RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11743
(551 letters)
>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 = 416 bits (1072), Expect = e-145
Identities = 162/240 (67%), Positives = 185/240 (77%), Gaps = 8/240 (3%)
Query: 59 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVP--------FS 110
V+ +GQYSTGK+TFI YLL +D+PG+ GPEPTTDRF VM+ E +G++P
Sbjct: 2 VLFLGQYSTGKSTFINYLLGQDYPGLRTGPEPTTDRFTVVMHGEDDGTIPGNALVVDPDK 61
Query: 111 PLDKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAE 170
P KFGN FLN+F+ S + P+L+ ++IVDTPGILSGEKQR RGYDF V WFAE
Sbjct: 62 PFRGLSKFGNGFLNKFEGSTLPHPLLESVTIVDTPGILSGEKQRQSRGYDFNAVCRWFAE 121
Query: 171 RVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRVYGALMWSL 230
R D I LLFD HKLDISDEFRR IE L+GH+ KIRIVLNKADMVD QQLMRVYGALMWSL
Sbjct: 122 RADLIFLLFDPHKLDISDEFRRVIEQLKGHESKIRIVLNKADMVDTQQLMRVYGALMWSL 181
Query: 231 GKVLQTPEVARVYIGSFWDQPLVHDVNRRLFEDEEQDLFKDLQSLPRNAALRKLNDLIKR 290
KV+ TPEV RVYIGSFWDQP D NR+LF +EE DL +DL SLPRNAALRKLNDLIKR
Sbjct: 182 SKVINTPEVPRVYIGSFWDQPYEPDTNRKLFLEEEIDLLRDLNSLPRNAALRKLNDLIKR 241
Score = 158 bits (402), Expect = 5e-45
Identities = 54/88 (61%), Positives = 69/88 (78%)
Query: 309 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPGNALVVDPKK 368
V+ +GQYSTGK+TFI YLL +D+PG+ GPEPTTDRF VM+ E +G++PGNALVVDP K
Sbjct: 2 VLFLGQYSTGKSTFINYLLGQDYPGLRTGPEPTTDRFTVVMHGEDDGTIPGNALVVDPDK 61
Query: 369 QFRPLDKFGNSFLNRFQCSLVNSPVLKG 396
FR L KFGN FLN+F+ S + P+L+
Sbjct: 62 PFRGLSKFGNGFLNKFEGSTLPHPLLES 89
Score = 60.0 bits (146), Expect = 4e-10
Identities = 22/33 (66%), Positives = 25/33 (75%)
Query: 396 GKVLQTPEVARVYIGSFWDQPLVHDVNRRLFED 428
KV+ TPEV RVYIGSFWDQP D NR+LF +
Sbjct: 182 SKVINTPEVPRVYIGSFWDQPYEPDTNRKLFLE 214
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 116 bits (292), Expect = 2e-30
Identities = 37/177 (20%), Positives = 66/177 (37%), Gaps = 33/177 (18%)
Query: 59 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDE-------------REG 105
+ +VG S GK++ + LL RD GP PTT R + + E ++G
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDIL--PRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDG 58
Query: 106 SVPFSPLDKFGK-----------FGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQR 154
F + + G + + SP++ G+++VDTPG+ S
Sbjct: 59 LKKFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPGLDSVAVGD 118
Query: 155 VDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKA 211
+ E + + D I+ + DA+ + E + + + VL K
Sbjct: 119 -------QDLTEEYIKPADIILAVVDANHDLSTSEALFLAREVDPNGKRTIGVLTKD 168
Score = 69.6 bits (171), Expect = 7e-14
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 8/102 (7%)
Query: 309 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPG--NALVVDP 366
+ +VG S GK++ + LL RD GP PTT R + + E G++PG D
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDIL--PRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDG 58
Query: 367 KKQFRPLDKFGNSFLNRFQCSLVNSPVLKGKVLQTPEVARVY 408
K+F + + + P + +
Sbjct: 59 LKKFEDFSELREEIEDETDK----ISGTGKGISSEPIILEIL 96
>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 = 66.3 bits (162), Expect = 7e-13
Identities = 26/171 (15%), Positives = 54/171 (31%), Gaps = 38/171 (22%)
Query: 61 LVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFGKFGN 120
+VG+ GK++ + LL + + P T D +
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDV------------------------ 37
Query: 121 SFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFD 180
+ +VDTPG+ + D I+L+ D
Sbjct: 38 -------YVKELDKGKVKLVLVDTPGLDEFGGLGREELA------RLLLRGADLILLVVD 84
Query: 181 AHKLDISDEFRRSI-EALRGHDDKIRIVLNKADMVDHQQLMRVYGALMWSL 230
+ + ++ + I LR I +V NK D+++ +++ + +
Sbjct: 85 STDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAK 135
Score = 34.0 bits (78), Expect = 0.10
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 311 LVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTD 343
+VG+ GK++ + LL + + P T D
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRD 34
>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 = 52.2 bits (126), Expect = 7e-08
Identities = 44/165 (26%), Positives = 67/165 (40%), Gaps = 48/165 (29%)
Query: 58 TVMLVGQYSTGKTTFIRYLLERDF-PGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFG 116
+ +VG++S GK+T + LL + P G PTT
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLP---TGVTPTT------------------------ 34
Query: 117 KFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRII 176
+ R+ LKG+ +VDTPG+ S + T + E F R D +I
Sbjct: 35 --AVITVLRYGL-------LKGVVLVDTPGLNSTIEHH-------TEITESFLPRADAVI 78
Query: 177 LLFDA-HKLDISD-EFRRSIEALRGHDDKIRIVLNKADMVDHQQL 219
+ A L S+ EF + I L+ KI VLNK D++ ++L
Sbjct: 79 FVLSADQPLTESEREFLKEI--LKWSGKKIFFVLNKIDLLSEEEL 121
Score = 33.3 bits (77), Expect = 0.18
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 308 TVMLVGQYSTGKTTFIRYLLERDF-PGIHIGPEPTTDRFIAVMYDEREGSV----PG 359
+ +VG++S GK+T + LL + P G PTT + Y +G V PG
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLP---TGVTPTTAVITVLRYGLLKGVVLVDTPG 55
>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 = 47.3 bits (113), Expect = 1e-06
Identities = 38/159 (23%), Positives = 55/159 (34%), Gaps = 48/159 (30%)
Query: 58 TVMLVGQYSTGKTTFIRYLLER------DFPGIHIGPEPTTDRFIAVMYDEREGSVPFSP 111
V LVG+ + GK+T I L D+PG T D + V+ R+
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGT------TRDPILGVLGLGRQ------- 47
Query: 112 LDKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAER 171
I +VDTPG++ G + F LE
Sbjct: 48 ---------------------------IILVDTPGLIEGASEG-KGVEGFNRFLEA-IRE 78
Query: 172 VDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNK 210
D I+L+ DA + D+ E + I +VLNK
Sbjct: 79 ADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
Score = 29.6 bits (67), Expect = 1.4
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 308 TVMLVGQYSTGKTTFIRYLLER------DFPGIHIGPEPTTDRFIAVMYDERE 354
V LVG+ + GK+T I L D+PG T D + V+ R+
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGT------TRDPILGVLGLGRQ 47
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 46.2 bits (110), Expect = 4e-06
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 136 LKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIE 195
G+ ++D PG+ GE+ R DR Y + D ++ L DA ++ + +
Sbjct: 44 GDGLVLLDLPGV--GERGRRDREY--EELYRRLLPEADLVLWLLDADDRALAADHDFYLL 99
Query: 196 ALRGHDDKIRIVLNKADMV 214
L GHD + VLN+ D V
Sbjct: 100 PLAGHDAPLLFVLNQVDPV 118
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 40.6 bits (96), Expect = 0.001
Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 11/66 (16%)
Query: 308 TVMLVGQYSTGKTTFIRYLLERDF--------PGIHIGPEPTTDRFIAVMYDEREGSVPG 359
+M+VG+ GK+TFI L PG HI T + E V
Sbjct: 6 NIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHI---TKTVEIKISKAELEENGVKL 62
Query: 360 NALVVD 365
