RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027757
(219 letters)
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 235 bits (601), Expect = 4e-79
Identities = 85/195 (43%), Positives = 113/195 (57%), Gaps = 6/195 (3%)
Query: 19 IKEVEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLI 78
I EFV S+ + + P DD PE A GRSNVGKSSLINAL +K LA TSK PG+TQLI
Sbjct: 4 IHNAEFVTSAPKLEQLPPDDGPEIAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQLI 63
Query: 79 NHFLVNKSWYIVDLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKI 138
N F VN +VDLPGYG+AK + W + Y RE+L GV+LLID+ P +++
Sbjct: 64 NFFEVNDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTRENLKGVVLLIDSRHPLKEL 123
Query: 139 DLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSV 198
DL WL IP+ V TK DK+K KG R + +K ++ ++ I+ SS+
Sbjct: 124 DLQMIEWLKEYGIPVLIVLTKADKLK--KGER-KKQLKKVRKALKFGDDEV---ILFSSL 177
Query: 199 TGLGRDELLLHMSQL 213
G DEL +++
Sbjct: 178 KKQGIDELRAAIAKW 192
>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 = 225 bits (577), Expect = 1e-75
Identities = 80/183 (43%), Positives = 110/183 (60%), Gaps = 5/183 (2%)
Query: 22 VEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHF 81
EFVKS+ + K P DD PE A GRSNVGKSSLINAL +K+LA TSK PG+TQLIN F
Sbjct: 1 AEFVKSAVKLKQLPPDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFF 60
Query: 82 LVNKSWYIVDLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLD 141
VN + +VDLPGYG+AK + W + Y RE+L GV+LL+D P +++DL+
Sbjct: 61 EVNDGFRLVDLPGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLE 120
Query: 142 CANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGL 201
WL IP+ V TK DK+K K ++ +K ++ ++++ + SS+
Sbjct: 121 MIEWLRERGIPVLIVLTKADKLK--KSEL-NKQLKKIKKALKKDADDSV--QLFSSLKKT 175
Query: 202 GRD 204
G D
Sbjct: 176 GID 178
>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 = 215 bits (549), Expect = 1e-71
Identities = 79/173 (45%), Positives = 101/173 (58%), Gaps = 4/173 (2%)
Query: 41 EFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGYGFAKA 100
E A GRSNVGKSSLINAL +K+LA TSK PG+TQLIN F V + +VDLPGYG+AK
Sbjct: 1 EVAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKV 60
Query: 101 PDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIPLTFVFTKC 160
R W + Y NRE+L GV+LLIDA P IDL+ +L IP V TK
Sbjct: 61 SKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKA 120
Query: 161 DKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHMSQL 213
DK+K K + +K ++ + + PP I+ SS G G DEL +++
Sbjct: 121 DKLK--KSEL-AKVLKKIKEEL-NLFNILPPVILFSSKKGTGIDELRALIAEW 169
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 192 bits (490), Expect = 3e-62
Identities = 82/193 (42%), Positives = 107/193 (55%), Gaps = 11/193 (5%)
Query: 19 IKEVEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLI 78
+ +F+ S+ K P+DD PE A GRSNVGKSSLINAL +K LA TSK PG+TQLI
Sbjct: 4 YHKAKFITSAPDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLI 63
Query: 79 NHFLVNKSWYIVDLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKI 138
N F V+ +VDLPGYG+AK P + W + Y R +L GV+LLIDA PP+ +
Sbjct: 64 NFFEVDDELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDL 123
Query: 139 DLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW----IM 194
D + +L IP+ V TK DK+K E K + + E PP ++
Sbjct: 124 DREMIEFLLELGIPVIVVLTKADKLK------KSERNKQLNK-VAEELKKPPPDDQWVVL 176
Query: 195 TSSVTGLGRDELL 207
SS+ G DEL
Sbjct: 177 FSSLKKKGIDELK 189
>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 = 91.6 bits (228), Expect = 6e-24
Identities = 33/120 (27%), Positives = 53/120 (44%), Gaps = 8/120 (6%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQ--LINHFLVNKSWYIVDLPGYGFAKA 100
A++GR NVGKS+LINAL K +A+ S PG T+ ++ + + +VD PG +
Sbjct: 3 ALVGRPNVGKSTLINALTGAK-VAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGAS 61
Query: 101 PDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGR-NNIPLTFVFTK 159
+ +LL++DAS + D + L + P+ V K
Sbjct: 62 EG----KGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>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 = 84.6 bits (210), Expect = 9e-21
Identities = 44/171 (25%), Positives = 65/171 (38%), Gaps = 23/171 (13%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLIN----HFLVNKSWYIVDLPGYGFA 98
AI GR NVGKSSL+NAL+ + + + S PG T+ L ++D PG
Sbjct: 1 AIFGRPNVGKSSLLNALLGQN-VGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEE 59
Query: 99 KAPDVTR--MDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIPLTFV 156
R + VLL++D+ + P + + L P+ V
Sbjct: 60 GGLGRERVEEARQVADR--------ADLVLLVVDSDLTPVEEEAKL-GLLRERGKPVLLV 110
Query: 157 FTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELL 207
K D E + ++ E P P I S++ G G DEL
Sbjct: 111 LNKIDL------VPESEEEELLRERKLELLPDLPV-IAVSALPGEGIDELR 154
>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 = 84.0 bits (208), Expect = 2e-20
Identities = 40/174 (22%), Positives = 63/174 (36%), Gaps = 27/174 (15%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSW-------YIVDLPGY 95
++GR VGKSSL+NAL+ E+ S PG T+ + + K +VD PG
Sbjct: 1 VVVGRGGVGKSSLLNALL-GGEVGEVSDVPGTTRDPD--VYVKELDKGKVKLVLVDTPGL 57
Query: 96 GFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPP--QKIDLDCANWLGRNNIPL 153
+ +LL++D++ + L L + IP+
Sbjct: 58 DEFGGLGREELARLLLRG--------ADLILLVVDSTDRESEEDAKLLILRRLRKEGIPI 109
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELL 207
V K D + ++ +L P S+ TG G DEL
Sbjct: 110 ILVGNKID-------LLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELF 156
>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 = 68.3 bits (168), Expect = 1e-14
Identities = 51/183 (27%), Positives = 77/183 (42%), Gaps = 46/183 (25%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKP-------------GKTQLINHFLVNKSWYI 89
AI+GR NVGKS+L+NALV +K +++ S KP Q+I
Sbjct: 7 AIIGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIYTDDDAQII----------F 55
Query: 90 VDLPGYGFAKAPDVTRMD---WSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWL 146
VD PG K RM WS+ ++ + VL ++DAS + D L
Sbjct: 56 VDTPGIHKPKKKLGERMVKAAWSAL-------KDVDL-VLFVVDASEWIGEGDEFILELL 107
Query: 147 GRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW--IMTSSVTGLGRD 204
++ P+ V K D +K E++ + ++E HP S++ G D
Sbjct: 108 KKSKTPVILVLNKIDLVK------DKEDLLPLLEKLKE---LHPFAEIFPISALKGENVD 158
Query: 205 ELL 207
ELL
Sbjct: 159 ELL 161
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 67.8 bits (167), Expect = 1e-13
Identities = 48/190 (25%), Positives = 67/190 (35%), Gaps = 60/190 (31%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKP-------------GKTQLINHFLVNKSWYI 89
AI+GR NVGKS+L+NALV +K +++ S KP Q+I
Sbjct: 9 AIVGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRHRIRGIVTEDDAQII----------F 57
Query: 90 VDLPGYGFAKAPDVTRMDWSSFTKGYFLNR-------ESLVGV---LLLIDASVPPQKID 139
VD PG LNR SL V L ++DA D
Sbjct: 58 VDTPGI---------------HKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGD 102
Query: 140 LDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW--IMTSS 197
L + P+ V K D +K E + + + E + S+
Sbjct: 103 EFILEKLKKVKTPVILVLNKIDLVK------DKEELLPLLEELSE---LMDFAEIVPISA 153
Query: 198 VTGLGRDELL 207
+ G DELL
Sbjct: 154 LKGDNVDELL 163
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 63.8 bits (156), Expect = 1e-12
Identities = 38/123 (30%), Positives = 59/123 (47%), Gaps = 9/123 (7%)
Query: 32 KDCPKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVD 91
+ D +PE +GRSNVGKS+L+ L KK K+PG T+ NH+ + + D
Sbjct: 2 FETRPDRKPEIVFVGRSNVGKSTLVRELTGKK--VRVGKRPGVTRKPNHYDW-GDFILTD 58
Query: 92 LPGYGF-AKAPDVTRMDWSSFTKGYFL-NRESLVGVLLLIDASVPPQKIDLDCANWLGRN 149
LPG+GF + P + Y N + ++ +L++D + I+ W GR
Sbjct: 59 LPGFGFMSGVPKEVQEKIKDEIVRYIEDNADRILAAVLVVDGKSFIEIIE----RWEGRG 114
Query: 150 NIP 152
IP
Sbjct: 115 EIP 117
>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 = 62.1 bits (152), Expect = 4e-12
Identities = 48/177 (27%), Positives = 82/177 (46%), Gaps = 17/177 (9%)
Query: 38 DRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-----LINHFLVNKSWYIVDL 92
D + AI+GR NVGKSSL+NAL+ +E + S G T+ + + + ++D
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALL-GEERVIVSDIAGTTRDSIDVPFEYD--GQKYTLIDT 57
Query: 93 PGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIP 152
G K ++ S + + V VLL++DAS + DL A +
Sbjct: 58 AGIR-KKGKVTEGIEKYSVLRTLKAIERADV-VLLVLDASEGITEQDLRIAGLILEEGKA 115
Query: 153 LTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPH--HPPWIMTSSVTGLGRDELL 207
L V K D ++ + ++ +K F++ +R P + P + S++TG G D+L
Sbjct: 116 LIIVVNKWDLVE-----KDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLF 167
>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 = 63.3 bits (155), Expect = 8e-12
Identities = 56/188 (29%), Positives = 76/188 (40%), Gaps = 47/188 (25%)
Query: 35 PKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
PK +R I GR N GKSSLINAL +++A+ S PG T V K+ ++L
Sbjct: 2 PKGNRLHIGIFGRRNAGKSSLINALTG-QDIAIVSDVPGTTTDP----VYKA---MELLP 53
Query: 95 YGFAKAPDVTRMDWSSFTKGYFLNRESLVG----------------VLLLIDASVPPQKI 138
G P V +D T G L+ E +G LL++DA V P +
Sbjct: 54 LG----P-VVLID----TAG--LDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEY 102
Query: 139 DLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSV 198
+L+ L IP V K D + + E P I S++
Sbjct: 103 ELELIEELKERKIPYIVVINKIDLGEESAELEKLEKKFGL------------PPIFVSAL 150
Query: 199 TGLGRDEL 206
TG G DEL
Sbjct: 151 TGEGIDEL 158
>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 = 60.1 bits (147), Expect = 1e-11
Identities = 38/175 (21%), Positives = 66/175 (37%), Gaps = 35/175 (20%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINH---FLVNKSWYIVDLPGYGFAK 99
AI+GR NVGKS+L N L +++ A+ S PG T+ + + + ++D G
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRD-AIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPDD 59
Query: 100 APDVTRMDWSSFTKGYFLNRESLVG------VLLLIDASVPPQKIDLDCANWLGRNNIPL 153
+ ++ + +L ++D D + A +L ++ P+
Sbjct: 60 EGISKEI-----------REQAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPV 108
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQL-IRENYPHHPPWIMTSSVTGLGRDELL 207
V K D + +E F L E P S+ G G +LL
Sbjct: 109 ILVVNKID------NIKEEEEAAEFYSLGFGEPIP-------ISAEHGRGIGDLL 150
