), Expect = 2.9
Identities = 10/34 (29%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 259 SEESESDESEWEDISEEEEEDDGQKVLENDLKIK 292
+ES+ DE + E+ +EE++D+ + E + +K
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDES-EEEESPVK 143
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 30.9 bits (70), Expect = 2.1
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 238 SATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQ 282
+ + D++ ED + ES+ D+S+ +D+S+E+ ED
Sbjct: 246 GIDSDDEGDGSDDDDDEDAI---ESDLDDSD-DDVSDEDGEDLFD 286
>gnl|CDD|235030 PRK02315, PRK02315, adaptor protein; Provisional.
Length = 233
Score = 30.2 bits (69), Expect = 2.3
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 2/72 (2%)
Query: 244 DDIPEGDEELEDEVVSEESES--DESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLNRE 301
D+P E+L D E+ E E ++ + + E+ D K + + +
Sbjct: 80 LDLPLNFEDLIDLPSDEDIEDLFPEDFFKLLEQSLEDKDDLDATAKQEKEEKEAEDEVQL 139
Query: 302 ELISLFKSFHDV 313
+ F F DV
Sbjct: 140 TYVLKFDDFEDV 151
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 30.6 bits (70), Expect = 2.3
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 325 IGLVGYPNVGKSSTINAL 342
IG+ G P VGKS+ I AL
Sbjct: 59 IGITGVPGVGKSTFIEAL 76
>gnl|CDD|227674 COG5384, Mpp10, U3 small nucleolar ribonucleoprotein component
[Translation, ribosomal structure and biogenesis].
Length = 569
Score = 30.8 bits (69), Expect = 2.4
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 239 ATNIYDDIPEGDEELEDEVV-------SEESESDESEWEDISEEEEEDD 280
+I D+ +G +EL+D + S ES+ E E + +E++
Sbjct: 63 LDSIDGDLIQGIQELKDPSLDGSTLNSSSGEESELEEAESVFKEKQMLS 111
>gnl|CDD|234673 PRK00166, apaH, diadenosine tetraphosphatase; Reviewed.
Length = 275
Score = 30.5 bits (70), Expect = 2.5
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 113 RRPKWDKNTTAEQLQAMERDEFLQWRRELNLLQ--EEDGLVIT 153
+R K K+T L+A +RDE L W R LL EE GLV+
Sbjct: 78 KRNK-KKDTLDPILEAPDRDELLDWLRHQPLLHVDEELGLVMV 119
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 30.3 bits (68), Expect = 2.5
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDL 289
+G EE EDE V +S E E EEEEE +G E+ +
Sbjct: 186 DGREEEEDEEVGSDSYG-EGNRELNEEEEEEAEGSDDGEDVV 226
>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 = 2.6
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEED 279
+++PE DE+ E E D+ + E+ EEE+
Sbjct: 14 EELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQI 49
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 30.8 bits (69), Expect = 2.7
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEED 279
E DE+ E + SE+ DESE + EE+ ED
Sbjct: 951 ETDEDEESDESSEDLSEDESENDSSDEEDGED 982
Score = 30.4 bits (68), Expect = 3.1
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 237 FSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEND 288
F D+ E +EE+ + S + ESDE++ ++ S+E ED + END
Sbjct: 922 FLMVGSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESEND 973
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 30.6 bits (69), Expect = 2.7
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 15/75 (20%)
Query: 248 EGDEELEDEVVSEESESDE--SEWEDISEEEEE--DDGQKVLENDLKIKSSPK------- 296
E +E+ ++ EE ++D+ +EW+DIS EE E + +N LK + +
Sbjct: 710 ESEEDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEV 769
Query: 297 ----LLNREELISLF 307
+L +EL+ LF
Sbjct: 770 TGQMILESQELLRLF 784
>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 = 30.1 bits (69), Expect = 2.8
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 207 ILLNKADLLTRKQRCYWTKYFNSVNVAVAFFSATNIYDDIPEGDEELEDE 256
I+LNKADL+ ++ + + + V SA EG +EL +
Sbjct: 38 IVLNKADLVDDEELEELLEIYEKLGYPVLAVSAKT-----GEGLDELREL 82
Score = 29.3 bits (67), Expect = 4.3