V+D
Sbjct: 63 KLTVID 68
Score = 37.1 bits (87), Expect = 0.014
Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 11/61 (18%)
Query: 58 TVMLVGQYSTGKTTFIRYLLERDF--------PGIHIGPEPTTDRFIAVMYDEREGSVPF 109
+M+VG+ GK+TFI L PG HI T + E V
Sbjct: 6 NIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHI---TKTVEIKISKAELEENGVKL 62
Query: 110 S 110
Sbjct: 63 K 63
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 38.0 bits (89), Expect = 0.003
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 136 LKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIE 195
L + ++DTPG+ +R + + A+R D ++L+ D+ L +E + +
Sbjct: 45 LGPVVLIDTPGLDEEGGLGRERVEE---ARQV-ADRADLVLLVVDS-DLTPVEEEAK-LG 98
Query: 196 ALRGHDDKIRIVLNKADMVDHQQ 218
LR + +VLNK D+V +
Sbjct: 99 LLRERGKPVLLVLNKIDLVPESE 121
>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 = 37.5 bits (88), Expect = 0.016
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 15/82 (18%)
Query: 134 PVLKGISIVDTPGIL-SGE--KQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEF 190
PV+ ++DT G+ GE + RV++ + VL+ + D +L+ DA E
Sbjct: 56 PVV----LIDTAGLDDEGELGELRVEKTRE---VLD----KTDLALLVVDAGVGPGEYE- 103
Query: 191 RRSIEALRGHDDKIRIVLNKAD 212
IE L+ +V+NK D
Sbjct: 104 LELIEELKERKIPYIVVINKID 125
>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 = 35.4 bits (82), Expect = 0.029
Identities = 38/169 (22%), Positives = 50/169 (29%), Gaps = 45/169 (26%)
Query: 61 LVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFGKFGN 120
LVG + GK+T + L + I P T V G F
Sbjct: 2 LVGLPNVGKSTLLSALTSAK---VEIASYPFTTLEPNV-----------------GVFEF 41
Query: 121 SFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFD 180
Q I+D PG+L G + G L R D I+ + D
Sbjct: 42 GDGVDIQ-------------IIDLPGLLDGASEGRGLGEQILAHL----YRSDLILHVID 84
Query: 181 AHKLDISDEFRR--------SIEALRGHDDKIRIVLNKADMVDHQQLMR 221
A + + D S L + IV NK DM L R
Sbjct: 85 ASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIVANKIDMASENNLKR 133
>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 = 35.1 bits (82), Expect = 0.041
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 142 VDTPGILSGEKQRVDR-GYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALRGH 200
VDTPGI +K+ +R L + VD ++ + DA + I + +E L+
Sbjct: 56 VDTPGIHKPKKKLGERMVKAAWSAL----KDVDLVLFVVDASE-WIGEGDEFILELLKKS 110
Query: 201 DDKIRIVLNKADMVDHQQ 218
+ +VLNK D+V ++
Sbjct: 111 KTPVILVLNKIDLVKDKE 128
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 35.7 bits (83), Expect = 0.048
Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 18/99 (18%)
Query: 171 RVDRIILLFDA-----HKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRVYGA 225
R+D ++ + DA I++ + D IVLNK D+VD ++L +
Sbjct: 116 RLDGVVTVVDAAHFLEGLDAIAELAEDQLAFA----D--VIVLNKTDLVDAEELEAL--- 166
Query: 226 LMWSLGKVLQTPEVARVYIGSFWDQPLVHDVNRRLFEDE 264
++ + AR+ S+ D L ++ LF+ +
Sbjct: 167 ----EARLRKLNPRARIIETSYGDVDLAELLDEGLFDLD 201
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 35.6 bits (83), Expect = 0.056
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 15/94 (15%)
Query: 135 VLKGIS--IVDTPGILSG----EKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISD 188
L GI +VDT GI E+ ++R + E D ++ + DA + +
Sbjct: 261 NLNGIPVRLVDTAGIRETDDVVERIGIERA------KKA-IEEADLVLFVLDASQP-LDK 312
Query: 189 EFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRV 222
E IE L I +VLNKAD+V +L
Sbjct: 313 EDLALIELLP-KKKPIIVVLNKADLVSKIELESE 345
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein
[General function prediction only].
Length = 398
Score = 35.8 bits (83), Expect = 0.057
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 1 MFSWMSKNEDSSPEMYETVLEGLKKVYKNKLLPLEQAYHFHDFHSPPYEDADFDAKPTVM 60
+ + S T L +V +++ PLE+ + S VM
Sbjct: 24 GLREV-EGGALSVARVRTTYHQLVEVPEDRSEPLEEIADTWE--SKSESAGK---VGVVM 77
Query: 61 LVGQYSTGKTTFIRYLLER 79
+VG +GK+T YL +
Sbjct: 78 VVGPVDSGKSTLTTYLANK 96
Score = 32.0 bits (73), Expect = 0.81
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 306 KPTVMLVGQYSTGKTTFIRYLLER 329
VM+VG +GK+T YL +
Sbjct: 73 VGVVMVVGPVDSGKSTLTTYLANK 96
>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 = 34.3 bits (80), Expect = 0.064
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 13/84 (15%)
Query: 141 IVDTPGILSGEKQRVDRGYDFTGVLEWFA--ERVDRIILLFDAHKLDISDE----FRRSI 194
++DT GI +K +V G + VL ER D ++L+ DA I+++ +
Sbjct: 54 LIDTAGIR--KKGKVTEGIEKYSVLRTLKAIERADVVLLVLDA-SEGITEQDLRIAGLIL 110
Query: 195 EALRGHDDKIRIVLNKADMVDHQQ 218
E + + IV+NK D+V+ +
Sbjct: 111 EEGKA----LIIVVNKWDLVEKDE 130
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.6 bits (79), Expect = 0.084
Identities = 33/170 (19%), Positives = 54/170 (31%), Gaps = 47/170 (27%)
Query: 59 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFGKF 118
++++G GKTT + L+ +FP G PT I + + P + K
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFP---EGYPPT----IGNLDPAKT----IEPYRRNIKL 56
Query: 119 GNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILL 178
+ DT G R + G I+++
Sbjct: 57 ---------------------QLWDTAGQEEYRSLRPEYYRGANG-----------ILIV 84
Query: 179 FDAHKLDISDEFRRS----IEALRGHDDKIRIVLNKADMVDHQQLMRVYG 224
+D+ + SDE + L D I +V NK D+ D Q
Sbjct: 85 YDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEIL 134
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 34.9 bits (81), Expect = 0.12
Identities = 35/183 (19%), Positives = 62/183 (33%), Gaps = 52/183 (28%)
Query: 55 AKPTVMLVGQYSTGKTTFIRYLLER------DFPGIHIGPEPTTDRFIAVMYDEREGSVP 108
+ P V +VG+ + GK+T L R D PG+ T DR G
Sbjct: 2 STPVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGV------TRDR--------IYGD-- 45
Query: 109 FSPLDKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWF 168
++ + ++DT G+ G++ +
Sbjct: 46 -------AEWLG----------------REFILIDTGGLDDGDEDELQE--LIREQALIA 80
Query: 169 AERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRVYGALMW 228
E D I+ + D + I+ + LR + +V+NK D + ++L +
Sbjct: 81 IEEADVILFVVDG-REGITPADEEIAKILRRSKKPVILVVNKIDNLKAEELA----YEFY 135
Query: 229 SLG 231
SLG
Sbjct: 136 SLG 138
Score = 32.2 bits (74), Expect = 0.66
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 25/90 (27%)
Query: 141 IVDTPGILSGEKQRVDRGYDFTGVLEWFA--------ERVDRIILLFDAHKLDISDEFRR 192
++DT GI K ++ T +E ++ ER D ++L+ DA + IS++ R
Sbjct: 230 LIDTAGI--RRKGKI------TESVEKYSVARTLKAIERADVVLLVIDATE-GISEQDLR 280
Query: 193 S----IEALRGHDDKIRIVLNKADMVDHQQ 218
EA RG I IV+NK D+V+ +
Sbjct: 281 IAGLIEEAGRG----IVIVVNKWDLVEEDE 306
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 33.4 bits (77), Expect = 0.16
Identities = 34/172 (19%), Positives = 56/172 (32%), Gaps = 44/172 (25%)
Query: 58 TVMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDERE-------GSVPFS 110
V ++G GKTT LL + G + F+ + +ERE G V F
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTR--KETFLDTLKEERERGITIKTGVVEFE 58