>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 = 60.9 bits (149), Expect = 6e-11
Identities = 51/189 (26%), Positives = 82/189 (43%), Gaps = 36/189 (19%)
Query: 35 PKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-----LINHFLVNKSWYI 89
+D + AI+GR NVGKS+L+NAL+ +E + S G T+ K + +
Sbjct: 168 EEDGPIKIAIIGRPNVGKSTLVNALL-GEERVIVSDIAGTTRDSIDIPFERN--GKKYTL 224
Query: 90 VDLPGYGFAKAPDVTRMDWSSFTKG---YFLNR------ESLVGVLLLIDASVPPQKIDL 140
+D G + R T+G Y + R + V VLL++DA+ + DL
Sbjct: 225 IDTAG--------IRRK--GKVTEGVEKYSVLRTLKAIERADV-VLLVLDATEGITEQDL 273
Query: 141 DCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPH--HPPWIMTSSV 198
A L V K D +K ++ + F++ +R P P + S++
Sbjct: 274 RIAGLALEAGKALVIVVNKWDLVK------DEKTREEFKKELRRKLPFLDFAPIVFISAL 327
Query: 199 TGLGRDELL 207
TG G D+LL
Sbjct: 328 TGQGVDKLL 336
Score = 57.5 bits (140), Expect = 7e-10
Identities = 41/175 (23%), Positives = 67/175 (38%), Gaps = 35/175 (20%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV---NKSWYIVDLPGYGFAK 99
AI+GR NVGKS+L N L K+ A+ S PG T+ + + + ++D G
Sbjct: 3 AIVGRPNVGKSTLFNRLTGKR-DAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEEDD 61
Query: 100 APDVTRMDWSSFTKGYFLNRESLVG------VLLLIDASVPPQKIDLDCANWLGRNNIPL 153
++ ++ + +L ++D D + A WL ++ P+
Sbjct: 62 DGLDKQI-----------REQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPV 110
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQL-IRENYPHHPPWIMTSSVTGLGRDELL 207
V K D G++ D F L E P S+ G G +LL
Sbjct: 111 ILVANKID------GKKEDAVAAEFYSLGFGEPIP-------ISAEHGRGIGDLL 152
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 59.9 bits (146), Expect = 8e-11
Identities = 48/174 (27%), Positives = 74/174 (42%), Gaps = 28/174 (16%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQL-INHFLVNKSWYI--VDLPGYGFAK 99
AI+GR NVGKS+L+NALV +K +++ S KP T+ I + + I VD PG K
Sbjct: 10 AIIGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIHKPK 68
Query: 100 APDVTRMDWSSFTKGYFLNRE---SLVGV---LLLIDASVPPQKIDLDCANWLGRNNIPL 153
+ G +N+ +L V L ++DA D L + P+
Sbjct: 69 ----HAL-------GELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPV 117
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELL 207
V K DK+K P + +++ P + S++ G D LL
Sbjct: 118 ILVVNKIDKVK------PKTVLLKLIAFLKKLLPFKEI-VPISALKGDNVDTLL 164
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 59.7 bits (145), Expect = 1e-10
Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGYGF 97
++G NVGKS+LIN L+ KK +A TS +PG T+ I ++ Y++D PG
Sbjct: 137 VVGYPNVGKSTLINRLLGKK-VAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIP 189
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 58.7 bits (143), Expect = 2e-10
Identities = 49/191 (25%), Positives = 72/191 (37%), Gaps = 57/191 (29%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-------LINHFLVNKSWYIVDLPGY 95
I+GR NVGKSSL+NAL+ ++ A+ + G T+ +N V +VD G
Sbjct: 221 VIIGRPNVGKSSLLNALLG-RDRAIVTDIAGTTRDVIEEDINLNGIPVR----LVDTAGI 275
Query: 96 ----------GFAKAPDVTRMDWSSFTKGYFLNRESLV---GVLLLIDASVPPQKIDLDC 142
G +A ++++ VL ++DAS P K DL
Sbjct: 276 RETDDVVERIGIERA------------------KKAIEEADLVLFVLDASQPLDKEDLA- 316
Query: 143 ANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLG 202
L P+ V K D + S +L E + I S+ TG G
Sbjct: 317 LIELLPKKKPIIVVLNKAD-------------LVSKIELESEKLANGDAIISISAKTGEG 363
Query: 203 RDELLLHMSQL 213
D L + QL
Sbjct: 364 LDALREAIKQL 374
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 57.6 bits (140), Expect = 6e-10
Identities = 42/179 (23%), Positives = 67/179 (37%), Gaps = 42/179 (23%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINH---FLVNKSWYIVDLPGYGFAK 99
AI+GR NVGKS+L N L ++ +A+ S PG T+ + + + + ++D G
Sbjct: 7 AIVGRPNVGKSTLFNRLTGRR-IAIVSDTPGVTRDRIYGDAEWLGREFILIDTGG----- 60
Query: 100 APDVTRMDWSSFTKGYFLNR----------ESLVGVLLLIDASVPPQKIDLDCANWLGRN 149
+ E+ V +L ++D D + A L R+
Sbjct: 61 --------LDDGDEDELQELIREQALIAIEEADV-ILFVVDGREGITPADEEIAKILRRS 111
Query: 150 NIPLTFVFTKCDKMKVAKGRRPDENIKSFQQL-IRENYPHHPPWIMTSSVTGLGRDELL 207
P+ V K D +K +E F L E P S+ G G +LL
Sbjct: 112 KKPVILVVNKIDNLK------AEELAYEFYSLGFGEPVP-------ISAEHGRGIGDLL 157
Score = 53.3 bits (129), Expect = 2e-08
Identities = 49/197 (24%), Positives = 83/197 (42%), Gaps = 41/197 (20%)
Query: 30 RAKDCPKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-LIN-HFLVN-KS 86
++ + D + AI+GR NVGKSSLINA++ +E + S G T+ I+ F + +
Sbjct: 169 EEEEEEETDPIKIAIIGRPNVGKSSLINAIL-GEERVIVSDIAGTTRDSIDIEFERDGRK 227
Query: 87 WYIVDLPG-------------YGFAKA-PDVTRMDWSSFTKGYFLNRESLVGVLLLIDAS 132
+ ++D G Y A+ + R D VLL+IDA+
Sbjct: 228 YVLIDTAGIRRKGKITESVEKYSVARTLKAIERADV----------------VLLVIDAT 271
Query: 133 VPPQKIDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHP-- 190
+ DL A + + V K D + + ++ F++ +R P
Sbjct: 272 EGISEQDLRIAGLIEEAGRGIVIVVNKWDLV-----EEDEATMEEFKKKLRRKLPFLDFA 326
Query: 191 PWIMTSSVTGLGRDELL 207
P + S++TG G D+L
Sbjct: 327 PIVFISALTGQGLDKLF 343
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 57.0 bits (139), Expect = 1e-09
Identities = 39/175 (22%), Positives = 68/175 (38%), Gaps = 35/175 (20%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINH---FLVNKSWYIVDLPGYGFAK 99
AI+GR NVGKS+L N L K+ A+ + PG T+ + + + + ++D G
Sbjct: 5 AIVGRPNVGKSTLFNRLTGKR-DAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPDD 63
Query: 100 APDVTRMDWSSFTKGYFLNRESLVG------VLLLIDASVPPQKIDLDCANWLGRNNIPL 153
++ ++ + +L ++D D + A L ++N P+
Sbjct: 64 DGFEKQI-----------REQAELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPV 112
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQL-IRENYPHHPPWIMTSSVTGLGRDELL 207
V K D + + F L + E YP S+ G G +LL
Sbjct: 113 ILVVNKVDGPD------EEADAYEFYSLGLGEPYP-------ISAEHGRGIGDLL 154
Score = 53.9 bits (131), Expect = 1e-08
Identities = 52/194 (26%), Positives = 83/194 (42%), Gaps = 47/194 (24%)
Query: 35 PKDDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-----LINHFLVNKSWYI 89
+D+ + AI+GR NVGKSSLINAL+ +E + S G T+ + + +
Sbjct: 169 EEDEPIKIAIIGRPNVGKSSLINALL-GEERVIVSDIAGTTRDSIDTPFERD--GQKYTL 225
Query: 90 VDLPGYGFAKAPDVTRMDWSSFTKG--------YFLNR------ESLVGVLLLIDASVPP 135
+D G + R KG Y + R + V VLL+IDA+
Sbjct: 226 IDTAG--------IRR-------KGKVTEGVEKYSVIRTLKAIERADV-VLLVIDATEGI 269
Query: 136 QKIDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPH--HPPWI 193
+ DL A L V K D + ++ ++ F++ +R P + P +
Sbjct: 270 TEQDLRIAGLALEAGRALVIVVNKWDLVD-------EKTMEEFKKELRRRLPFLDYAPIV 322
Query: 194 MTSSVTGLGRDELL 207
S++TG G D+LL
Sbjct: 323 FISALTGQGVDKLL 336
>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 = 53.5 bits (129), Expect = 4e-09
Identities = 38/173 (21%), Positives = 67/173 (38%), Gaps = 30/173 (17%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLIN--HFLVNKSWY---IVDLPGYGF 97
I+G NVGKS+L+N L ++++T KPG T+ + Y ++D G
Sbjct: 5 VIVGDPNVGKSTLLNRL-LGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG--- 60
Query: 98 AKAPDVTRMDWSSFTKGYFLNRESLVGV----LLLIDASVPPQKIDLDCANWLGRNNIPL 153
+ D+ + + Y+ ES + V +L++D +K + +P+
Sbjct: 61 -------QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEK-QTKEIIHHAESGVPI 112
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDEL 206
V K D D +K+ + + P I S+ TG D
Sbjct: 113 ILVGNKIDL--------RDAKLKTHVAFLFAKL-NGEPIIPLSAETGKNIDSA 156
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 52.8 bits (128), Expect = 3e-08
Identities = 50/200 (25%), Positives = 64/200 (32%), Gaps = 79/200 (39%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIV-DLPGYGFAKAP 101
I GR NVGKSSL+NAL+ +E A IV D+ G
Sbjct: 219 VIAGRPNVGKSSLLNALLG-EERA----------------------IVTDIAG------- 248
Query: 102 DVTRMDW--SSFT-KGYFLN-------RES--LV---G-------------VLLLIDASV 133
TR D G L RE+ V G VLL++DAS
Sbjct: 249 -TTR-DVIEEHINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASE 306
Query: 134 PPQKIDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWI 193
P + D + P+ V K D + P I
Sbjct: 307 PLTEEDD--EILEELKDKPVIVVLNKADLTGEIDLEEEN----------------GKPVI 348
Query: 194 MTSSVTGLGRDELLLHMSQL 213
S+ TG G DEL + +L
Sbjct: 349 RISAKTGEGIDELREAIKEL 368
>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 = 49.6 bits (119), Expect = 1e-07
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 10/62 (16%)
Query: 44 ILGRSNVGKSSLINALVRK----------KELALTSKKPGKTQLINHFLVNKSWYIVDLP 93
++G +NVGKS+LINAL++ + S PG T + + + + D P
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTP 189
Query: 94 GY 95
G
Sbjct: 190 GI 191
>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 = 49.2 bits (118), Expect = 1e-07
Identities = 40/191 (20%), Positives = 72/191 (37%), Gaps = 44/191 (23%)
Query: 42 FAILGRSNVGKSSLINALVRK----------KELALTSKKP----G---KTQLINHFLVN 84
++G + GK++L +L+ + KE L + K G KT ++
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 85 KSWYIVDLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLV---GVLLLIDASVPPQKIDLD 141
+ +D PG+ D+S T L G LL++DA+ + +
Sbjct: 62 RRINFIDTPGHE----------DFSKETVR------GLAQADGALLVVDANEGVEPQTRE 105
Query: 142 CANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRE-----NYPHHPPWIMTS 196
N +P+ K D+ DE ++ ++L++ P I S
Sbjct: 106 HLNIALAGGLPIIVAVNKIDR---VGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPIS 162
Query: 197 SVTGLGRDELL 207
++TG G +ELL
Sbjct: 163 ALTGEGIEELL 173
>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 = 49.1 bits (118), Expect = 2e-07
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
++G NVGKS+LIN L KK +A KPG T+ + + ++D PG
Sbjct: 120 VVGIPNVGKSTLINRLRGKK-VAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
>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 = 1e-06
Identities = 35/134 (26%), Positives = 51/134 (38%), Gaps = 29/134 (21%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKT--------QLINHFLVNKSWYIVDLPG 94
++G++ GKSSL NAL E+A + T Q LV ++DLPG
Sbjct: 1 GLMGKTGAGKSSLCNALFG-TEVAAVGDRRPTTRAAQAYVWQTGGDGLV-----LLDLPG 54
Query: 95 YGFAKAPDVTRMDWSSFTKGYFLNRESLVG----VLLLIDASVPPQKIDLDC-ANWLGRN 149
G + + Y L+ VL L+DA D D L +
Sbjct: 55 VG----------ERGRRDREYEELYRRLLPEADLVLWLLDADDRALAADHDFYLLPLAGH 104
Query: 150 NIPLTFVFTKCDKM 163
+ PL FV + D +
Sbjct: 105 DAPLLFVLNQVDPV 118
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes.