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 333 VGKSSTINALLNAKKV---SVSATPGKTKHFQT------LFVDDELLLCDCPG 376
VGKS+ +NALL + +S G+ +H T + L+ D PG
Sbjct: 96 VGKSTLLNALLPELVLATGEISEKLGRGRH--TTTHRELFPLPGGGLIIDTPG 146
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 30.3 bits (69), Expect = 2.8
Identities = 16/55 (29%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLL 298
DDI D+E E+ V+++E + DE + D+ ++++E++ +E IK + L
Sbjct: 223 DDI---DDEEEERVLADEDDDDEDDMFDM-DDDDEEESDPEVERTSTIKEVSEKL 273
>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 = 30.5 bits (69), Expect = 3.1
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 249 GDEELEDEVVSEESESDESEWEDISEEEEEDDGQ 282
E+ED + E +E E E+ EEE+ED+G
Sbjct: 377 SALEIEDANTERDDEEEEDEEEE--EEEDEDEGP 408
Score = 30.1 bits (68), Expect = 3.7
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 247 PEGDEELEDEV---VSEESESDESEWEDISEEEEEDDGQKVL 285
E +EE EDE E S+ +E E +D+ + E+ DG L
Sbjct: 395 DEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSL 436
Score = 29.3 bits (66), Expect = 6.9
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 237 FSATNIYDDIPEG-DEELEDEVVSEESESDESEWEDISEEEE-EDDGQKVLENDLKIKSS 294
FSA I D E DEE EDE EE + DE ++ S++EE E+D + D SS
Sbjct: 376 FSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSS 435
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.2 bits (69), Expect = 3.2
Identities = 45/177 (25%), Positives = 57/177 (32%), Gaps = 77/177 (43%)
Query: 189 CEDLERYVKEVSPHKRNMILLNKADLLTRKQRCYWTKYFNSVNVAVAFFSATNIYDDIPE 248
CE L + P +I+LNK DLL + R VN + IY +I
Sbjct: 146 CETLG-----IEP----LIVLNKIDLLDDEGR-------AFVNEQLD------IYRNI-- 181
Query: 249 GDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLLNREELISLFK 308
G L VS + +G + LE L + IS+F
Sbjct: 182 GYRVLM---VSSHTG----------------EGLEELEAALTGR-----------ISIF- 210
Query: 309 SFHDVNIPRMNPDVMTIGLVGYPNVGKSSTINALL---NAKKVSVSATPGKTKHFQT 362
VG VGKSS INALL VS G +H T
Sbjct: 211 -------------------VGQSGVGKSSLINALLPEAEILVGDVSDNSGLGQHTTT 248
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 29.5 bits (67), Expect = 3.6
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 324 TIGLVGYPNVGKSSTINALLNAKK-VSVSATPGKTKHFQT 362
I LVG GKS+T N++L K S G TK Q
Sbjct: 2 RIVLVGKTGNGKSATGNSILGRKAFESKLRAQGVTKTCQL 41
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 30.4 bits (68), Expect = 3.6
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDG 281
DD + DE+ +DE EE E +E E + +E+EED+G
Sbjct: 155 DDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEG 192
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 30.0 bits (68), Expect = 3.7
Identities = 10/50 (20%), Positives = 22/50 (44%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKS 293
DDI + D++ +D+ ++ + D+ + E +E E + S
Sbjct: 145 DDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDS 194
Score = 29.6 bits (67), Expect = 5.2
Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 10/84 (11%)
Query: 235 AFFSATNIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEED-DGQKVLE----ND- 288
+ DD + ++E + E E SD+ ++ ++ E +K + D
Sbjct: 153 DEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADP 212
Query: 289 ----LKIKSSPKLLNREELISLFK 308
LK KLLN EE + L K
Sbjct: 213 VKAYLKQIGKVKLLNAEEEVELAK 236
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 28.4 bits (64), Expect = 3.8
Identities = 9/42 (21%), Positives = 22/42 (52%)
Query: 247 PEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEND 288
P D E + +E + D+ +D +++++DD + ++D
Sbjct: 46 PAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDD 87
Score = 28.4 bits (64), Expect = 4.0
Identities = 6/37 (16%), Positives = 22/37 (59%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