Query: 111 PLDKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAE 170
+ I+ +DTPG DF+
Sbjct: 59 WPKR-----------------------RINFIDTPGHE-----------DFSKETVRGLA 84
Query: 171 RVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRV 222
+ D +L+ DA++ + + R + I + +NK D V + V
Sbjct: 85 QADGALLVVDANE-GVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEV 135
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 116
Score = 32.4 bits (74), Expect = 0.19
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 59 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTT 92
V+++G +GK++ + L+ +FP + + T
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDT 35
Score = 32.4 bits (74), Expect = 0.19
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 309 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTT 342
V+++G +GK++ + L+ +FP + + T
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDT 35
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 33.9 bits (79), Expect = 0.22
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 11/89 (12%)
Query: 137 KGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIIL-LFDAHKLDISDEFRRSIE 195
K I D PG++ G + G+ F +E R R++L L D +D ++++
Sbjct: 206 KSFVIADIPGLIEGASEGAGLGHRFLKHIE----RT-RLLLHLVDIEAVDPVEDYKTIRN 260
Query: 196 ALRGHD----DKIRI-VLNKADMVDHQQL 219
L + DK RI VLNK D++D ++
Sbjct: 261 ELEKYSPELADKPRILVLNKIDLLDEEEE 289
>gnl|CDD|212009 cd11619, HR1_CIP4-like, Protein kinase C-related kinase homology
region 1 (HR1) Rho-binding domain of Cdc42-Interacting
Protein 4 and similar proteins. This subfamily is
composed of Cdc42-Interacting Protein 4 (CIP4), Formin
Binding Protein 17 (FBP17), FormiN Binding Protein
1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L
are Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. It functions downstream of Cdc42 in
PDGF-dependent actin reorganization and cell migration,
and also regulates the activity of PDGFRbeta. It uses
Src as a substrate in regulating the invasiveness of
breast tumor cells. CIP4 may also play a role in the
pathogenesis of Huntington's disease. Members of this
subfamily typically contain an N-terminal F-BAR
(FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain,
central HR1 domain, and a C-terminal SH3 domain. HR1
domains are anti-parallel coiled-coil (ACC) domains that
bind small GTPases from the Rho family; the HR1 domain
of CIP4 binds Cdc42 and TC10. Translocation of CIP4 is
facilitated by its binding to TC10 at the plasma
membrane.
Length = 77
Score = 30.7 bits (70), Expect = 0.33
Identities = 12/44 (27%), Positives = 28/44 (63%), Gaps = 7/44 (15%)
Query: 455 EGKKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQ 498
E ++K+L +K+DE+ K+I++E + ++ + K+ +Y+Q
Sbjct: 2 EQRRKKLQQKIDELEKEIEKETK-------SRDGLMKMKGVYEQ 38
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 32.7 bits (75), Expect = 0.40
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 58 TVMLVGQYSTGKTTFIRYLLERD 80
T+M+VG+ GKTT I L D
Sbjct: 6 TLMVVGESGLGKTTLINTLFLTD 28
Score = 32.7 bits (75), Expect = 0.40
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 308 TVMLVGQYSTGKTTFIRYLLERD 330
T+M+VG+ GKTT I L D
Sbjct: 6 TLMVVGESGLGKTTLINTLFLTD 28
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 33.0 bits (75), Expect = 0.41
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 51 ADFDAKPTVMLVGQYSTGKTTFIRYL 76
+++ PTVM+VG GKT+F L
Sbjct: 94 FNYEKGPTVMVVGGSQNGKTSFCFTL 119
Score = 33.0 bits (75), Expect = 0.41
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 301 ADFDAKPTVMLVGQYSTGKTTFIRYL 326
+++ PTVM+VG GKT+F L
Sbjct: 94 FNYEKGPTVMVVGGSQNGKTSFCFTL 119
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 32.8 bits (76), Expect = 0.43
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 18/85 (21%)
Query: 135 VLKGIS--IVDTPGILSG----EKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISD 188
L GI ++DT GI EK ++R + E D ++L+ DA + +
Sbjct: 259 NLDGIPLRLIDTAGIRETDDEVEKIGIERSREA-------IEEADLVLLVLDASEPLTEE 311
Query: 189 EFRRSIEALRGHDDKIRI-VLNKAD 212
+ E L DK I VLNKAD
Sbjct: 312 DD----EILEELKDKPVIVVLNKAD 332
>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 = 31.6 bits (72), Expect = 0.48
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 141 IVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALRGH 200
++DT G E R + V D +IL+ D +I ++ + I
Sbjct: 55 LLDTAGQ---EDYDAIRRLYYRAVES-SLRVFDIVILVLDV--EEILEKQTKEIIHHAES 108
Query: 201 DDKIRIVLNKADMVD 215
I +V NK D+ D
Sbjct: 109 GVPIILVGNKIDLRD 123
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 32.2 bits (74), Expect = 0.72
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 45 SPPYEDADFDAKP--TVMLVGQYSTGKTTFIRYLLERDF 81
ED F+AKP TV +VG GK+T I LL+R F
Sbjct: 348 RQGVEDVSFEAKPGQTVAIVGPTGAGKSTLIN-LLQRVF 385
Score = 31.9 bits (73), Expect = 0.92
Identities = 18/35 (51%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 299 EDADFDAKP--TVMLVGQYSTGKTTFIRYLLERDF 331
ED F+AKP TV +VG GK+T I LL+R F
Sbjct: 352 EDVSFEAKPGQTVAIVGPTGAGKSTLIN-LLQRVF 385
>gnl|CDD|225922 COG3387, SGA1, Glucoamylase and related glycosyl hydrolases
[Carbohydrate transport and metabolism].
Length = 612
Score = 32.4 bits (74), Expect = 0.74
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 404 VARVYIGSFWDQPLVHDVNRRLFEDRSSTSNSVQAYIISALRK--DMPSVFGKEGKKKEL 461
I + P + L+E+R +A + + L D+ FG +G +
Sbjct: 391 RRMEKIKANLPTP-----DFDLWEERGGHFTYTKATVYAGLDAAADLAEEFGDKGSAEHW 445
Query: 462 IKKLDEIYKQI 472
K DE+ + +
Sbjct: 446 RKTADELKEAV 456
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 30.8 bits (70), Expect = 0.77
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 57 PTVMLVGQYSTGKTTFIRYLLER 79
P V++VG +GKTT IR LL
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNY 23
Score = 30.8 bits (70), Expect = 0.77
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 307 PTVMLVGQYSTGKTTFIRYLLER 329
P V++VG +GKTT IR LL
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNY 23
>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 = 30.8 bits (69), Expect = 0.78
Identities = 22/156 (14%), Positives = 43/156 (27%), Gaps = 20/156 (12%)
Query: 56 KPTVMLVGQYSTGKTTFI----RYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSP 111
+++VG +GKTT R L I+I E + + + G S
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 112 LD-KFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAE 170
+ + + + ++ I+D L +Q L +
Sbjct: 62 SGELRLRLALALARKLKPDVL---------ILDEITSLLDAEQEALLLLLEELRLLLLLK 112
Query: 171 RVDRIILLFDAHKLDISDE------FRRSIEALRGH 200
+ ++ + F R I L
Sbjct: 113 SEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|220222 pfam09403, FadA, Adhesion protein FadA. FadA (Fusobacterium
adhesin A) is an adhesin which forms two alpha helices.