TrmE contains a GTPase domain that forms a canonical
Ras-like fold. It functions a molecular switch GTPase,
and apparently uses a conformational change associated
with GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 45.9 bits (110), Expect = 2e-06
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKT 75
I G+ NVGKSSL+NAL ++ A+ S G T
Sbjct: 7 VIAGKPNVGKSSLLNALAG-RDRAIVSDIAGTT 38
Score = 41.3 bits (98), Expect = 8e-05
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 17/89 (19%)
Query: 125 VLLLIDASVPPQKIDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRE 184
VLL++DAS + D P+ V K D + A+G
Sbjct: 86 VLLVVDASEGLDE--EDLEILELPAKKPVIVVLNKSDLLSDAEGISELNG---------- 133
Query: 185 NYPHHPPWIMTSSVTGLGRDELLLHMSQL 213
P I S+ TG G DEL + +L
Sbjct: 134 -----KPIIAISAKTGEGIDELKEALLEL 157
>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 = 46.5 bits (111), Expect = 4e-06
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 44 ILGRSNVGKSSLINALVR----KKELALTSKKPGKTQLINHFLVNKSWYIVDLPGY 95
++G +NVGKSSLIN L++ K++ TS PG T + ++ + D PG
Sbjct: 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGI 214
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 45.9 bits (109), Expect = 4e-06
Identities = 46/188 (24%), Positives = 74/188 (39%), Gaps = 35/188 (18%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVN---KSWYIVDLPGYGFAKA 100
++G + GKSSLINAL + E+ SK T + ++ ++ + D PG G K
Sbjct: 44 LMGATGAGKSSLINALF-QGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGLGDGKD 102
Query: 101 PDVTRMDWSSFTKGY--FLNRESLVGVLLLIDASVPPQKIDLDCANWLGRN--NIPLTFV 156
D + + Y +L + L VL LI A D D + + + FV
Sbjct: 103 KD------AEHRQLYRDYLPKLDL--VLWLIKADDRALGTDEDFLRDVIILGLDKRVLFV 154
Query: 157 FTKCDK-MKV----AKGRRPDENIKSF--------QQLIRENYPHHPPWIMTSSV-TGLG 202
T+ D+ + G +P IK F +L +E P ++ S G
Sbjct: 155 VTQADRAEPGREWDSAGHQPSPAIKQFIEEKAEALGRLFQEVKP-----VVAVSGRLPWG 209
Query: 203 RDELLLHM 210
EL+ +
Sbjct: 210 LKELVRAL 217
>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 = 44.1 bits (105), Expect = 6e-06
Identities = 22/49 (44%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 46 GRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
G NVGKSSLINALV K+++ S PGKT+ + + D PG
Sbjct: 89 GYPNVGKSSLINALVGSKKVS-VSSTPGKTKHFQTIFLEPGITLCDCPG 136
>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 = 43.8 bits (104), Expect = 9e-06
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSK---KPGKTQLINHFLVNKSWYIVDLPG 94
++G VGKSS+INAL + + A TS PG T+ I ++ Y++D PG
Sbjct: 103 GVVGYPKVGKSSIINAL-KGRHSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 22/52 (42%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
++G NVGKSS INAL+ K +L PG T+L ++K Y+ D PG
Sbjct: 95 GVVGLPNVGKSSFINALLNKFKL-KVGSIPGTTKLQQDVKLDKEIYLYDTPG 145
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 43.3 bits (103), Expect = 2e-05
Identities = 44/193 (22%), Positives = 71/193 (36%), Gaps = 50/193 (25%)
Query: 42 FAILGRSNVGKSSLINALV---------RKKELALTSKKP-----GKTQLINH--FLVNK 85
I+G + GK++L +AL+ K + K G T I F K
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKK 65
Query: 86 SWY-IVDLPGY-GFAKAPDVTR----MDWSSFTKGYFLNRESLVGVLLLIDAS--VPPQK 137
I+D PG+ F K ++ R D G +L++DA V PQ
Sbjct: 66 RLINIIDTPGHVDFTK--EMIRGASQAD----------------GAILVVDAVEGVMPQT 107
Query: 138 IDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHP---PWIM 194
+ +P+ K D++ +E ++ + + E Y P +
Sbjct: 108 REH--LLLAKTLGVPIIVFINKIDRVD---DAELEEVVEEISRELLEKYGFGGETVPVVP 162
Query: 195 TSSVTGLGRDELL 207
S++TG G DELL
Sbjct: 163 GSALTGEGIDELL 175
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 44.2 bits (105), Expect = 2e-05
Identities = 48/193 (24%), Positives = 66/193 (34%), Gaps = 71/193 (36%)
Query: 43 AILGRSNVGKSSLINAL--------------VRKKELALTSKKPGKTQLINHFLVNKSWY 88
A++G NVGK++L NAL V KKE L K
Sbjct: 7 ALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYK-------------GHEIE 53
Query: 89 IVDLPG-YGF-AKAPD--VTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCAN 144
IVDLPG Y A + D V R FL ++ ++DA+
Sbjct: 54 IVDLPGTYSLTAYSEDEKVAR---------DFLLEGKPDLIVNVVDATN----------- 93
Query: 145 WLGRN----------NIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIM 194
L RN IP+ D AK R +I+ +L+ P +
Sbjct: 94 -LERNLYLTLQLLELGIPMILALNMID---EAKKRGIRIDIEKLSKLLG------VPVVP 143
Query: 195 TSSVTGLGRDELL 207
T + G G +EL
Sbjct: 144 TVAKRGEGLEELK 156
>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 = 41.7 bits (99), Expect = 5e-05
Identities = 50/199 (25%), Positives = 72/199 (36%), Gaps = 71/199 (35%)
Query: 43 AILGRSNVGKSSLINAL--------------VRKKELALTSKKPGKTQLINHFLVNKSWY 88
A++G NVGK++L NAL V KKE K
Sbjct: 1 ALVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKLG-------------GKEIE 47
Query: 89 IVDLPG-YGF-AKAPD--VTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCAN 144
IVDLPG Y + D V R D FL E ++ ++DA+ N
Sbjct: 48 IVDLPGTYSLTPYSEDEKVAR-D--------FLLGEEPDLIVNVVDAT-----------N 87
Query: 145 WLGRN----------NIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIM 194
L RN +P+ D A+ R ++ +L+ P +
Sbjct: 88 -LERNLYLTLQLLELGLPVVVALNMID---EAEKRGIKIDLDKLSELLG------VPVVP 137
Query: 195 TSSVTGLGRDELLLHMSQL 213
TS+ G G DELL +++L
Sbjct: 138 TSARKGEGIDELLDAIAKL 156
>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 = 42.5 bits (101), Expect = 6e-05
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
I+G NVGKS+LIN L KK +A +PG T+ ++ ++D PG
Sbjct: 123 IVGIPNVGKSTLINRLAGKK-VAKVGNRPGVTKGQQWIKLSDGLELLDTPG 172
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 42.9 bits (101), Expect = 7e-05
Identities = 49/189 (25%), Positives = 78/189 (41%), Gaps = 23/189 (12%)
Query: 40 PEFAILGRSNVGKSSLINALVRKK-----ELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
A++GR NVGKSSL+N L ++ +LA T++ P +++ + + W +D G
Sbjct: 451 RRVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDP-VDEIVE--IDGEDWLFIDTAG 507
Query: 95 YGFAKAPDVTRMD-WSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIPL 153
+ +T + +SS + R L L L DAS P + DL + L
Sbjct: 508 IK-RRQHKLTGAEYYSSLRTQAAIERSEL--ALFLFDASQPISEQDLKVMSMAVDAGRAL 564
Query: 154 TFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW---IMTSSVTGLGRDELLLHM 210
VF K D M DE + + + + W + S+ TG + L M
Sbjct: 565 VLVFNKWDLM--------DEFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPAM 616
Query: 211 SQLRNYWDQ 219
+ WDQ
Sbjct: 617 QEALESWDQ 625
Score = 41.3 bits (97), Expect = 2e-04
Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 9/122 (7%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQ---LINHFLVNKSWYIVDLPGYGFAK 99
AI+GR NVGKS+L+N ++ ++E A+ PG T+ + + +VD G+
Sbjct: 279 AIVGRPNVGKSTLVNRILGRRE-AVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGW---- 333
Query: 100 APDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIPLTFVFTK 159
DV +D S+ + V+ ++D V D L R P+ K
Sbjct: 334 EADVEGID-SAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNK 392
Query: 160 CD 161
D
Sbjct: 393 ID 394
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 42.1 bits (100), Expect = 8e-05
Identities = 24/54 (44%), Positives = 31/54 (57%), Gaps = 7/54 (12%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKT---QLINHFLVNKSWYIVDLPG 94
I+G NVGKS+LIN L KK +A T +PG T Q I + K ++D PG
Sbjct: 126 IIGIPNVGKSTLINRLAGKK-IAKTGNRPGVTKAQQWIK---LGKGLELLDTPG 175
>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 = 9e-05
Identities = 47/194 (24%), Positives = 67/194 (34%), Gaps = 71/194 (36%)
Query: 42 FAILGRSNVGKSSLINAL--------------VRKKELALTSKKPGKTQLINHFLVNKSW 87
A++G NVGK++L NAL V KKE K
Sbjct: 3 IALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYK-------------GYEI 49
Query: 88 YIVDLPG-YGF-AKAPD--VTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCA 143
IVDLPG Y + + V R +L E ++ ++DA+
Sbjct: 50 EIVDLPGTYSLSPYSEEEKVARD---------YLLEEKPDVIINVVDAT----------- 89
Query: 144 NWLGRN----------NIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWI 193
N L RN IP+ D A+ + +IK +L+ P +
Sbjct: 90 N-LERNLYLTLQLLELGIPVVVALNMMD---EAEKKGIKIDIKKLSELLG------VPVV 139
Query: 194 MTSSVTGLGRDELL 207
TS+ G G DEL