D + ++E +++ V + + D+ + +D+ + +++D
Sbjct: 52 DAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDV 88
Score = 27.3 bits (61), Expect = 9.7
Identities = 8/37 (21%), Positives = 19/37 (51%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDD 280
D+ E D L+D+ ++ + +D + +++DD
Sbjct: 59 DEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDD 95
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 30.3 bits (68), Expect = 3.9
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 244 DDIPEGDEELE----DEVVSEESESDESEWEDISEEEEEDDGQKVLENDL 289
DD P +E+ E + E S ESE D E E++ + ++DL
Sbjct: 217 DDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDL 266
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 29.3 bits (67), Expect = 3.9
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 333 VGKSSTINALLNAK---KVSVSAT 353
GKS+ + ALL ++SVSAT
Sbjct: 16 AGKSTLVKALLERDPNLQLSVSAT 39
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 30.0 bits (68), Expect = 3.9
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 242 IYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLK 290
+ E EEL ++ EE E D SE ED E+EE++D ++ ++D
Sbjct: 271 VVGGDEEDLEELLEKAEEEEEEDDYSESED--EDEEDEDEEEEEDDDEG 317
Score = 29.2 bits (66), Expect = 6.7
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQK 283
E EE E+E ESE ++ E ED EEE++D+G K
Sbjct: 284 EKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
Score = 28.9 bits (65), Expect = 8.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 249 GDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSS 294
G +E + E + E++E +E E +D SE E+ED+ + E +
Sbjct: 273 GGDEEDLEELLEKAEEEEEE-DDYSESEDEDEEDEDEEEEEDDDEG 317
>gnl|CDD|236071 PRK07638, PRK07638, acyl-CoA synthetase; Validated.
Length = 487
Score = 29.7 bits (67), Expect = 4.3
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 111 IPRRPKWDKNTTAEQLQAMERDEFLQWRRELNLLQEEDGLVITPYEKNLDFWRQLWRVIE 170
+P KW ++ E+L D + R +LN L +E+G VI +D W+++ IE
Sbjct: 78 VPLDIKWKQDELKERLAISNADMIVTERYKLNDLPDEEGRVI-----EIDEWKRM---IE 129
Query: 171 R-SDVIVQIVDARN 183
+ I + +N
Sbjct: 130 KYLPTYAPIENVQN 143
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 29.2 bits (66), Expect = 5.1
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 169 IERSDVIVQIVDARNP-LLFRCEDLERYVKEVSPHKRNMILLNKADLLTRKQ--RCY 222
ER+D+I + D + + +K R I+LNKAD++ +Q R Y
Sbjct: 120 AERADLIFLLFDPHKLDISDEFRRVIEQLKGHESKIR--IVLNKADMVDTQQLMRVY 174
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 29.8 bits (68), Expect = 5.3
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKI 291
D E++ SE +E + ++ EEEEED+ L D
Sbjct: 173 FVDPNAEEDPAHVGSELEELDDDE-DEEEEEDENDDSLAADESE 215
Score = 29.4 bits (67), Expect = 6.5
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDG 281
++ +G + E S+ E +D +EEEE+D
Sbjct: 167 RELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDE 204
Score = 29.0 bits (66), Expect = 8.5
Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 20/88 (22%)
Query: 244 DDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIKSSPKLL----- 298
+D ELE+ E+ E +E E +D +E + +KVLE + K L
Sbjct: 180 EDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239
Query: 299 ---------------NREELISLFKSFH 311
RE+L KS
Sbjct: 240 KKVEGRLAQHKKYAKLREKLKEELKSLR 267
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 29.5 bits (66), Expect = 5.4
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 245 DIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQK 283
++ E +L E EE+ +S+ ED E+ ED K
Sbjct: 234 NLEERRRDLRKEQELEENVERDSDDEDEHGEDSEDGETK 272
>gnl|CDD|224478 COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism].