Length = 126
Score = 30.6 bits (69), Expect = 0.85
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 454 KEGKKKELIKKLDEIYKQIQREYQISPVFGKKK-------ELIKKLDEIYKQIQREYQIS 506
KE +KE+ + L E + Y K + +L+K+ DE +++++
Sbjct: 54 KETAEKEVQE-LKERQLGREELYAKLKEESKTRFHKDEYKKLLKRYDEYLNKLEQKITDK 112
Query: 507 PGDFPKVEKMQELL 520
+ EK+QE+
Sbjct: 113 EQQISEFEKIQEVR 126
>gnl|CDD|218408 pfam05062, RICH, RICH domain. This presumed domain is about 85
residues in length and very rich in charged residues,
hence the name RICH (Rich In CHarged residues). It is
found in secreted proteins such as PspC, SpsA, and IgA
FC receptor from Streptococcus agalactiae. This domain
could be involved in bacterial adherence or cell wall
binding.
Length = 81
Score = 29.6 bits (67), Expect = 0.91
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 7/74 (9%)
Query: 458 KKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQIQREYQISPGDFPKVEKMQ 517
++ L K L EIYKQ+ + V LIKKL I + E + E +
Sbjct: 12 EEYLEKILSEIYKQLDKRKHTQNV-----ALIKKLSAIKTEYLYELDVLKTKVELEELVS 66
Query: 518 ELLQHHD--FTKFQ 529
+ D F KF+
Sbjct: 67 KTKSELDAAFEKFK 80
>gnl|CDD|224691 COG1777, COG1777, Predicted transcriptional regulators
[Transcription].
Length = 217
Score = 31.2 bits (71), Expect = 0.98
Identities = 27/104 (25%), Positives = 47/104 (45%), Gaps = 8/104 (7%)
Query: 444 LRKDMPSVFGKEGKKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQIQREY 503
R ++ +F ELI +L EI + E + EL K+L+E+ +I+ E
Sbjct: 106 ERSEVSKLFKSPEGISELISRLLEI-NREIEELSR-----AQTELQKQLNELMDRIKEEI 159
Query: 504 QISPGDFPKVEKMQELLQHHDFTKFQTLR--PRLIEVADKMLAE 545
+ GD + ++ LL++ +T R IE ++LAE
Sbjct: 160 EDKDGDMTERIVLEYLLKNGAADVEETSRRTVLKIEEVLEILAE 203
>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 = 31.0 bits (71), Expect = 1.0
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 23/110 (20%)
Query: 139 ISIVDTPGILSGEKQRVDRGYDFTGVLEWFA----ERVDRIILLFDAHKLDISDEFRRSI 194
++DTPGIL DR + +E A + +L F +D S+ SI
Sbjct: 49 WQVIDTPGIL-------DRPLEERNTIEMQAITALAHLRAAVLFF----IDPSETCGYSI 97
Query: 195 EA-------LRGHDDK-IRIVLNKADMVDHQQLMRVYGALMWSLGKVLQT 236
E ++ +K + +VLNK D++ + L + L +V++
Sbjct: 98 EEQLSLFKEIKPLFNKPVIVVLNKIDLLTEEDLSEIEKELEKEGEEVIKI 147
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 31.6 bits (73), Expect = 1.0
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 11/83 (13%)
Query: 142 VDTPGILSGEK---QRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALR 198
VDTPGI ++ + +++ + VD ++ + DA + I +E L+
Sbjct: 58 VDTPGIHKPKRALNRAMNKA-----AWSSLKD-VDLVLFVVDADE-KIGPGDEFILEKLK 110
Query: 199 GHDDKIRIVLNKADMV-DHQQLM 220
+ +VLNK D+V D ++L+
Sbjct: 111 KVKTPVILVLNKIDLVKDKEELL 133
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 31.5 bits (72), Expect = 1.1
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 58 TVMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIA 97
T+M+VG+ GKTTFI L + E D A
Sbjct: 25 TIMVVGESGLGKTTFINTLFGT-----SLVDETEIDDIRA 59
Score = 31.5 bits (72), Expect = 1.1
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 308 TVMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIA 347
T+M+VG+ GKTTFI L + E D A
Sbjct: 25 TIMVVGESGLGKTTFINTLFGT-----SLVDETEIDDIRA 59
>gnl|CDD|218615 pfam05504, Spore_GerAC, Spore germination B3/ GerAC like,
C-terminal. The GerAC protein of the Bacillus subtilis
spore is required for the germination response to
L-alanine. Members of this family are thought to be
located in the inner spore membrane. Although the
function of this family is unclear, they are likely to
encode the components of the germination apparatus that
respond directly to this germinant, mediating the
spore's response.
Length = 171
Score = 30.6 bits (70), Expect = 1.1
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 10/51 (19%)
Query: 459 KELIKKLDEIYKQIQREYQISPV-FGKK---------KELIKKLDEIYKQI 499
KE+ K+++++ K++Q+EY++ FG+ K++ K DEI+
Sbjct: 104 KEIKKEIEKLIKKLQKEYKVDIFGFGEYLRRKYPKLWKKIKKNWDEIFPNA 154
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 31.1 bits (71), Expect = 1.1
Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 32/100 (32%)
Query: 58 TVMLVGQYSTGKTTFIRYLLE---RDFPGIHIGPEPT--TD-RFIAVMYDEREGSVPFSP 111
V + G GKT+ + L+E + P + +G +P TD R ER S+ +P
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQ---ERGISIKSNP 58
Query: 112 L-----DKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPG 146
+ D GK S+L I+I+DTPG
Sbjct: 59 ISLVLEDSKGK---SYL---------------INIIDTPG 80
>gnl|CDD|238560 cd01140, FatB, Siderophore binding protein FatB. These proteins
have been shown to function as ABC-type initial
receptors in the siderophore-mediated iron uptake in
some eubacterial species. They belong to the TroA
superfamily of periplasmic metal binding proteins that
share a distinct fold and ligand binding mechanism. A
typical TroA protein is comprised of two globular
subdomains connected by a single helix and can bind
their ligands in the cleft between these domains.
Length = 270
Score = 31.1 bits (71), Expect = 1.2
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 446 KDMPSVFGKEGKKKELIKKLDEIYKQIQREYQISPVFGKKKELI 489
+ + +FGKE + KEL+ ++D + + + GKKK L+
Sbjct: 114 ETLGKIFGKEEEAKELVAEIDASIAEAKSAAK-----GKKKALV 152
>gnl|CDD|148602 pfam07088, GvpD, GvpD gas vesicle protein. This family consists of
several archaeal GvpD gas vesicle proteins. GvpD is
thought to be involved in the regulation of gas vesicle
formation.
Length = 484
Score = 31.4 bits (71), Expect = 1.2
Identities = 34/139 (24%), Positives = 53/139 (38%), Gaps = 29/139 (20%)
Query: 53 FDAKP--TVMLVGQYSTGKTTF-IRYL--LERDFPGIHIGPEPTTDRFIAVMYDEREGSV 107
FD T+++ G TGKT F IR L L R +++ + MY E GS
Sbjct: 5 FDGDFGKTLLINGAPGTGKTLFTIRGLDVLRRHHDVLYVSTR-VDQETVHEMYFEGHGS- 62
Query: 108 PFSPLDKFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEW 167
LDK + L+ Q I+ T + EK +D ++ +
Sbjct: 63 ----LDK-----TAILDLLQDPF----------ILPTDVDVPFEKLNLDSLLEWVDAINA 103
Query: 168 FAERVDRIILLFDAHKLDI 186
E R+ + FD+ +L
Sbjct: 104 AGE---RLTIAFDSWELIY 119
Score = 29.1 bits (65), Expect = 6.5
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 303 FDAKP--TVMLVGQYSTGKTTF-IRYL--LERDFPGIHIGPEPTTDRFIAVMYDEREGSV 357
FD T+++ G TGKT F IR L L R +++ + MY E GS+
Sbjct: 5 FDGDFGKTLLINGAPGTGKTLFTIRGLDVLRRHHDVLYVSTR-VDQETVHEMYFEGHGSL 63
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 30.7 bits (70), Expect = 1.4
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 9/56 (16%)
Query: 170 ERVDRIILLFDA---HKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRV 222
+D ++ + D DI ++ I D IV+NK D+ +
Sbjct: 113 LGLDGVVTVVDVAETEGEDIPEKAPDQIAF----AD--LIVINKTDLAPAVADLEK 162
>gnl|CDD|215682 pfam00055, Laminin_N, Laminin N-terminal (Domain VI).