Sbjct: 140 PTSARKGEGIDELK 153
>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 = 40.4 bits (95), Expect = 1e-04
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 38 DRPEFAI--LGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG 94
D+ + ++ +G NVGKSS+IN L R K++ + PG+T++ + + K Y++D PG
Sbjct: 99 DKKQISVGFIGYPNVGKSSVINTL-RSKKVCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
>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 = 40.8 bits (96), Expect = 2e-04
Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 4/56 (7%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQL-INHFLVNKSWYI--VDLPGY 95
AILGR NVGKS+L+N L +K +++TS K T+ I+ + I +D PG+
Sbjct: 4 AILGRPNVGKSTLLNQLHGQK-ISITSPKAQTTRNRISGIHTTGASQIIFIDTPGF 58
>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 = 39.3 bits (92), Expect = 4e-04
Identities = 45/181 (24%), Positives = 69/181 (38%), Gaps = 37/181 (20%)
Query: 43 AILGRSNVGKSSLINALVRKK-ELALTSKKPGKTQLIN----HFLVNKSWYIVDLPGYGF 97
++G NVGKS+L++AL K E+A P T N F I+DLPG
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIA---SYPFTTLEPNVGVFEFGDGVDIQIIDLPGL-- 55
Query: 98 AKAPDVTRMDWSSFTKGYFLNRESLVGVLL-LIDAS-------VPPQKI---DLDCANWL 146
+ L ++L +IDAS + QK ++ + L
Sbjct: 56 -----LDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSF-L 109
Query: 147 GRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDEL 206
N P V K D + N+K +L + P + TS++T LG D +
Sbjct: 110 FLKNKPEMIVANKIDMAS-------ENNLK---RLKLDKLKRGIPVVPTSALTRLGLDRV 159
Query: 207 L 207
+
Sbjct: 160 I 160
>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 = 40.2 bits (94), Expect = 5e-04
Identities = 36/124 (29%), Positives = 57/124 (45%), Gaps = 14/124 (11%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQ-LINHFLVNKSWYIVDLPGYGFAKAP 101
AI+G NVGKSSL+NAL++ ++ A+ S G T+ ++ I L G +
Sbjct: 207 AIVGSPNVGKSSLLNALLK-QDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHA 265
Query: 102 D-VTRMDWSSFTKGYFLNRESLVG---VLLLIDASVPPQKIDLDCANWLGRNNIPLTFVF 157
D V R+ G + +++ V+ ++DAS P K D L ++ P V
Sbjct: 266 DFVERL-------GIEKSFKAIKQADLVIYVLDASQPLTK-DDFLIIDLNKSKKPFILVL 317
Query: 158 TKCD 161
K D
Sbjct: 318 NKID 321
>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 = 38.1 bits (90), Expect = 0.001
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 12/61 (19%)
Query: 43 AILGRSNVGKSSLINALVRKKELA--LTSKKPGK-------TQLINHFLVNKSWYIVDLP 93
++G+S VGKS+L+NAL+ + LA S+K G+ +L F + I+D P
Sbjct: 89 VLVGQSGVGKSTLLNALLPELVLATGEISEKLGRGRHTTTHREL---FPLPGGGLIIDTP 145
Query: 94 G 94
G
Sbjct: 146 G 146
Score = 30.1 bits (69), Expect = 0.58
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 12/59 (20%)
Query: 149 NNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRE-NYPHHPPWIMTSSVTGLGRDEL 206
+ I V K D + DE ++ ++ + YP + S+ TG G DEL
Sbjct: 32 SGIEPVIVLNKADLV-------DDEELEELLEIYEKLGYP----VLAVSAKTGEGLDEL 79
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 37.9 bits (89), Expect = 0.001
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 12/61 (19%)
Query: 43 AILGRSNVGKSSLINALVRKKELAL--TSKKPGK-------TQLINHFLVNKSWYIVDLP 93
+ G+S VGKS+L+NAL+ + +L S+K G+ +L F + ++D P
Sbjct: 39 VLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVEL---FPLPGGGLLIDTP 95
Query: 94 G 94
G
Sbjct: 96 G 96
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 38.0 bits (89), Expect = 0.002
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 43 AILGRSNVGKSSLINALVRKKELAL--TSKKPGK-------TQLINHFLVNKSWYIVDLP 93
+LG+S VGKS+LINAL+ + S+K G+ +L +I+D P
Sbjct: 168 VLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELF-PL--PGGGWIIDTP 224
Query: 94 G 94
G
Sbjct: 225 G 225
>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 = 37.1 bits (87), Expect = 0.002
Identities = 26/129 (20%), Positives = 51/129 (39%), Gaps = 24/129 (18%)
Query: 42 FAILGRSNVGKSSLINALVRKKEL-----ALTSKKPGKTQLINH--FLVNKSWYIVDLPG 94
A++G + GKS+L+NAL+ ++ L T+ I + + K +VD PG
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAV-------ITVLRYGLLKGVVLVDTPG 55
Query: 95 YGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLD-CANWLGRNNIPL 153
+ + T+ + + V+ ++ A P + + + L + +
Sbjct: 56 LN---STIEHHTEI---TESFLPRAD---AVIFVLSADQPLTESEREFLKEILKWSGKKI 106
Query: 154 TFVFTKCDK 162
FV K D
Sbjct: 107 FFVLNKIDL 115
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 37.9 bits (89), Expect = 0.003
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 6/56 (10%)
Query: 44 ILGRSNVGKSSLINALVR----KKELALTSKKPGKT-QLINHFLVNKSWYIVDLPG 94
++G +NVGKS+LIN +++ +K++ TS+ PG T I L + S ++ D PG
Sbjct: 165 VVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGS-FLYDTPG 219
>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 = 36.8 bits (86), Expect = 0.003
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGY 95
++G NVGKSS+IN+L R + PG T+ + ++K ++D PG
Sbjct: 120 GVVGYPNVGKSSVINSLKRSRACN-VGATPGVTKSMQEVHLDKHVKLLDSPGV 171
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 37.3 bits (87), Expect = 0.005
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 40 PEFAILGRSNVGKSSLINALVRKKELALTSKKPGKT 75
P A++GR NVGKS+L+N ++ ++E A+ PG T
Sbjct: 39 PVVAVVGRPNVGKSTLVNRILGRRE-AVVEDVPGVT 73
Score = 34.2 bits (79), Expect = 0.047
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 43 AILGRSNVGKSSLINAL 59
A++G+ NVGKSSL+N L
Sbjct: 215 ALVGKPNVGKSSLLNKL 231
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 36.1 bits (84), Expect = 0.005
Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 13/100 (13%)
Query: 40 PEFAILGRSNVGKSSLINALVRKKELA-LTSKKPGKTQLINHFLVNKSWYIVDLPGYGFA 98
P +LG S+ GK++L L K + +TS +P ++ K +VD+PG+
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKL 60
Query: 99 KAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKI 138
+ + + SL ++ ++D++ + I
Sbjct: 61 R---------DKLLEYL---KASLKAIVFVVDSATFQKNI 88
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 35.2 bits (82), Expect = 0.015
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 14/61 (22%)
Query: 44 ILGRSNVGKSSLINALVRKKELALT---SKKPGK-------TQLINHFLVNKSWYIVDLP 93
+ G+S VGKS+L+NAL EL T S+ G+ +L + + ++D P
Sbjct: 169 LAGQSGVGKSTLLNALAPDLELK-TGEISEALGRGKHTTTHVELYD---LPGGGLLIDTP 224
Query: 94 G 94
G
Sbjct: 225 G 225
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 35.2 bits (82), Expect = 0.016
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV 83
AI GRS GK+SLINA+ LT + G+ L L
Sbjct: 28 AIFGRSGAGKTSLINAIS-----GLTRPQKGRIVLNGRVLF 63
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 35.2 bits (81), Expect = 0.020
Identities = 47/193 (24%), Positives = 83/193 (43%), Gaps = 39/193 (20%)
Query: 40 PEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV-------NKSWYIVDL 92
P ILG + GK++L++ +RK ++A + G TQ I + V N+ +D
Sbjct: 245 PIVTILGHVDHGKTTLLDK-IRKTQIA-QKEAGGITQKIGAYEVEFEYKDENQKIVFLDT 302
Query: 93 PGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIP 152
PG+ +A R ++G N + +++ D V PQ I+ N++ N+P
Sbjct: 303 PGH---EAFSSMR------SRG--ANVTDIAILIIAADDGVKPQTIE--AINYIQAANVP 349
Query: 153 LTFVFTKCDKMKVAKGRRPDENIKSFQQ------LIRENYPHHPPWIMTSSVTGLGRDEL 206
+ K DK + N + +Q LI E + P I S+ G D+L
Sbjct: 350 IIVAINKIDK--------ANANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKL 401
Query: 207 L---LHMSQLRNY 216
L L ++++ +
Sbjct: 402 LETILLLAEIEDL 414
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.5 bits (80), Expect = 0.037
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 156 VFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHM 210
VF K D + +E + + I E P + S+ +GLG EL +
Sbjct: 281 VFNKIDLL-------DEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDL 328
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7
is a small Rab GTPase that regulates vesicular traffic
from early to late endosomal stages of the endocytic
pathway. The yeast Ypt7 and mammalian Rab7 are both
involved in transport to the vacuole/lysosome, whereas
Ypt7 is also required for homotypic vacuole fusion.
Mammalian Rab7 is an essential participant in the
autophagic pathway for sequestration and targeting of
cytoplasmic components to the lytic compartment.