Length = 288
Score = 29.3 bits (66), Expect = 5.6
Identities = 18/80 (22%), Positives = 24/80 (30%), Gaps = 17/80 (21%)
Query: 131 RDEFLQWRRELNLLQEEDGLVITPYEKNLDFWRQLWRVIERSDVIVQIVDA--------- 181
+ L WRREL+ P L V R + + A
Sbjct: 63 AEILLAWRRELDGDFSGQPASDHPVLAALV------EVARRFGLPREAFPALIDAMRMDL 116
Query: 182 -RNPLLFRCEDLERYVKEVS 200
R L E+LE Y V+
Sbjct: 117 DRTRYLDF-EELEEYCYGVA 135
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 28.4 bits (63), Expect = 5.6
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 244 DDIPEGDEELE-DEVVSEESESDESEWEDISEEEEED 279
D E DEE E DE V E ++ ++E E+ EEE+E+
Sbjct: 92 DAADEADEEEETDEAVDETADEADAEAEEADEEEDEE 128
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.2 bits (65), Expect = 5.6
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 8/61 (13%)
Query: 322 VMTIGLVGYPNVGKSSTINALL------NAKKVSVSATPGKTKHFQTLFVDDELLLCDCP 375
I ++G VGK++ +N L+ + P KT + +L L D
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIE--PYRRNIKLQLWDTA 62
Query: 376 G 376
G
Sbjct: 63 G 63
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.1 bits (63), Expect = 5.8
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 323 MTIGLVGYPNVGKSSTINALLN 344
+ +VG + GK++ I LLN
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLN 22
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 29.8 bits (66), Expect = 6.3
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 241 NIYDDIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEN 287
NI +++ E DEE +EV E DE E+I E EE+ + + EN
Sbjct: 1014 NIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEEN 1060
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 28.9 bits (65), Expect = 6.4
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDLKIK 292
E +EE E + ++SE DE E +D E E+E ++ L+ ++K
Sbjct: 47 EEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKKRVK 91
Score = 28.9 bits (65), Expect = 6.5
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 248 EGDEELEDEVVSEESESD----ESEWEDISEEEEEDDGQKVLENDLKIK 292
E DEE E E EE E D +SE ++ E ++E++G+K L+ + ++K
Sbjct: 38 EDDEEFEIEEEEEEEEVDSDFDDSEDDE-PESDDEEEGEKELQREERLK 85
>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 = 29.1 bits (65), Expect = 6.6
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 244 DDIPEGD---EELEDEVVSEESESDESEWEDISEEEEEDDGQKVLENDL 289
+ EGD EE DE +E E DES E+++E E + L L
Sbjct: 335 VEKQEGDVVTEESTDEESEDEVEIDESVIEEVAEMELLEVQVDDLAERL 383
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 28.7 bits (65), Expect = 7.1
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 327 LVGYPNVGKSSTINALLNAKK--VSVSAT 353
L G VGKS+ + ALL K SVSAT
Sbjct: 9 LSGPSGVGKSTLVKALLEDDKLRFSVSAT 37
>gnl|CDD|217357 pfam03079, ARD, ARD/ARD' family. The two acireductone dioxygenase
enzymes (ARD and ARD', previously known as E-2 and E-2')
from Klebsiella pneumoniae share the same amino acid
sequence, but bind different metal ions: ARD binds Ni2+,
ARD' binds Fe2+. ARD and ARD' can be experimentally
interconverted by removal of the bound metal ion and
reconstitution with the appropriate metal ion. The two
enzymes share the same substrate,
1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield
different products. ARD' yields the alpha-keto precursor
of methionine (and formate), thus forming part of the
ubiquitous methionine salvage pathway that converts
5'-methylthioadenosine (MTA) to methionine. This pathway
is responsible for the tight control of the
concentration of MTA, which is a powerful inhibitor of
polyamine biosynthesis and transmethylation reactions.