Length = 237
Score = 30.9 bits (70), Expect = 1.4
Identities = 28/113 (24%), Positives = 40/113 (35%), Gaps = 25/113 (22%)
Query: 17 ETVLEGLKKVYKNKLLPLEQAYHFH----DFHSPPYEDADFDAKPTVMLVGQYSTGKT-- 70
ET+ G++ L LE +HF F + +P M+ + S T
Sbjct: 75 ETMQNGVQYPNVTITLDLEAEFHFTYVIIKFKTF---------RPAAMIYERSSDFGTWI 125
Query: 71 --TFIRYLLERDFPGIHIGPEPTTDRFIAVMYDER--------EGSVPFSPLD 113
+ Y E +PGI P T V+ R EG V FS L+
Sbjct: 126 PYQYYAYSCESTYPGIPRRPIRTGRAEDDVICTSRYSDIEPLTEGEVIFSTLE 178
>gnl|CDD|191140 pfam04960, Glutaminase, Glutaminase. This family of enzymes
deaminates glutamine to glutamate EC:3.5.1.2.
Length = 286
Score = 31.1 bits (71), Expect = 1.4
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 9/65 (13%)
Query: 335 HIGPEPTTDRFIAVMYDEREGSVPGN------ALVV-DPKKQFRPLDKFGNSFLNRFQCS 387
+G EP+ D F +++ E E P N A+VV K ++ FL F
Sbjct: 65 RVGKEPSGDPFNSIVQLETEKGKPRNPMINAGAIVVTSLLKGRTSAERLD--FLLSFVRK 122
Query: 388 LVNSP 392
L +
Sbjct: 123 LAGNE 127
Score = 30.7 bits (70), Expect = 1.6
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 85 HIGPEPTTDRFIAVMYDEREGSVPFSPL 112
+G EP+ D F +++ E E P +P+
Sbjct: 65 RVGKEPSGDPFNSIVQLETEKGKPRNPM 92
>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 = 30.6 bits (70), Expect = 1.5
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 12/73 (16%)
Query: 139 ISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEA-L 197
I ++D PGI+ G RG V A D I+++ DA K + R +E L
Sbjct: 49 IQLLDLPGIIEGASDGKGRGRQVIAV----ARTADLILIVLDATK---PEGQREILEREL 101
Query: 198 RGHDDKIRIVLNK 210
G + I LNK
Sbjct: 102 EG----VGIRLNK 110
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of RNase
L inhibitor. The ABC ATPase RNase L inhibitor (RLI) is
a key enzyme in ribosomal biogenesis, formation of
translation preinitiation complexes, and assembly of HIV
capsids. RLI's are not transport proteins, and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains, which
are arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity more than 48%. The high degree of evolutionary
conservation suggests that RLI performs a central role
in archaeal and eukaryotic physiology.
Length = 177
Score = 29.8 bits (67), Expect = 2.1
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 286 DLIKRARLAKAPYEDADFDAKPTVMLVGQYSTGKTTFIRYL 326
D +KR + E + +VG TGKTT ++ L
Sbjct: 5 DCVKRYGVFFLLVELGVVKEGEVIGIVGPNGTGKTTAVKIL 45
>gnl|CDD|226966 COG4607, CeuA, ABC-type enterochelin transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 320
Score = 30.4 bits (69), Expect = 2.4
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 450 SVFGKEGKKKELIKKLDEIYKQIQREYQISPVFGKK 485
+FGKE + KEL+ +D I + + GK
Sbjct: 164 KIFGKEEEAKELLADID---ASIAAAKEKAAGKGKT 196
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 30.3 bits (69), Expect = 2.5
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 139 ISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDI 186
I ++D PGI+ G RG V A D II++ D +
Sbjct: 112 IQLLDLPGIIEGASSGRGRGRQVLSV----ARNADLIIIVLDVFEDPH 155
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 30.5 bits (69), Expect = 2.7
Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 20/116 (17%)
Query: 440 IISALRKDMPSVFGKEGKKKELIKKLDEIYKQIQREYQISP------VFGKKKELIKKLD 493
I+ L+K++ V+G K I++L E+Y + ++ YQ+S + + + L
Sbjct: 96 ILEELKKELK-VYGSLADKSGFIEQLAELYTEFKK-YQLSVEDLEDTADEQSLKKLHDLS 153
Query: 494 EIYKQI-QREY--QISPGDF-----PKVEKMQELLQHH----DFTKFQTLRPRLIE 537
IY++ Y + P D K++K ++L Q FT+F R+IE
Sbjct: 154 LIYEEFEANLYNNYLDPEDSLSRLADKIKKSEQLKQAAIVIDGFTRFSPEEYRVIE 209
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 29.4 bits (67), Expect = 2.8
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 170 ERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRV 222
E + ++LL DA + +E L IVL KAD + +L +V
Sbjct: 80 ENLKGVVLLIDARHG-PTPIDLEMLEFLEELGIPFLIVLTKADKLKKSELAKV 131
>gnl|CDD|172739 PRK14251, PRK14251, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 30.0 bits (67), Expect = 2.8
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 52 DFDAKPTVMLVGQYSTGKTTFIRYL--LERDFPGIHIGPE 89
DF+ K L+G GK+TF+R L + D I I E
Sbjct: 26 DFEEKELTALIGPSGCGKSTFLRCLNRMNDDIENIKITGE 65
Score = 30.0 bits (67), Expect = 2.8
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 302 DFDAKPTVMLVGQYSTGKTTFIRYL--LERDFPGIHIGPE 339
DF+ K L+G GK+TF+R L + D I I E
Sbjct: 26 DFEEKELTALIGPSGCGKSTFLRCLNRMNDDIENIKITGE 65
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 29.5 bits (66), Expect = 2.9
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 277 RNAALRKLNDLIKRARLAKAPYEDADFDAKPTVMLVGQYSTGKTTFIRYLLER 329
R L +L D ++RAR P+V+L G TGKT+ +R LLE
Sbjct: 5 REEELERLLDALRRARS----------GGPPSVLLTGPSGTGKTSLLRELLEG 47
>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 = 30.1 bits (69), Expect = 3.0
Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 12/93 (12%)
Query: 131 VNSPVLKGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISD-- 188
V + I D PG++ G + G+ F +E R ++ L D D SD
Sbjct: 199 VRVDDGRSFVIADIPGLIEGASEGAGLGHRFLKHIE----RTRVLLHLIDISPEDGSDPI 254
Query: 189 -EFRRSIEALRGHD----DKIRI-VLNKADMVD 215
++ L+ + +K RI VLNK D++D
Sbjct: 255 EDYEIIRNELKKYSPELAEKPRIVVLNKIDLLD 287
>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 = 29.3 bits (67), Expect = 3.1
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 137 KGISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFD-AHKLDISDEFRRSIE 195
+ I D PG++ G + G+ F +E R ++ + D + + D +++
Sbjct: 48 RSFVIADIPGLIEGASEGKGLGHRFLRHIE----RTRVLLHVIDLSGEDDPVEDYETIRN 103
Query: 196 ALRGHDDKIR-----IVLNKADMVD 215
L ++ + +VLNK D++D
Sbjct: 104 ELEAYNPGLAEKPRIVVLNKIDLLD 128
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 3.4
Identities = 14/61 (22%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 441 ISALRKDMPSVFGKEGKKKELIKKLDEIYKQI-QREYQISPVFGKKKELIKKLDEIYKQI 499
I+ + ++P + + K ++ +K+L+E+ ++I + E ++ + G K++L +K+ E+ ++I
Sbjct: 209 INEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERI 268
Query: 500 Q 500
+
Sbjct: 269 E 269
>gnl|CDD|238932 cd01972, Nitrogenase_VnfE_like, Nitrogenase_VnfE_like: VnfE subunit
of the VnfEN complex_like. This group in addition to
VnfE contains a subset of the alpha subunit of the
nitrogenase MoFe protein and NifE-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protein
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 426
Score = 29.7 bits (67), Expect = 3.9
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 424 RLFEDRSSTSNSVQAYIISAL-RKDMPSVFGKEGKKKELIKKLDEIYK 470
RL+ + + + L KD+ VFG E K ++ IK+ YK
Sbjct: 44 RLYRCGEMRRGLNEPVLSTNLTEKDV--VFGGEKKLEDTIKEAYSRYK 89
>gnl|CDD|236600 PRK09636, PRK09636, RNA polymerase sigma factor SigJ; Provisional.