Mammalian Rab7 is also proposed to function as a tumor
suppressor. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 172
Score = 33.4 bits (77), Expect = 0.038
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 44 ILGRSNVGKSSLINALVRKK 63
ILG S VGK+SL+N V KK
Sbjct: 5 ILGDSGVGKTSLMNQYVNKK 24
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 33.0 bits (76), Expect = 0.051
Identities = 48/181 (26%), Positives = 72/181 (39%), Gaps = 46/181 (25%)
Query: 51 GKSSLINALV-----RKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGYGFAKAPDVTR 105
GK++LI AL R E KK G T +DL G+ + PD R
Sbjct: 11 GKTTLIKALTGIETDRLPE----EKKRGIT--------------IDL-GFAYLDLPDGKR 51
Query: 106 MDWSSF--TKGY--FLNRESLVG------VLLLIDAS--VPPQKID-LDCANWLGRNNIP 152
+ F G+ F+ + L G VLL++ A + PQ + L+ LG
Sbjct: 52 L---GFIDVPGHEKFV-KNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGL 107
Query: 153 LTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHMSQ 212
+ V TK D R + + +L+ + P SSVTG G +EL ++ +
Sbjct: 108 V--VLTKADL---VDEDRLELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNYLDE 162
Query: 213 L 213
L
Sbjct: 163 L 163
>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 = 33.2 bits (77), Expect = 0.067
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 11/54 (20%)
Query: 18 QIKEVEFVKSSGRAKDCPKDDR-----PEFAILGRSNVGKSSLINALVRKKELA 66
++++V+ + RA+ R P A++G +N GKS+L NAL LA
Sbjct: 21 ELEKVKKQRELQRAR------RKRSGVPTVALVGYTNAGKSTLFNALTGADVLA 68
Score = 30.5 bits (70), Expect = 0.40
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 17/87 (19%)
Query: 125 VLLLIDASVPPQKIDLDCANW----LGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQ 180
+L ++DAS P ++ ++ LG ++IP+ V K D + DE +
Sbjct: 124 LLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLL-------DDE------E 170
Query: 181 LIRENYPHHPPWIMTSSVTGLGRDELL 207
L P + S+ TG G D L
Sbjct: 171 LEERLRAGRPDAVFISAKTGEGLDLLK 197
>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 = 32.8 bits (76), Expect = 0.10
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 18 QIKEVEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVRKKELA 66
++++VE + R + + D P A++G +N GKS+L NAL A
Sbjct: 169 ELEKVEKQRERQRRRR-KRADVPTVALVGYTNAGKSTLFNALTGADVYA 216
Score = 27.4 bits (62), Expect = 6.4
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 14/68 (20%)
Query: 146 LGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDE 205
LG +IP V+ K D + + I + + E YP + S+ TG G D
Sbjct: 297 LGAEDIPQLLVYNKIDLL-------DEPRI----ERLEEGYPEA---VFVSAKTGEGLDL 342
Query: 206 LLLHMSQL 213
LL +++
Sbjct: 343 LLEAIAER 350
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 32.9 bits (76), Expect = 0.11
Identities = 12/14 (85%), Positives = 13/14 (92%)
Query: 46 GRSNVGKSSLINAL 59
G+S VGKSSLINAL
Sbjct: 212 GQSGVGKSSLINAL 225
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 32.2 bits (73), Expect = 0.12
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLP 93
+LG VGK++L+N LV + P L + + L
Sbjct: 9 VVLGDGGVGKTTLLNRLVGDEF--PEGYPPTIGNLDPAKTIEPYRRNIKLQ 57
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 32.0 bits (73), Expect = 0.13
Identities = 20/106 (18%), Positives = 38/106 (35%), Gaps = 22/106 (20%)
Query: 39 RPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV------NKSWYIVDL 92
+P I G + GK+SL L + K T S+ ++D
Sbjct: 3 QPAVIIAGLCDSGKTSLFTLLTTG------TVKKTVTSQEPSAAYKYMLHKGFSFTLIDF 56
Query: 93 PGYGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKI 138
PG+ R + SL G++ ++D++ P+++
Sbjct: 57 PGH------VKLRQKLLE----TIKDSSSLRGIVFVVDSTAFPKEV 92
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 32.0 bits (72), Expect = 0.19
Identities = 36/123 (29%), Positives = 54/123 (43%), Gaps = 13/123 (10%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIV--DLPGYGFAKAP 101
I+GR N GKS+L+N ++ +K +T K +I + K ++ D PG K
Sbjct: 57 IIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPKGS 116
Query: 102 ---DVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGRNNIPLTFVFT 158
+ R WSS L+ L VLL+ID+ I + + L NI F+
Sbjct: 117 LEKAMVRCAWSS------LHSADL--VLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLN 168
Query: 159 KCD 161
K D
Sbjct: 169 KID 171
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 31.8 bits (73), Expect = 0.21
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 43 AILGRSNVGKSSLINAL 59
A+LG S VGKS+L+NAL
Sbjct: 199 ALLGSSGVGKSTLVNAL 215
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 32.1 bits (74), Expect = 0.22
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 43 AILGRSNVGKSSLINAL 59
A++G S GK+SL+NAL
Sbjct: 380 ALVGPSGAGKTSLLNAL 396
>gnl|CDD|130874 TIGR01815, TrpE-clade3, anthranilate synthase, alpha
proteobacterial clade. This model represents a small
clade of anthranilate synthases from alpha
proteobacteria and Nostoc (a cyanobacterium). This
enzyme is the first step in the pathway for the
biosynthesis of tryprophan from chorismate [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 717
Score = 32.2 bits (73), Expect = 0.23
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 1 MILPGSNIVVGPYAGHSQIKEVEFVKSSGRAKDCPKDDRPE 41
+ LP +VV PYAG +++ +F+ ++G + R
Sbjct: 177 LYLPDELVVVDPYAGLARLVAYDFITAAGSTEGLECGGRDH 217
>gnl|CDD|224586 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 359
Score = 31.7 bits (72), Expect = 0.25
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 20 KEVEFVKSSGRAKDCPKDDRPEF-AILGRSNVGKSSLINALVRKKEL 65
KE+E + + + P I GR VGK+SL+ +++K
Sbjct: 9 KELEELLK------IIESEPPSIVFIYGRRRVGKTSLLKEFIKEKLG 49
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 31.8 bits (72), Expect = 0.27
Identities = 40/179 (22%), Positives = 64/179 (35%), Gaps = 24/179 (13%)
Query: 42 FAILGRSNVGKSSLINALVRKKELAL-TSKKPGKTQLINHF---LVNKSWYIVDLPGYGF 97
A G + GK++L+ AL L KK G T + L + +D+PG+
Sbjct: 3 IATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPGH-- 60
Query: 98 AKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDAS--VPPQKID-LDCANWLGRNNIPLT 154
F + LL++DA V Q + L + LG
Sbjct: 61 -----------EKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLG--IPHTI 107
Query: 155 FVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHMSQL 213
V TK D++ + +R + +K + + TS+ TG G EL + L
Sbjct: 108 VVITKADRVNEEEIKRTEMFMKQILN--SYIFLKNAKIFKTSAKTGQGIGELKKELKNL 164
>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 = 0.28
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 44 ILGRSNVGKSSLINALVRKK----ELALTSKKPGKTQLINHFLVN-KSWYIVDLPG 94
I G NVGKSSL+N L R K T+K + HF W ++D PG
Sbjct: 5 IAGYPNVGKSSLVNKLTRAKPEVAPYPFTTKS----LFVGHFDYKYLRWQVIDTPG 56
Score = 27.1 bits (61), Expect = 4.8
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 10/57 (17%)
Query: 150 NIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDEL 206
N P+ V K D ++ + ++L +E I S++T G DEL
Sbjct: 112 NKPVIVVLNKIDL------LTEEDLSEIEKELEKEGE----EVIKISTLTEEGVDEL 158
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 31.5 bits (72), Expect = 0.29
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 43 AILGRSNVGKSSLINALVR 61
AILGRS GKS+L+ L
Sbjct: 368 AILGRSGSGKSTLLQLLAG 386
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 31.6 bits (72), Expect = 0.29
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 153 LTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHMSQ 212
LT TK D+ V + R E + + ++RE +T++ G G D L H+ Q
Sbjct: 107 LTVALTKADR--VDEARI-AEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHLLQ 163
Query: 213 L 213
L
Sbjct: 164 L 164
>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 = 31.6 bits (72), Expect = 0.33
Identities = 20/55 (36%), Positives = 23/55 (41%), Gaps = 11/55 (20%)
Query: 46 GRSNVGKSSLINALVRKKELALTSKKPGKT------QLINHFLVNKSWYIVDLPG 94
G NVGKS+L NAL PG T +L + IVDLPG
Sbjct: 1 GNPNVGKSTLFNALT--GANQTVGNWPGVTVEKKEGKLG---FQGEDIEIVDLPG 50
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 30.8 bits (70), Expect = 0.33
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 42 FAILGRSNVGKSSLINALVRK 62
I+G N GK++LI LVRK
Sbjct: 5 LGIVGYKNSGKTTLIEKLVRK 25
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.5 bits (72), Expect = 0.34
Identities = 43/187 (22%), Positives = 72/187 (38%), Gaps = 50/187 (26%)
Query: 40 PEFAILGRSNVGKSSLINALVRKKELA-------L--TSKK---PGKTQLINHFLVNKSW 87
P A++G +N GKS+L NAL L T+++ +++ L +
Sbjct: 193 PLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVL---LTDTVG 249
Query: 88 YIVDLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLVG---VLLLIDASVP--PQKID--L 140
+I DLP + +F E + +L ++DAS P +K++
Sbjct: 250 FIRDLP-------HPLV----EAF----KSTLEEVKEADLLLHVVDASDPEILEKLEAVE 294
Query: 141 DCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTG 200
D +G + IP+ V K D + DE I + P+ + S+ TG
Sbjct: 295 DVLAEIGADEIPIILVLNKIDLL-------EDEEI---LAELERGSPNP---VFISAKTG 341
Query: 201 LGRDELL 207
G D L
Sbjct: 342 EGLDLLR 348
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 31.0 bits (71), Expect = 0.35
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 42 FAILGRSNVGKSSLINALVRKKELALT------SKKPGKTQLINHFLVNK 85
+ G S VGKS+L+ AL+ +L + +PG+ +++F V +
Sbjct: 7 IVLSGPSGVGKSTLVKALLEDDKLRFSVSATTRKPRPGEVDGVDYFFVTE 56
>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 = 30.8 bits (70), Expect = 0.39
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 46 GRSNVGKSSLINALV 60
G+S VGKSSLINAL
Sbjct: 127 GQSGVGKSSLINALD 141
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 30.9 bits (71), Expect = 0.39
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 43 AILGRSNVGKSSLINALVR 61
I+GR+ GKSSL+ AL R
Sbjct: 34 GIVGRTGSGKSSLLLALFR 52
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 31.2 bits (71), Expect = 0.40
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 44 ILGRSNVGKSSLINALVRKKEL 65
I+GR+ GKSS++NAL R EL
Sbjct: 1270 IVGRTGAGKSSMLNALFRIVEL 1291
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter
family is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 30.6 bits (70), Expect = 0.40
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 43 AILGRSNVGKSSLINAL 59
AI+G S GKS+L+NAL
Sbjct: 39 AIMGPSGAGKSTLLNAL 55
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 31.2 bits (70), Expect = 0.43
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 35 PKDDRPEF--AILGRSNVGKSSLINALVRK 62
PKD P F A++G GKS+LI +LVR+
Sbjct: 63 PKDLPPPFIVAVVGPPGTGKSTLIRSLVRR 92
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 29.9 bits (68), Expect = 0.45
Identities = 34/113 (30%), Positives = 46/113 (40%), Gaps = 32/113 (28%)
Query: 46 GRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPG-Y----GFAKA 100
GRS GK++L AL +EL K KTQ I S ++D PG Y F A
Sbjct: 8 GRSGCGKTTLTQAL-NGEEL-----KYKKTQAIEF-----SDNMIDTPGEYLENRRFYSA 56
Query: 101 PDVTRMD-------------WSSFTKGY--FLNRESLVGVLLLIDASVPPQKI 138
VT D WS F G+ N+ ++G++ ID + I
Sbjct: 57 LIVTAADADVIALVQDATEPWSVFPPGFASMFNKP-VIGIITKIDLAKDEANI 108
>gnl|CDD|225586 COG3044, COG3044, Predicted ATPase of the ABC class [General
function prediction only].