ARD yields methylthiopropanoate, carbon monoxide and
formate, and thus prevents the conversion of MTA to
methionine. The role of the ARD catalyzed reaction is
unclear: methylthiopropanoate is cytotoxic, and carbon
monoxide can activate guanylyl cyclase, leading to
increased intracellular cGMP levels. This family also
contains other members, whose functions are not well
characterized.
Length = 157
Score = 28.5 bits (64), Expect = 7.1
Identities = 14/85 (16%), Positives = 26/85 (30%), Gaps = 15/85 (17%)
Query: 242 IYDDIPEGDEELEDEVVSEESESDESEWEDISE--------EEEEDDGQKVLE------- 286
I DD P GD+ L +E + + EE ++ ++ +
Sbjct: 4 IMDDSPCGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEELLRIRKYKHYDDV 63
Query: 287 NDLKIKSSPKLLNREELISLFKSFH 311
+ N +E + F H
Sbjct: 64 DIDVTVCPETTPNFDEKLKKFFEEH 88
>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase 19
kDa subunit. This family contains several DNA-directed
RNA polymerase 19 kDa polypeptides. The Poxvirus
DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes
DNA-template-directed extension of the 3'-end of an RNA
strand by one nucleotide at a time.
Length = 167
Score = 28.5 bits (64), Expect = 7.2
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 253 LEDEVVSEESESDESEWEDISEEEEEDDGQKVLEND 288
+ED + ESD+ + E+ EEEE+++ + LE+
Sbjct: 1 MEDSDDIIDYESDDDDSEEYEEEEEDEEDAESLESS 36
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.1 bits (62), Expect = 7.3
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 324 TIGLVGYPNVGKSSTINALLN 344
I +VG P GK++ AL
Sbjct: 4 VILIVGPPGSGKTTLARALAR 24
>gnl|CDD|224843 COG1932, SerC, Phosphoserine aminotransferase [Coenzyme metabolism
/ Amino acid transport and metabolism].
Length = 365
Score = 28.8 bits (65), Expect = 7.7
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 72 TAEKLNITFVNPKSGVGLLS---KEEKELALQAHKEKRELLKIP 112
A+K + + V +S KE K + +A K+ RELL IP
Sbjct: 23 QAQKELLDWNGLGMSVMEISHRSKEFKNVLEEAEKDLRELLNIP 66
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.2 bits (65), Expect = 7.9
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEN-DLKIKSSPKLLNREELISL 306
+ D + +++ EE D ++I + +E++ Q EN DL + KL +E +S
Sbjct: 3947 DKDRQEKED--EEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSK 4004
Query: 307 FKSFHDVNIPRMNPD 321
D+++ + +
Sbjct: 4005 DSDLEDMDMEAADEN 4019
>gnl|CDD|163665 cd07422, MPP_ApaH, Escherichia coli ApaH and related proteins,
metallophosphatase domain. ApaH (also known as
symmetrically cleaving Ap4A hydrolase and
bis(5'nucleosyl)-tetraphosphatase) is a bacterial member
of the PPP (phosphoprotein phosphatase) family of
serine/threonine phosphatases that hydrolyzes the
nucleotide-signaling molecule diadenosine tetraphosphate
(Ap(4)A) into two ADP and also hydrolyzes Ap(5)A,
Gp(4)G, and other extending compounds. Null mutations
in apaH result in high intracellular levels of Ap(4)A
which correlate with multiple phenotypes, including a
decreased expression of catabolite-repressible genes, a
reduction in the expression of flagellar operons, and an
increased sensitivity to UV and heat. Ap4A hydrolase
is important in responding to heat shock and oxidative
stress via regulating the concentration of Ap4A in
bacteria. Ap4A hydrolase is also thought to play a role
in siderophore production, but the mechanism by which
ApaH interacts with siderophore pathways in unknown.