Length = 293
Score = 29.5 bits (67), Expect = 4.0
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 5/25 (20%)
Query: 528 FQTLRPRLIEVADKML-----AEDI 547
F+ LRP L+ VA +ML AEDI
Sbjct: 10 FEPLRPHLLSVAYRMLGSVADAEDI 34
>gnl|CDD|233913 TIGR02536, eut_hyp, ethanolamine utilization protein. This family
of proteins is found in operons for the polyhedral
organelle-based degradation of ethanolamine. This family
is not found in proteobacterial species which otherwise
have the same suite of genes in the eut operon.
Proteobacteria have two genes that are not found in
non-proteobacteria which may complement this genes
function, a phosphotransacetylase (pfam01515) and the
EutJ protein (TIGR02529) of unknown function.
Length = 207
Score = 29.4 bits (66), Expect = 4.1
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 465 LDEIYKQIQREYQISPVFGKKKELIKKLD---EIYKQIQREYQISPGDFPKVEKMQELL 520
+DE+ K+I E S +KK ++ D I +++ +E+ +S +K+ ++L
Sbjct: 1 MDELIKRITEEICTSQQLEEKKYIVALGDSKHAIPEEMLKEFDVSWVT--SEQKLADIL 57
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.9 bits (68), Expect = 4.2
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 421 VNRRLFEDRSSTSNSVQAYIISALRKDMPSVFGKEGKKKELIKKLDEIYKQIQ-REYQIS 479
V E+ S+ IS + + V KEL +++E K++ ++
Sbjct: 152 VPEDKLEELKLESDVENVEYISTDKGYVYVVVVVL---KELSDEVEEELKKLGFERLEL- 207
Query: 480 PVFGKKKELIKKLDEIYKQIQREYQ 504
G ELI+++ E ++I++E +
Sbjct: 208 EEEGTPSELIREIKEELEEIEKERE 232
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 29.1 bits (65), Expect = 4.4
Identities = 12/54 (22%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 454 KEGKKKELIKKLDEIYKQIQREYQISPVFGK---KKELIKKLDEIYKQIQREYQ 504
+ K+KE ++L+E+ K+++ + K +KE K+L+E+ ++++ +
Sbjct: 148 LKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEELEELLE 201
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 28.7 bits (65), Expect = 4.5
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 309 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPGNALVVDPKK 368
+++ G STGKTT + L R +P + PE Y E + + G+AL
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVV---PEY------GREYIEEQLADGGDALPWADLL 52
Query: 369 QFR 371
F
Sbjct: 53 AFA 55
Score = 27.9 bits (63), Expect = 8.7
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 59 VMLVGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFGK 117
+++ G STGKTT + L R +P + PE + +I + ++P++ L F +
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVV---PEYGRE-YIEEQLADGGDALPWADLLAFAE 56
>gnl|CDD|205044 pfam12725, DUF3810, Protein of unknown function (DUF3810). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 333 and 377 amino
acids in length. There is a conserved HEXXH sequence
motif that is characteristic of metallopeptidases. This
family may therefore belong to an as yet uncharacterized
family of peptidase enzymes.
Length = 317
Score = 29.5 bits (67), Expect = 4.8
Identities = 11/59 (18%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 459 KELIKKLDEIYKQIQR-EYQISPVFGKKKELIKKLDEIYKQIQREYQISPGDFPKVEKM 516
+ LI++L+E+ Q+ + + + K+E+ K+ + Y+++ +Y +P +
Sbjct: 104 EYLIERLNELRLQLTEDDSGVVKLPYSKEEIFKEAVKGYEKLSEKYPFLSYYYPSPKPS 162
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family
is characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins),
and a characteristic second domain called COR
(C-terminal of Roc). A kinase domain and diverse
regulatory domains are also often found in Roco
proteins. Their functions are diverse; in Dictyostelium
discoideum, which encodes 11 Roco proteins, they are
involved in cell division, chemotaxis and development,
while in human, where 4 Roco proteins (LRRK1, LRRK2,
DAPK1, and MFHAS1) are encoded, these proteins are
involved in epilepsy and cancer. Mutations in LRRK2
(leucine-rich repeat kinase 2) are known to cause
familial Parkinson's disease.
Length = 161
Score = 28.8 bits (65), Expect = 4.8
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 54 DAKPTVMLVGQYSTGKTTFIRYLLERDFPG 83
+AK +MLVGQ GKT+ + L+ F G
Sbjct: 1 EAK--LMLVGQGGVGKTSLCKQLIGEKFDG 28
Score = 28.8 bits (65), Expect = 4.8
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 304 DAKPTVMLVGQYSTGKTTFIRYLLERDFPG 333
+AK +MLVGQ GKT+ + L+ F G
Sbjct: 1 EAK--LMLVGQGGVGKTSLCKQLIGEKFDG 28
>gnl|CDD|234298 TIGR03659, IsdE, heme ABC transporter, heme-binding protein isdE.
This family of ABC substrate-binding proteins is
observed primarily in close proximity with proteins
localized to the cell wall and bearing the NEAT (NEAr
Transporter, pfam05031) heme-binding domain. IsdE has
been shown to bind heme and is involved in the process
of scavenging heme for the purpose of obtaining iron.
Length = 289
Score = 29.5 bits (67), Expect = 4.8
Identities = 9/41 (21%), Positives = 26/41 (63%), Gaps = 5/41 (12%)
Query: 446 KDMPSVFGKEGKKKELIKKLDEIYKQIQREYQISPVFGKKK 486
++ +G+E + ++L+K+++E +++++ + GKKK
Sbjct: 132 TELGEKYGREEQAEKLVKEINEKEAEVKKKVK-----GKKK 167
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 29.8 bits (68), Expect = 4.9
Identities = 16/102 (15%), Positives = 49/102 (48%), Gaps = 19/102 (18%)
Query: 459 KELIKKLDEIYKQIQREYQISPVFGKKK----ELIKKLDEIYKQIQRE-------YQISP 507
+E+ +++D++Y ++RE + K + ++ E K+++ E Y ++
Sbjct: 285 EEIQERIDQLYDILEREVKARKYVEKNSDTLPDFLEHAKEQNKELKEEIDRVKQSYTLNE 344
Query: 508 GDFPKVEKMQELLQHHDFTKFQTLRPRLIEVADKMLAEDIAH 549
+ V ++++ L ++L + E+ +++ ++IA+
Sbjct: 345 SELESVRQLEKQL--------ESLEKQYDEITERIAEQEIAY 378
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 29.6 bits (67), Expect = 4.9
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 15/59 (25%)
Query: 49 EDADFDAKPTVMLVGQYSTGKTTFIRYLLER------DFPGIHIGPEPTTDRFIAVMYD 101
E A+ P V +VG+ + GK+T + +L R D PG+ T DR V YD
Sbjct: 31 EAAEGGPLPVVAVVGRPNVGKSTLVNRILGRREAVVEDVPGV------TRDR---VSYD 80
Score = 29.6 bits (67), Expect = 4.9
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 15/59 (25%)
Query: 299 EDADFDAKPTVMLVGQYSTGKTTFIRYLLER------DFPGIHIGPEPTTDRFIAVMYD 351
E A+ P V +VG+ + GK+T + +L R D PG+ T DR V YD
Sbjct: 31 EAAEGGPLPVVAVVGRPNVGKSTLVNRILGRREAVVEDVPGV------TRDR---VSYD 80
>gnl|CDD|183486 PRK12381, PRK12381, bifunctional succinylornithine
transaminase/acetylornithine transaminase; Provisional.