Length = 554
Score = 31.0 bits (70), Expect = 0.45
Identities = 27/103 (26%), Positives = 39/103 (37%), Gaps = 16/103 (15%)
Query: 42 FAILGRSNVGKSSLINALVRK---------KELALTSKKPGKTQLINHFLVNK---SWYI 89
I G + GK++L+ A+ R +E +T K K + V+ S +I
Sbjct: 245 TLITGGNFHGKTTLLTAIERGVDNHIPGDGRERVVTDVKLAKAEAEEGRCVSGLDLSLFI 304
Query: 90 VDLPGYGFAKAPDVTRMDWSSFTK-GYFLNRESLVGV-LLLID 130
LPG PD D S T ++ G LLID
Sbjct: 305 NHLPGG--KDTPDFVTGDASGSTSMAAWIQEAIEAGAKTLLID 345
>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 = 29.7 bits (67), Expect = 0.46
Identities = 25/126 (19%), Positives = 38/126 (30%), Gaps = 18/126 (14%)
Query: 42 FAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGYGFAKAP 101
++G GKSSL++ LV + + G T ++ V D
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEV-----DGDTGLLNIWDFG 56
Query: 102 DVTRMDWSSFTKGYFLNRESLVGVLLLID-------ASVPPQKIDLDCANWLGRNNIPLT 154
+ F F+ +LL+ D V L LG IP+
Sbjct: 57 GREEL---KFEHIIFMKW--ADAILLVYDLTDRESLNEVSRLIAWLPNLRKLG-GKIPVI 110
Query: 155 FVFTKC 160
V K
Sbjct: 111 LVGNKL 116
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 30.8 bits (71), Expect = 0.46
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 44 ILGRSNVGKSSLINALVRKKELA 66
I+G NVGKS+L NAL + A
Sbjct: 7 IVGLPNVGKSTLFNALTKAGAEA 29
>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 = 30.1 bits (69), Expect = 0.56
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 44 ILGRSNVGKSSLINALVRKK----ELALTSKKPGKTQL-INHFLVNKSWYIVDLPG 94
++G N GKS+L++A+ K + T+ P L + +S+ I D+PG
Sbjct: 5 LVGLPNAGKSTLLSAISNAKPKIADYPFTTLVP---NLGVVRVDDGRSFVIADIPG 57
>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 = 30.5 bits (70), Expect = 0.59
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 44 ILGRSNVGKSSLINALVRKKELA 66
I+G NVGKS+L NAL + A
Sbjct: 3 IVGLPNVGKSTLFNALTKSNAEA 25
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 30.6 bits (70), Expect = 0.60
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 43 AILGRSNVGKSSLINALVR 61
A+LGR+ GKS+L+ L R
Sbjct: 370 ALLGRTGCGKSTLLQLLTR 388
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 30.4 bits (69), Expect = 0.61
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 46 GRSNVGKSSLINALV 60
G S VGKSSLIN L+
Sbjct: 179 GPSGVGKSSLINRLI 193
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 30.5 bits (69), Expect = 0.65
Identities = 47/184 (25%), Positives = 78/184 (42%), Gaps = 45/184 (24%)
Query: 40 PEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV----NKSWYIVDLPGY 95
P I+G + GK+SL++++ RK ++A + G TQ I + V K +D PG+
Sbjct: 88 PVVTIMGHVDHGKTSLLDSI-RKTKVAQG-EAGGITQHIGAYHVENEDGKMITFLDTPGH 145
Query: 96 -GF-------AKAPDVTRMDWSSFTKGYFLNRESLVGVLLLI--DASVPPQKIDLDCANW 145
F AK D+ V+L++ D V PQ I+ +
Sbjct: 146 EAFTSMRARGAKVTDI---------------------VVLVVAADDGVMPQTIE--AISH 182
Query: 146 LGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQ--LIRENYPHHPPWIMTSSVTGLGR 203
N+P+ K DK + PD + + L+ E++ ++ S++TG G
Sbjct: 183 AKAANVPIIVAINKIDKPEA----NPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGI 238
Query: 204 DELL 207
DELL
Sbjct: 239 DELL 242
>gnl|CDD|213256 cd03289, ABCC_CFTR2, ATP-binding cassette domain 2 of
CFTR,subfamily C. The cystic fibrosis transmembrane
regulator (CFTR), the product of the gene mutated in
patients with cystic fibrosis, has adapted the ABC
transporter structural motif to form a tightly
regulated anion channel at the apical surface of many
epithelia. Use of the term assembly of a functional ion
channel implies the coming together of subunits or at
least smaller not-yet functional components of the
active whole. In fact, on the basis of current
knowledge only the CFTR polypeptide itself is required
to form an ATP- and protein kinase A-dependent
low-conductance chloride channel of the type present in
the apical membrane of many epithelial cells. CFTR
displays the typical organization (IM-ABC)2 and carries
a characteristic hydrophilic R-domain that separates
IM1-ABC1 from IM2-ABC2.
Length = 275
Score = 30.2 bits (68), Expect = 0.65
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 14 AGHSQIKEVEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVR 61
G++ ++ + F S G+ +LGR+ GKS+L++A +R
Sbjct: 15 GGNAVLENISFSISPGQ----------RVGLLGRTGSGKSTLLSAFLR 52
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.5 bits (69), Expect = 0.67
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 37 DDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPG 73
D F I+G + GKSS+++A+ AL K P
Sbjct: 23 FDSGIFLIVGPNGAGKSSILDAI----TFALYGKTPR 55
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 29.7 bits (67), Expect = 0.75
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 42 FAILGRSNVGKSSLINALVR 61
I+G N GK++LI LV+
Sbjct: 2 LQIVGPKNSGKTTLIERLVK 21
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 30.0 bits (68), Expect = 0.82
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 38 DRPEFAILGRSNVGKSSLINALVRKK-ELA---LTSKKPGKTQL-INHF-LVNKSWYIVD 91
D P + G NVGKSSL+ L K E+A T+K + + HF ++D
Sbjct: 167 DLPTIVVAGYPNVGKSSLVRKLTTAKPEVAPYPFTTK-----GIHVGHFERGYLRIQVID 221
Query: 92 LPG 94
PG
Sbjct: 222 TPG 224
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 29.6 bits (67), Expect = 0.91
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 43 AILGRSNVGKSSLINALVR 61
A+LGRS GKS+L+ L
Sbjct: 32 ALLGRSGSGKSTLLQLLTG 50
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 29.4 bits (67), Expect = 0.93
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 44 ILGRSNVGKSSLINALVRKK 63
++G S VGKSSL++ K
Sbjct: 5 LIGDSGVGKSSLLSRFTDGK 24
>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 = 29.8 bits (68), Expect = 0.97
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 14/70 (20%)
Query: 41 EFAIL--GRSNVGKSSLINALVRKK--------ELALTSKKPGKTQLINHFLVNK--SWY 88
+F I+ G S +GKS+ IN L K K + ++ L
Sbjct: 4 QFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLK 63
Query: 89 --IVDLPGYG 96
++D PG+G
Sbjct: 64 LTVIDTPGFG 73
>gnl|CDD|215099 PLN00197, PLN00197, beta-amylase; Provisional.
Length = 573
Score = 30.0 bits (67), Expect = 0.99
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 139 DLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPH 188
DL + GR N +V CD + V KGR P + F + R+N+ H
Sbjct: 214 DLAYTDQWGRRN--YEYVSLGCDTLPVLKGRTPVQCYADFMRAFRDNFKH 261
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 29.8 bits (68), Expect = 0.99
Identities = 46/199 (23%), Positives = 79/199 (39%), Gaps = 56/199 (28%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGK------TQLINHFLV-----NKSWYIVDL 92
++G N GKS+L++ A+++ KP K T L+ + V +S+ + D+
Sbjct: 164 LVGLPNAGKSTLLS--------AVSAAKP-KIADYPFTTLVPNLGVVRVDGGESFVVADI 214
Query: 93 PGY--GFAKAPDVTRMDWSSFTKG---YFLNRESLVGVLL-LIDAS----VPP----QKI 138
PG G +S G FL VLL +ID S P Q I
Sbjct: 215 PGLIEG------------ASEGVGLGLRFLRHIERTRVLLHVIDLSPIDGRDPIEDYQTI 262
Query: 139 --DLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTS 196
+L+ + P V K D +E ++ ++ + E +++ S
Sbjct: 263 RNELEKYS-PKLAEKPRIVVLNKIDLP------LDEEELEELKKALAEALGWEVFYLI-S 314
Query: 197 SVTGLGRDELLLHMSQLRN 215
++T G DELL +++L
Sbjct: 315 ALTREGLDELLRALAELLE 333
>gnl|CDD|184590 PRK14249, PRK14249, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 29.6 bits (66), Expect = 1.0
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 38 DRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLVNKSWYIVDL 92
+R AI+G S GKS+L+ AL R ++ ++ G L N + + + +V+L
Sbjct: 29 ERQITAIIGPSGCGKSTLLRALNRMNDIVSGARLEGAVLLDNENIYSPNLDVVNL 83
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. 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 = 171
Score = 29.3 bits (67), Expect = 1.0
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 43 AILGRSNVGKSSLINALVR 61
AI+G S GKS+L+ L+R
Sbjct: 32 AIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 29.1 bits (66), Expect = 1.0
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 40 PEFAILGRSNVGKSSLINALVRK 62
+G S GK++L+ L+
Sbjct: 2 KVIGFVGYSGSGKTTLLEKLIPA 24
>gnl|CDD|214735 smart00591, RWD, domain in RING finger and WD repeat containing
proteins and DEXDc-like helicases subfamily related to
the UBCc domain.
Length = 107
Score = 28.5 bits (64), Expect = 1.1
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 184 ENYPHHPPWIMTSSVTGLGRDELLLHMSQLRNYWDQ 219
ENYP P I + GL ++L + +L ++
Sbjct: 51 ENYPDEAPPISLLNSEGLSDEQLAELLKKLEEIAEE 86
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a
novel subfamily of Ras that were identified based on
their behavior in breast and prostate tumors,
respectively. RERG expression was decreased or lost in
a significant fraction of primary human breast tumors
that lack estrogen receptor and are correlated with
poor clinical prognosis. Elevated RERG expression
correlated with favorable patient outcome in a breast
tumor subtype that is positive for estrogen receptor
expression. In contrast to most Ras proteins, RERG
overexpression inhibited the growth of breast tumor
cells in vitro and in vivo. RasL11 was found to be
ubiquitously expressed in human tissue, but
down-regulated in prostate tumors. Both RERG and RasL11
lack the C-terminal CaaX prenylation motif, where a =
an aliphatic amino acid and X = any amino acid, and are
localized primarily in the cytoplasm. Both are believed
to have tumor suppressor activity.
Length = 166
Score = 29.2 bits (66), Expect = 1.1
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 3/19 (15%)
Query: 43 AILGRSNVGKSSLINALVR 61
A+LG S VGKS+L VR
Sbjct: 3 AVLGASGVGKSALT---VR 18
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. 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 = 157
Score = 29.1 bits (66), Expect = 1.2
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 42 FAILGRSNVGKSSLINALVR 61
A++G + GKS+L+ A+
Sbjct: 28 VALVGPNGSGKSTLLRAIAG 47
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 29.1 bits (65), Expect = 1.2
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 42 FAILGRSNVGKSSLINALVRKKELALTSKKPG 73
I G + GK+++++A+ AL K
Sbjct: 22 TLIYGPNGSGKTTILDAI----RWALYGKTSR 49
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 28.7 bits (65), Expect = 1.4
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 43 AILGRSNVGKSSLINALVRKKEL 65
A++G + GKSS++NAL+ + L
Sbjct: 2 AVVGDQSAGKSSVLNALLGRDIL 24
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.4 bits (66), Expect = 1.5
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 35 PKDDRPEF----AILGRSNVGKSSLINALVRK 62
P++ RP F AILG + GKS+L+N L
Sbjct: 154 PREVRPFFVKTVAILGGESTGKSTLVNKLAAV 185
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 29.6 bits (67), Expect = 1.5
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 43 AILGRSNVGKSSLINALVR 61
A++G S GKS+L+N L+
Sbjct: 352 ALVGPSGAGKSTLLNLLLG 370
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 29.5 bits (67), Expect = 1.5
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 43 AILGRSNVGKSSLINAL 59
A++G S GKS+L+N L
Sbjct: 351 ALVGASGAGKSTLLNLL 367
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 29.6 bits (66), Expect = 1.6
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 44 ILGRSNVGKSSLINALVRKKEL 65
++GR+ GKSS++NAL R EL
Sbjct: 1267 VVGRTGAGKSSMLNALFRIVEL 1288
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 29.1 bits (66), Expect = 1.6
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 43 AILGRSNVGKSSLINALVRK 62
I+G NVGKS+L NAL +
Sbjct: 6 GIVGLPNVGKSTLFNALTKA 25
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 29.2 bits (66), Expect = 1.7
Identities = 14/66 (21%), Positives = 20/66 (30%), Gaps = 8/66 (12%)
Query: 155 FVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIM----TSSVTGLGRDELLLHM 210
V K D+ K R + W TS++ G G DEL +
Sbjct: 194 IVINKADRKGAEKAARE----LRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAI 249
Query: 211 SQLRNY 216
R +
Sbjct: 250 EDHRKF 255
>gnl|CDD|183108 PRK11377, PRK11377, dihydroxyacetone kinase subunit M; Provisional.