The PPP (phosphoprotein phosphatase) family, to which
ApaH belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, and PrpA/PrpB. The
PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 28.6 bits (65), Expect = 8.2
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 113 RRPKWDKNTTAEQLQAMERDEFLQWRRELNLLQEEDGL 150
++PK K+T + L A +RDE L W R LL + L
Sbjct: 76 KKPK-KKDTLDDILNAPDRDELLDWLRHQPLLHRDPEL 112
>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 = 27.6 bits (61), Expect = 8.4
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 245 DIPEGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKV 284
+ + E E+EV ++ E + E+ EEEEE +G
Sbjct: 45 QEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATG 84
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 28.8 bits (64), Expect = 8.6
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 248 EGDEELEDEVVSEESESDESEWEDISEEEEEDDGQKVLEND 288
E +EE +E +E + D+ + ED +++++DD E+D
Sbjct: 44 EAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDD 84
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 28.2 bits (63), Expect = 8.6
Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 243 YDDIPEGDEELEDE---VVSEESESDESEWEDISEEEEED 279
DD + ++E +DE ++ E+ E DE E +D EE+EED
Sbjct: 135 LDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDEED 174
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 28.7 bits (65), Expect = 9.2
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 328 VGYPNVGKSSTINALLNAKK-----VSVSATPGKTKHFQTLFVDDELLLCDCPGLV---- 378
VG NVGKS+ IN ++ ++ S PG T + +DD L D PG++
Sbjct: 166 VGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLYDTPGIIHRHQ 225
Query: 379 MPSFVFSK 386
M ++ +K
Sbjct: 226 MAHYLSAK 233
>gnl|CDD|99824 cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of
Sulfurisphaera ohwakuensis DNA polymerase B3 and similar
archaeal family-B DNA polymerases. The 3'-5'
exonuclease domain of archaeal proteins with similarity
to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a
family-B DNA polymerase. Family-B DNA polymerases
contain an N-terminal DEDDy DnaQ-like exonuclease domain
in the same polypeptide chain as the polymerase domain,
similar to family-A DNA polymerases. B3 exhibits both
polymerase and 3'-5' exonuclease activities. This
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, with a specific YX(3)D pattern
at ExoIII. These motifs are clustered around the active
site and are involved in metal binding and catalysis.
The exonuclease domain of family B polymerases also
contains a beta hairpin structure that plays an
important role in active site switching in the event of
nucleotide misincorporation. Archaeal proteins that are
involved in DNA replication are similar to those from
eukaryotes. Some archaea possess multiple family-B DNA
polymerases. B3 is mainly found in crenarchaea.
Phylogenetic analyses of eubacterial, archaeal, and
eukaryotic family B-DNA polymerases support independent
gene duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 188
Score = 28.1 bits (63), Expect = 9.7
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 117 WDKNTTAEQLQAMERDEFLQWRRELNLLQEEDGLVITPYEKNLDFWRQLWRVIERSDVI 175
N E + A D+ R + ++E D +I Y N W L +ER+ V+
Sbjct: 32 ATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYL---VERARVL 87
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 0.134 0.391
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,735,867
Number of extensions: 3063386
Number of successful extensions: 4340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3890
Number of HSP's successfully gapped: 313
Length of query: 595
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 493
Effective length of database: 6,413,494
Effective search space: 3161852542
Effective search space used: 3161852542
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: 42 (22.0 bits)
S2: 62 (28.1 bits)