Length = 406
Score = 29.3 bits (66), Expect = 5.0
Identities = 31/111 (27%), Positives = 45/111 (40%), Gaps = 35/111 (31%)
Query: 81 FPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLDKFGKFGNSFLNRFQCSLVNSPVLKGIS 140
FP IG TT++ +VM G+ +G GN S V VL
Sbjct: 258 FP---IGAMLTTEKCASVMTVGTHGTT-------YG--GNPL-----ASAVAGKVL---E 297
Query: 141 IVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFR 191
+++TP +L+G KQR D WF ER++ I + + E R
Sbjct: 298 LINTPEMLNGVKQRHD----------WFVERLNTI-----NARYGLFSEIR 333
>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 = 29.4 bits (66), Expect = 5.1
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 11/84 (13%)
Query: 135 VLKG--ISIVDTPGILSGEKQRVDRGYDFTGVLEWF--AERVDRIILLFDAHKLDISDEF 190
L G I ++DT GI + + G+ + F ++ D +I + DA + D+F
Sbjct: 247 ELNGILIKLLDTAGI-----REHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDF 301
Query: 191 RRSIEALRGHDDKIRIVLNKADMV 214
I L +VLNK D+
Sbjct: 302 L--IIDLNKSKKPFILVLNKIDLK 323
>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 = 28.6 bits (65), Expect = 5.2
Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 8/93 (8%)
Query: 139 ISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALR 198
++DT GI ++ + E E D I+ + D + ++ + LR
Sbjct: 47 FILIDTGGIEPDDEGISKEIREQA---EIAIEEADVILFVVDG-REGLTPADEEIAKYLR 102
Query: 199 GHDDKIRIVLNKADMVDHQQLMRVYGALMWSLG 231
+ +V+NK D + ++ + +SLG
Sbjct: 103 KSKKPVILVVNKIDNIKEEEEAAEF----YSLG 131
>gnl|CDD|216245 pfam01015, Ribosomal_S3Ae, Ribosomal S3Ae family.
Length = 195
Score = 29.0 bits (66), Expect = 5.3
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 432 TSNSVQAYIISALRKDMPSVFGKEGKK---KELIKKL------DEIYKQIQREYQISPVF 482
T Q A+RK M + KE + KE ++KL +I K ++ Y + V
Sbjct: 125 TKKRAQTSQKRAIRKKMTEIITKEASELDFKEFVQKLIPGSIAKDIEKAAKKIYPLRRVE 184
Query: 483 GKKKELIKK 491
+K +++K+
Sbjct: 185 IRKVKVLKR 193
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 28.8 bits (65), Expect = 5.9
Identities = 31/148 (20%), Positives = 50/148 (33%), Gaps = 30/148 (20%)
Query: 58 TVMLVGQYSTGKTTF-IRYLLE---RDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPLD 113
+ +L G TGKTTF +++L R PG+++ E + + I L+
Sbjct: 1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENA---ESLGWDLERLE 57
Query: 114 KFGKFGNSFLNRFQCSLVNSPVLKGISIVDTPGILSGEKQRVDRGYD--FTGVLEWFAER 171
G +V+ D I E + E+ A+R
Sbjct: 58 DEGLLA----------IVD---------ADPDEIGPAESSLRLELIQRLKDAIEEFKAKR 98
Query: 172 V--DRIILLFDAHKLDISDEFRRSIEAL 197
V D + L + E RR + AL
Sbjct: 99 VVIDSVSGLLLMEQSTARLEIRRLLFAL 126
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 28.7 bits (65), Expect = 6.2
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 50 DADFDAKP--TVMLVGQYSTGKTTFIRYLL 77
D +F KP TV +VG GKTT I L+
Sbjct: 21 DINFSIKPGETVAIVGPTGAGKTTLINLLM 50
Score = 28.7 bits (65), Expect = 6.2
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 300 DADFDAKP--TVMLVGQYSTGKTTFIRYLL 327
D +F KP TV +VG GKTT I L+
Sbjct: 21 DINFSIKPGETVAIVGPTGAGKTTLINLLM 50
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 28.8 bits (65), Expect = 6.2
Identities = 27/128 (21%), Positives = 53/128 (41%), Gaps = 23/128 (17%)
Query: 210 KADMVDHQQLMRVYGALMWSLGKVLQTPEVARVY---IGSFWDQPLVHDVNRRLFEDEEQ 266
+ ++ ++L+ L+ L + PE A++ + + + L ++ +L ED +
Sbjct: 111 RKELSALRELLE---RLLAGLALQRRDPEGAKLLERLLEAGVSEELARELLEKLPEDLDA 167
Query: 267 DLFKDLQSLPRNAALRKLNDLIKRARLAKAPYEDADFDAKPTVMLVGQYSTGKTTFI--- 323
+ A R L + ++ L P ED + + LVG GKTT +
Sbjct: 168 E-----------DAWRWLREALEG-MLPVKPEEDPILERGGVIALVGPTGVGKTTTLAKL 215
Query: 324 --RYLLER 329
R++LE
Sbjct: 216 AARFVLEH 223
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 28.9 bits (65), Expect = 6.4
Identities = 34/171 (19%), Positives = 58/171 (33%), Gaps = 43/171 (25%)
Query: 170 ERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRVYGALMWS 229
+ VD ++ + DA D +E + K+ +VLNKAD+
Sbjct: 33 KSVDVVVEVVDA--RDPLGTRNPELERIVKEKPKL-LVLNKADLAP-------------- 75
Query: 230 LGKVLQTPEVARVYIGSFWDQPLVHDVNRRLFEDEEQDLFKDLQSLPRNAALRKLNDLIK 289
T + + + +P+ V+ + Q K R A + + IK
Sbjct: 76 ---KEVTKKWKKYFKKEEGIKPI--FVSAK----SRQGGKKI-----RKALEKLSEEKIK 121
Query: 290 RARLAKAPYEDADFDAKPTVMLVGQYSTGKTTFIRYLLER------DFPGI 334
R + V +VG + GK+T I LL + + PG
Sbjct: 122 RLKKKGLLKRKIR------VGVVGYPNVGKSTLINRLLGKKVAKTSNRPGT 166
>gnl|CDD|234537 TIGR04313, aro_clust_Mycop, aromatic cluster surface protein.
Members of this family are absolutely restricted to the
Mollicutes (Mycoplasma and Ureaplasma). All have a
signal peptide, usually of the lipoprotein type,
suggesting surface expression. Most members have lengths
of about 280 residues but some members have a nearly
full-length duplication. The mostly nearly invariant
residue, a Trp,is part of a strongly conserved 9-residue
motif, [ND]-W-[LY]-[WF]-X-[LF]-X-N-[LI], where X usually
is hydrophobic. Because the hydrophobic six-residue core
of this motif almost always contains three to four
aromatic residues, we name this family aromatic cluster
surface protein. Multiple paralogs may occur in a given
Mycoplasma, usually clustered on the genome.
Length = 297
Score = 28.9 bits (65), Expect = 6.7
Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 457 KKKELIKKLDEIYKQIQREYQISPVFGKK--KELIKKLDEIYKQ 498
+L+K E I F ++ KKL+E++ +
Sbjct: 89 LYLKLLKLSLEYLNNINNSSSNDSDFFSYLYEKSKKKLNELFSK 132
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 28.9 bits (65), Expect = 6.8
Identities = 12/51 (23%), Positives = 25/51 (49%)
Query: 457 KKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQIQREYQISP 507
K+ E+ KL E+ K+ + + F IK L+ ++++++ Q S
Sbjct: 77 KRDEINAKLQELRKEYRELKEKRNEFNLGGRSIKSLEREIERLEKKQQTSV 127
>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex. Med21 has been
known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in
Drosophila. The heterodimer of the two subunits Med7 and
Med21 appears to act as a hinge between the middle and
the tail regions of Mediator.