Length = 473
Score = 28.9 bits (65), Expect = 1.9
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 142 CANWLGRNNIPLTFVFTKCDKMK-VAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTG 200
C N I L V D ++ +AKG +E + +F+QL +N+ + ++
Sbjct: 195 CVTPESLNQIALLQV-RYNDTLRLIAKGPEAEEALIAFRQLAEDNFGETEE-VAPPTLRP 252
Query: 201 L 201
+
Sbjct: 253 V 253
>gnl|CDD|206690 cd04104, p47_IIGP_like, p47 GTPase family includes IGTP,
TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. The p47
GTPase family consists of several highly homologous
proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI,
LRG-47, and IIGP1. They are found in higher eukaryotes
where they play a role in immune resistance against
intracellular pathogens. p47 proteins exist at low
resting levels in mouse cells, but are strongly induced
by Type II interferon (IFN-gamma). ITGP is critical for
resistance to Toxoplasma gondii infection and in
involved in inhibition of Coxsackievirus-B3-induced
apoptosis. TGTP was shown to limit vesicular stomatitis
virus (VSV) infection of fibroblasts in vitro. IRG-47
is involved in resistance to T. gondii infection.
LRG-47 has been implicated in resistance to T. gondii,
Listeria monocytogenes, Leishmania, and mycobacterial
infections. IIGP1 has been shown to localize to the ER
and to the Golgi membranes in IFN-induced cells and
inflamed tissues. In macrophages, IIGP1 interacts with
hook3, a microtubule binding protein that participates
in the organization of the cis-Golgi compartment.
Length = 197
Score = 28.4 bits (64), Expect = 1.9
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 43 AILGRSNVGKSSLINAL 59
A+ G S GKSS INAL
Sbjct: 5 AVTGESGAGKSSFINAL 21
>gnl|CDD|184593 PRK14258, PRK14258, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 261
Score = 28.8 bits (64), Expect = 2.0
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINH 80
AI+G S GKS+ + L R EL + G+ + N
Sbjct: 37 AIIGPSGCGKSTFLKCLNRMNELESEVRVEGRVEFFNQ 74
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small
guanosine triphosphatases (GTPases). Rab GTPases form
the largest family within the Ras superfamily. There
are at least 60 Rab genes in the human genome, and a
number of Rab GTPases are conserved from yeast to
humans. Rab GTPases are small, monomeric proteins that
function as molecular switches to regulate vesicle
trafficking pathways. The different Rab GTPases are
localized to the cytosolic face of specific
intracellular membranes, where they regulate distinct
steps in membrane traffic pathways. In the GTP-bound
form, Rab GTPases recruit specific sets of effector
proteins onto membranes. Through their effectors, Rab
GTPases regulate vesicle formation, actin- and
tubulin-dependent vesicle movement, and membrane
fusion. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 28.2 bits (64), Expect = 2.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 44 ILGRSNVGKSSLINALVRKK 63
++G S VGK+SL+ V K
Sbjct: 5 LIGDSGVGKTSLLLRFVDNK 24
>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 = 28.9 bits (66), Expect = 2.1
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 20/62 (32%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGK------TQLINHFLV-----NKSWYIVDL 92
++G N GKS+LI+ A+++ KP K T L+ + V +S+ I D+
Sbjct: 162 LVGLPNAGKSTLIS--------AVSAAKP-KIADYPFTTLVPNLGVVRVDDGRSFVIADI 212
Query: 93 PG 94
PG
Sbjct: 213 PG 214
Score = 27.8 bits (63), Expect = 4.9
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 156 VFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHMSQL 213
V K D + +E ++ + ++E P S++TG G DELL +++L
Sbjct: 279 VLNKIDLL-------DEEELEELLKELKEALGK--PVFPISALTGEGLDELLYALAEL 327
>gnl|CDD|234199 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 230
Score = 28.6 bits (65), Expect = 2.1
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 43 AILGRSNVGKSSLINALV 60
+LGR+ VGK++L+ L+
Sbjct: 30 CVLGRNGVGKTTLLKTLM 47
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 28.6 bits (65), Expect = 2.2
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 156 VFTKCDKMKVAKGRRPDENIKSFQQLIRENYPH-HPPWIMTSSVTGLGRDEL 206
V K D RR +S +L+R P PP + S++ G G DE+
Sbjct: 200 VINKADGDNKTAARRAAAEYRSALRLLRPKDPGWQPPVLTCSALEGEGIDEI 251
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 28.7 bits (65), Expect = 2.3
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 41 EF-AILGRSNVGKSSLINAL 59
EF AILG S GKS+L+ +
Sbjct: 30 EFVAILGPSGCGKSTLLRLI 49
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 28.4 bits (64), Expect = 2.4
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 41 EF-AILGRSNVGKSSLINALVR 61
E AI+G S GKS+L+ +L
Sbjct: 31 EMVAIIGPSGAGKSTLLRSLNG 52
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 28.4 bits (64), Expect = 2.6
Identities = 7/23 (30%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 44 ILGRSNVGKSSLIN-ALVRKKEL 65
+ G GK++L+ L +EL
Sbjct: 25 VYGPRRCGKTALLREFLEELREL 47
>gnl|CDD|218953 pfam06245, DUF1015, Protein of unknown function (DUF1015). Family
of proteins with unknown function found in archaea and
bacteria.
Length = 415
Score = 28.7 bits (65), Expect = 2.7
Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 52 KSSLINAL-----VRKKELALTSKKPGKTQLINHFLVNKSWYIVDLPGYGFAKAPDVTRM 106
+ L V + AL KP K +L WY++ L + V R+
Sbjct: 266 PEEFLEKLEEYFEVEELGDALEPYKPAKKHTFGMYLDGGKWYLLTLKPELYDPEDPVRRL 325
Query: 107 D 107
D
Sbjct: 326 D 326
>gnl|CDD|184584 PRK14238, PRK14238, phosphate transporter ATP-binding protein;
Provisional.
Length = 271
Score = 28.3 bits (63), Expect = 2.8
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGK 74
AI+G S GKS+ I L R EL + K GK
Sbjct: 54 AIIGPSGCGKSTYIKTLNRMVELVPSVKTTGK 85
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 28.1 bits (63), Expect = 2.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 43 AILGRSNVGKSSLINALV 60
++G VGKSSLI +LV
Sbjct: 6 VLIGDEGVGKSSLIMSLV 23
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 28.5 bits (64), Expect = 2.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 43 AILGRSNVGKSSLINALVR 61
A++GRS GKS+L+N + R
Sbjct: 362 ALVGRSGSGKSTLVNLIPR 380
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins
involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules.
Length = 222
Score = 28.2 bits (64), Expect = 3.0
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 43 AILGRSNVGKSSLINALV 60
A+LGR+ GK++L+ ++
Sbjct: 30 ALLGRNGAGKTTLLKTIM 47
>gnl|CDD|177713 PLN00093, PLN00093, geranylgeranyl diphosphate reductase;
Provisional.
Length = 450
Score = 28.6 bits (64), Expect = 3.0
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 155 FVFTKCDKMKVAKG---RRPDENIKSFQQLIRE 184
+VF KCD + V G +P IK +Q+ R
Sbjct: 249 WVFPKCDHVAVGTGTVVNKPA--IKKYQRATRN 279
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.1 bits (64), Expect = 3.1
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 20/62 (32%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGK------TQLINHFLV-----NKSWYIVDL 92
++G N GKS+LI+ A+++ KP K T L + V KS+ I D+
Sbjct: 163 LVGLPNAGKSTLIS--------AVSAAKP-KIADYPFTTLHPNLGVVRVDDYKSFVIADI 213
Query: 93 PG 94
PG
Sbjct: 214 PG 215
Score = 27.0 bits (61), Expect = 7.8
Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 8/52 (15%)
Query: 156 VFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELL 207
V K D + +E + L P + S+VTG G DELL
Sbjct: 277 VLNKIDLL------DEEEEREKRAALELAALGG--PVFLISAVTGEGLDELL 320
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 28.3 bits (64), Expect = 3.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 42 FAILGRSNVGKSSLINALVR 61
I+G S GKS+L AL+
Sbjct: 38 LGIVGESGSGKSTLALALMG 57
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.4 bits (61), Expect = 3.7
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 40 PEFAILGRSNVGKSSLINALVRK 62
P ++G + GK++LI L+
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNY 23
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 27.9 bits (62), Expect = 4.0
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 38 DRPEFAILGRSNVGKSSLINALVRKKEL----ALTSKKPGKTQLIN 79
D P+ A++G + GKSS++ V + L + +++P QLI
Sbjct: 25 DLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLILQLIK 70
>gnl|CDD|213796 TIGR03316, ygeW, probable carbamoyltransferase YgeW. Members of
this protein family include the ygeW gene product of
Escherichia coli. The function is unknown. Members show
homology to ornithine carbamoyltransferase (TIGR00658)
and aspartate carbamoyltransferase
(carbamoyltransferase), and therefore may belong to the
carbamoyltransferases in function. Members often are
found in a large, conserved genomic region associated
with purine catabolism.
Length = 357
Score = 28.0 bits (62), Expect = 4.0
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 173 ENIKSFQQLIRENYPHHPPWIMTSSVTGLGRDELLLHM 210
E +K+ ++ H W T L RD L+M
Sbjct: 273 EGLKALEKQCLAQNAKHKDWHCTEERMELTRDGEALYM 310
>gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 27.9 bits (62), Expect = 4.1
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 42 FAILGRSNVGKSSLINALVRKKELALTSKKPGKTQL 77
FA++G S GKS+L+ R EL ++ G+ +L
Sbjct: 33 FALMGPSGCGKSTLLRTFNRLLELNEEARVEGEVRL 68
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 27.4 bits (62), Expect = 4.1
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHF 81
++GR+ GKS+L+ + + E G T I +F
Sbjct: 30 GLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYF 68
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 27.8 bits (61), Expect = 4.2
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 43 AILGRSNVGKSSLINAL 59
I+G + GKS+L+ AL
Sbjct: 3 VIIGPNGSGKSNLLKAL 19
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 27.7 bits (62), Expect = 4.5
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 41 EFAILGRSNVGKSSLINALVRK 62
E A G S GK++LI ALVR+
Sbjct: 7 EIAFCGYSGSGKTTLITALVRR 28
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 27.7 bits (62), Expect = 4.5
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 10/56 (17%)
Query: 155 FVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW----IMTSSVTGLGRDEL 206
+V K D + R + + P W + TS+VTG G DEL
Sbjct: 172 YVVNKADLPGAERTAR------ELRSALHLLTPKEAGWRPPVLTTSAVTGEGIDEL 221
>gnl|CDD|173630 cd05044, PTKc_c-ros, Catalytic domain of the Protein Tyrosine
Kinase, C-ros. Protein Tyrosine Kinases (PTK) family;
C-ros and Drosophila Sevenless proteins; catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. The
proto-oncogene c-ros encodes an orphan receptor tyr
kinase (RTK) with an unknown ligand. RTKs contain an
extracellular ligand-binding domain, a transmembrane
region, and an intracellular tyr kinase domain. RTKs are
usually activated through ligand binding, which causes
dimerization and autophosphorylation of the
intracellular tyr kinase catalytic domain. C-ros is
expressed in embryonic cells of the kidney, intestine
and lung, but disappears soon after birth. It persists
only in the adult epididymis. Male mice bearing inactive
mutations of c-ros lack the initial segment of the
epididymis and are infertile. The Drosophila protein,
Sevenless, is required for the specification of the R7
photoreceptor cell during eye development.