Length = 132
Score = 28.0 bits (63), Expect = 6.8
Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 439 YIISALRKDMPSVFGKEGKKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQ 498
Y+I +L P + E ++ IK+L+E ++++ E + +K++L+KK++ + ++
Sbjct: 75 YLIDSL----PGIESSEEEQLRRIKELEEELREVEAERE--EAVKEKEKLLKKVEALLRE 128
Query: 499 IQR 501
I R
Sbjct: 129 IAR 131
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 29.2 bits (65), Expect = 7.2
Identities = 15/49 (30%), Positives = 22/49 (44%)
Query: 340 PTTDRFIAVMYDEREGSVPGNALVVDPKKQFRPLDKFGNSFLNRFQCSL 388
P + +A M G GN P++ R L++ FL+RF SL
Sbjct: 335 PARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSL 383
>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 = 28.8 bits (65), Expect = 7.5
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 139 ISIVDTPGILSGEKQRVDR 157
++I+DTPG+L + QRV+R
Sbjct: 81 LNIIDTPGLLESQDQRVNR 99
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1); Provisional.
Length = 1466
Score = 29.2 bits (65), Expect = 7.7
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 46 PPYEDADF--DAKPTVMLVGQYSTGKTTFIRYLL 77
P Y+D F D+K T +VG+ +GK+T + L+
Sbjct: 1182 PIYKDLTFSCDSKKTTAIVGETGSGKSTVMSLLM 1215
>gnl|CDD|212008 cd00089, HR1, Protein kinase C-related kinase homology region 1
(HR1) domain that binds Rho family small GTPases. The
HR1 domain, also called the ACC (anti-parallel
coiled-coil) finger domain or Rho-binding domain binds
small GTPases from the Rho family. It is found in Rho
effector proteins including PKC-related kinases such as
vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases
C, as well as in rhophilins and Rho-associated kinase
(ROCK). Rho family members function as molecular
switches, cycling between inactive and active forms,
controlling a variety of cellular processes. HR1 domains
may occur in repeat arrangements (PKN contains three HR1
domains), separated by a short linker region.
Length = 68
Score = 26.5 bits (59), Expect = 8.1
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 454 KEGKKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKLDEIYKQIQRE 502
KE K +E + L ++Y + + ++ V KE +K+D + +Q++R
Sbjct: 16 KELKIREGAENLLKLYSNPKVKKDLAEVQLNLKESKEKIDLLKRQLERY 64
>gnl|CDD|214354 CHL00074, rps14, ribosomal protein S14.
Length = 100
Score = 27.1 bits (61), Expect = 8.7
Identities = 9/39 (23%), Positives = 22/39 (56%)
Query: 454 KEGKKKELIKKLDEIYKQIQREYQISPVFGKKKELIKKL 492
+E K+++L++K + +++E + +K E+ KL
Sbjct: 9 REKKRQKLVQKYHLKRRSLKKEIKKVSSLSEKWEIHGKL 47
>gnl|CDD|215096 PLN00192, PLN00192, aldehyde oxidase.
Length = 1344
Score = 28.9 bits (65), Expect = 8.9
Identities = 34/126 (26%), Positives = 49/126 (38%), Gaps = 22/126 (17%)
Query: 18 TVLEGLKKVYKNKLLPLEQAYHFH------DFHSPPYEDADFDAKPTVMLVGQYSTG--- 68
T E LKK K+ LL Y ++ + S E +FD ++VG TG
Sbjct: 214 TFPEFLKKEIKSSLLLDSSRYRWYTPVSVEELQSL-LESNNFDGVSVKLVVGNTGTGYYK 272
Query: 69 ------KTTFIRYLLE-----RDFPGIHIGPEPTTDRFIAVMYDEREGSVPFSPL-DKFG 116
K IR++ E RD GI IG T + I + +E + F + D
Sbjct: 273 DEELYDKYIDIRHIPELSMIRRDEKGIEIGAVVTISKAIEALREESKSEYVFKKIADHME 332
Query: 117 KFGNSF 122
K + F
Sbjct: 333 KIASRF 338
>gnl|CDD|212019 cd11629, HR1_FBP17, Protein kinase C-related kinase homology region
1 (HR1) Rho-binding domain of Formin Binding Protein 17.
FBP17, also called FormiN Binding Protein 1 (FNBP1), is
involved in dynamin-mediated endocytosis. It is
recruited to clathrin-coated pits late in the
endocytosis process and may play a role in the
invagination and scission steps. FBP17 binds in vivo to
tankyrase, a protein involved in telomere maintenance
and mitogen activated protein kinase (MAPK) signaling.
It also binds to the Fas ligand and may be implicated in
the inflammatory response. FBP17 contains an N-terminal
F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs)
domain, central HR1 domain, and a C-terminal SH3 domain.
HR1 domains are anti-parallel coiled-coil (ACC) domains
that bind small GTPases from the Rho family; the HR1
domain of the related protein, CIP4, binds Cdc42 and
TC10. Translocation of CIP4 is facilitated by its
binding to TC10 at the plasma membrane.
Length = 77
Score = 26.5 bits (58), Expect = 8.9
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 13/60 (21%)
Query: 455 EGKKKELIKKLDEIYKQIQRE-------------YQISPVFGKKKELIKKLDEIYKQIQR 501
E ++K+L +K+DE+ K IQ+E Y +P G + +L+EI + I++
Sbjct: 2 EQRRKKLQQKVDELNKDIQKEMDQRDALTKMKDVYIKNPQMGDPASVDHRLEEITQNIEK 61
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 28.6 bits (64), Expect = 9.3
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 454 KEGKKKELIKKLDEIYKQIQREYQISPVFGKKK-ELIKKLDEIYKQIQREYQIS 506
K+ + + L K+LDE+ K++Q++ Q + +KK E K + + + +++ + S
Sbjct: 112 KDKELELLEKELDELSKELQKQLQNTAEIIEKKRENNKNEERLKFENEKKLEES 165
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 28.7 bits (65), Expect = 9.4
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 446 KDMPSVFGKEGKKKELIKKLDEIYK 470
KD+ VFG E K K+ IK+ E +
Sbjct: 65 KDI--VFGGEKKLKKAIKEAYERFP 87
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 28.8 bits (65), Expect = 9.7
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 4/36 (11%)
Query: 487 ELIKKLDEIYKQIQREYQIS-PGD-FPKVEKMQELL 520
E++ KL+EIY +RE+ IS + F K+EK ++ L
Sbjct: 231 EVMDKLNEIYP--EREFVISRFENVFEKLEKQRDNL 264
>gnl|CDD|238629 cd01304, FMDH_A, Formylmethanofuran dehydrogenase (FMDH) subunit A;
Methanogenic bacteria and archea derive the energy for
autotrophic growth from methanogenesis, the reduction of
CO2 with molecular hydrogen as the electron donor. FMDH
catalyzes the first step in methanogenesis, the
formyl-methanofuran synthesis. In this step, CO2 is
bound to methanofuran and subsequently reduced to the
formyl state with electrons derived from hydrogen.
Length = 541
Score = 28.5 bits (64), Expect = 9.9
Identities = 34/119 (28%), Positives = 45/119 (37%), Gaps = 21/119 (17%)
Query: 13 PEMYETVLEGLKKVYKNKLLPLEQAYH-----FH--------DFHSPPYEDADF-DAKPT 58
P YET LE +K K P Q H FH DF S AD+ +A
Sbjct: 237 PGNYETTLETMKAAEGVKPDPRRQVLHLTHVQFHSYGGTSWRDFESGAERIADYVNANDH 296
Query: 59 VML-VGQYSTGKTTFIRYLLERDFPGIHIGPEPTTDRFI--AVMYDEREGSVPFSPLDK 114
V + VGQ G+TT + D P T +++ + + G VPF K
Sbjct: 297 VTIDVGQVIFGETTTM----TGDGPMQFDLHGLTGLKWVNCDIELETGSGVVPFIYSPK 351
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
0.321 0.139 0.412
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: 29,812,597
Number of extensions: 3077088
Number of successful extensions: 4729
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4675
Number of HSP's successfully gapped: 214
Length of query: 551
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 449
Effective length of database: 6,413,494
Effective search space: 2879658806
Effective search space used: 2879658806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.7 bits)