Length = 269
Score = 27.9 bits (62), Expect = 4.6
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 12 PYAGHSQIKEVEFVKSSGR---AKDCPKD 37
PY + + ++ V + GR ++CP
Sbjct: 213 PYPALNNQEVLQHVTAGGRLQKPENCPDK 241
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 28.0 bits (63), Expect = 4.6
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 44 ILGRSNVGKSSLINAL 59
I+G NVGKS+ NAL
Sbjct: 26 IVGLPNVGKSTTFNAL 41
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 28.1 bits (63), Expect = 4.7
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 43 AILGRSNVGKSSLINAL 59
A++G S GK++L+NAL
Sbjct: 55 AVMGSSGAGKTTLMNAL 71
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 27.7 bits (62), Expect = 5.3
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 42 FAILGRSNVGKSSLINAL 59
F +LG + GK++L+ L
Sbjct: 34 FGLLGPNGAGKTTLLKIL 51
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 27.2 bits (61), Expect = 5.6
Identities = 37/185 (20%), Positives = 64/185 (34%), Gaps = 45/185 (24%)
Query: 44 ILGRSNVGKSSLINALVRKKELALTSKKPGKTQLINHFLV------NKSWYIVDLPGYGF 97
+LG GK++++ L + T F V N + + D+ G
Sbjct: 4 MLGLDGAGKTTILY--------KLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGG--- 52
Query: 98 AKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQKIDLDCANWLGR-------NN 150
D R W Y+ E+ G++ ++D+S ++I+ + N L +
Sbjct: 53 ---QDKIRPLWKH----YY---ENTDGLIFVVDSS-DRERIE-EAKNELHKLLNEEELKG 100
Query: 151 IPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPWI--MTSSVTGLGRDELLL 208
PL + K D E +L+ W S+VTG G DE L
Sbjct: 101 APLLILANKQDL---PGALTESE----LIELLGLESIKGRRWHIQPCSAVTGDGLDEGLD 153
Query: 209 HMSQL 213
+ +
Sbjct: 154 WLIEQ 158
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 27.7 bits (62), Expect = 6.1
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 88 YIVDLPG---YGFAKAPDVTRMDWSSFTKGYFLNRESLVGVLLLIDASVPPQ 136
++ LP G R K YFLN V V L+I +
Sbjct: 451 FLSALPEDVVSGLKPFSASNRETNEEIVKQYFLNVYCSV-VFLVIKNTHEGG 501
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 27.4 bits (61), Expect = 6.2
Identities = 26/116 (22%), Positives = 40/116 (34%), Gaps = 23/116 (19%)
Query: 125 VLLLIDASVPPQKIDLDCANWLGRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLI-R 183
LL++ A K+ + +P+ V TK D + + + E I + + + R
Sbjct: 230 GLLVVAADDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGVVEEISALLKRVGR 289
Query: 184 ENYP------------------HHPPWIMTSSVTGLGRD---ELLLHMSQLRNYWD 218
P TSSVTG G D E L + + R WD
Sbjct: 290 IPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLLLPK-RRRWD 344
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain
of the nitrate and sulfonate transporters. NrtD and
SsuB are the ATP-binding subunits of the bacterial
ABC-type nitrate and sulfonate transport systems,
respectively. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. 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 = 220
Score = 27.1 bits (61), Expect = 6.6
Identities = 9/20 (45%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 41 EF-AILGRSNVGKSSLINAL 59
EF A++G S GKS+L+ +
Sbjct: 31 EFVALVGPSGCGKSTLLRII 50
>gnl|CDD|224058 COG1135, AbcC, ABC-type metal ion transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 339
Score = 27.2 bits (61), Expect = 6.6
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 42 FAILGRSNVGKSSLI 56
F I+G S GKS+L+
Sbjct: 35 FGIIGYSGAGKSTLL 49
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 27.0 bits (61), Expect = 7.0
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 43 AILGRSNVGKSSLINALV 60
A+LGR+ GK++L+ ++
Sbjct: 33 ALLGRNGAGKTTLLKTIM 50
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 27.3 bits (61), Expect = 7.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 43 AILGRSNVGKSSLINAL 59
A+ G S GK+SLIN +
Sbjct: 28 ALFGPSGSGKTSLINMI 44
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5
and Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of
plants. The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 26.7 bits (60), Expect = 7.1
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 44 ILGRSNVGKSSLINALVR 61
+LG S+VGKSS++ V+
Sbjct: 6 LLGDSSVGKSSIVLRFVK 23
>gnl|CDD|213201 cd03234, ABCG_White, White pigment protein homolog of ABCG
transporter subfamily. The White subfamily represents
ABC transporters homologous to the Drosophila white
gene, which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the
cells of red pigments, which are synthesized from
guanine, and brown pigments, which are synthesized from
tryptophan. The pigment precursors are encoded by the
white, brown, and scarlet genes, respectively. Evidence
from genetic and biochemical studies suggest that the
White and Brown proteins function as heterodimers to
import guanine, while the White and Scarlet proteins
function to import tryptophan. However, a recent study
also suggests that White may be involved in the
transport of a metabolite, such as 3-hydroxykynurenine,
across intracellular membranes. Mammalian ABC
transporters belonging to the White subfamily (ABCG1,
ABCG5, and ABCG8) have been shown to be involved in the
regulation of lipid-trafficking mechanisms in
macrophages, hepatocytes, and intestinal mucosa cells.
ABCG1 (ABC8), the human homolog of the Drosophila white
gene is induced in monocyte-derived macrophages during
cholesterol influx mediated by acetylated low-density
lipoprotein. It is possible that human ABCG1 forms
heterodimers with several heterologous partners.
Length = 226
Score = 26.9 bits (60), Expect = 7.2
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 43 AILGRSNVGKSSLINALVRK 62
AILG S GK++L++A+ +
Sbjct: 37 AILGSSGSGKTTLLDAISGR 56
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 26.9 bits (59), Expect = 7.3
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 43 AILGRSNVGKSSLINALVRKKELALTSKKPGKTQL 77
AI+G S GKS+++ ++ R +L +++ GK L
Sbjct: 34 AIIGPSGCGKSTVLRSINRMHDLVPSARVTGKILL 68
>gnl|CDD|236863 PRK11153, metN, DL-methionine transporter ATP-binding subunit;
Provisional.
Length = 343
Score = 27.1 bits (61), Expect = 7.4
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 42 FAILGRSNVGKSSLI 56
F ++G S GKS+LI
Sbjct: 34 FGVIGASGAGKSTLI 48
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 27.5 bits (61), Expect = 7.6
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 43 AILGRSNVGKSSLINALVRKKEL-----------ALTSKKPGKTQLINHF 81
AI+G GKS+ INA+V + L L PG+ + + HF
Sbjct: 73 AIVGTMKAGKSTTINAIVGTEVLPNRNRPMTALPTLIRHTPGQKEPVLHF 122
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 26.8 bits (60), Expect = 7.9
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 41 EF-AILGRSNVGKSSLINALVR 61
EF A++G S GKS+L+ L
Sbjct: 28 EFVALIGPSGAGKSTLLRCLNG 49
>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 = 26.9 bits (60), Expect = 8.0
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 44 ILGRSNVGKSSLINALV 60
+LG++ VGKSS IN++
Sbjct: 36 VLGKTGVGKSSTINSIF 52
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 26.7 bits (60), Expect = 8.6
Identities = 41/187 (21%), Positives = 68/187 (36%), Gaps = 47/187 (25%)
Query: 40 PEFAILGRSNVGKSSLINAL----VRKKELALTSKKPGKTQLINHFLVNKSWYI-----V 90
P ++G + GK++L++ + V E G TQ I + V I +
Sbjct: 1 PVVTVMGHVDHGKTTLLDKIRKTNVAAGE------AGGITQHIGAYQVPIDVKIPGITFI 54
Query: 91 DLPGYGFAKAPDVTRMDWSSFTKGYFLNRESLVG--VLLLIDA--SVPPQKIDLDCANWL 146
D PG+ +FT R + V +L++ A V PQ I+ N
Sbjct: 55 DTPGH-------------EAFTN--MRARGASVTDIAILVVAADDGVMPQTIE--AINHA 97
Query: 147 GRNNIPLTFVFTKCDKMKVAKGRRPDENIKSFQQLIRENYPHHPPW------IMTSSVTG 200
N+P+ K DK + + + + + E W + S+ TG
Sbjct: 98 KAANVPIIVAINKIDKP-----YGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTG 152
Query: 201 LGRDELL 207
G D+LL
Sbjct: 153 EGIDDLL 159
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 160
Score = 26.3 bits (59), Expect = 8.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 43 AILGRSNVGKSSLINALVRKK 63
+LG VGKS+L V +
Sbjct: 3 VVLGAGGVGKSALTIRFVSGE 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 = 26.6 bits (58), Expect = 8.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 43 AILGRSNVGKSSLINALVR 61
I+G GK++L AL R
Sbjct: 6 LIVGPPGSGKTTLARALAR 24
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 26.3 bits (59), Expect = 9.0
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 42 FAILGRSNVGKSSLINALVRKKELAL------TSKKP 72
+ G S VGKS+L+ L+ + + T++KP
Sbjct: 2 IVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKP 38
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 26.9 bits (60), Expect = 9.1
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 20/77 (25%)
Query: 24 FVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVRKK----ELALTSKKPGKTQLIN 79
VK SG A A++G +VGKS+L+N L K + T+ +P +
Sbjct: 57 AVKKSGDAT---------VALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEP-----VP 102
Query: 80 HFLVNKSWYI--VDLPG 94
L K I +DLPG
Sbjct: 103 GMLEYKGAQIQLLDLPG 119
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 26.5 bits (59), Expect = 9.5
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 37 DDRPEFAILGRSNVGKSSLINALVRKKELALTSKKPGK 74
D+ F I G + GKS++++A+ AL K P
Sbjct: 26 DNNGLFLICGPTGAGKSTILDAIT----YALYGKTPRY 59
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 26.7 bits (59), Expect = 9.5
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 16 HSQIKEVEFVKSSGRAKDCPKD---DRPEFAILGRSNVGKSSLINAL 59
+ ++E K K ++ + A+ G S GKSS INAL
Sbjct: 9 ETALREGNLQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFINAL 55
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se [Transport and binding proteins,
Anions].
Length = 1490
Score = 27.2 bits (60), Expect = 9.9
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 10/48 (20%)
Query: 14 AGHSQIKEVEFVKSSGRAKDCPKDDRPEFAILGRSNVGKSSLINALVR 61
AG + ++++ F G+ +LGR+ GKS+L++AL+R
Sbjct: 1230 AGRAVLQDLSFSVEGGQ----------RVGLLGRTGSGKSTLLSALLR 1267
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
0.320 0.137 0.425
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,253,409
Number of extensions: 1030503
Number of successful extensions: 1342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1297
Number of HSP's successfully gapped: 214
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
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: 57 (25.8 bits)