RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780484|ref|YP_003064897.1| GTPase EngB [Candidatus
Liberibacter asiaticus str. psy62]
(212 letters)
>gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily. This 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 = 220 bits (563), Expect = 2e-58
Identities = 81/180 (45%), Positives = 113/180 (62%), Gaps = 10/180 (5%)
Query: 31 EIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90
EIAF+GRSNVGKSSLIN L NRK LARTS PG+TQ +NFF N+ + LVD
Sbjct: 1 EIAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFF------NVNDKF---RLVD 51
Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAV 150
+PGYGYA+ K+ + WG LI YL R L+ V LLID RHG +ID ++ +L++ +
Sbjct: 52 LPGYGYAKVSKEVKEKWGKLIEEYLENRENLKGVVLLIDSRHGPTEIDLEMLDWLEELGI 111
Query: 151 SYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
+ +VLTK DKL + + L++ K ++ + P +I SS+K +GI+ LR I + +
Sbjct: 112 PFLVVLTKADKLKKSELAKALKEIKKELKLFE-IDPPIILFSSLKGQGIDELRALIEKWL 170
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 217 bits (553), Expect = 3e-57
Identities = 89/206 (43%), Positives = 120/206 (58%), Gaps = 9/206 (4%)
Query: 6 IFTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65
F+ P+I P+ PEIAF+GRSNVGKSSLIN L N+KNLARTS PGRT
Sbjct: 1 KLNYHKAKFITSAPDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRT 60
Query: 66 QHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVY 125
Q +NFF D + LVD+PGYGYA+ PK+ + W LI YL +R+ L+ V
Sbjct: 61 QLINFFEVDD---------ELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVV 111
Query: 126 LLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAH 185
LLID RH K +D+++ FL + + +VLTK DKL + + L K ++ P
Sbjct: 112 LLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDD 171
Query: 186 PEVIPTSSVKRKGIEVLRKAILETIN 211
V+ SS+K+KGI+ L+ ILE +
Sbjct: 172 QWVVLFSSLKKKGIDELKAKILEWLK 197
>gnl|CDD|37697 KOG2486, KOG2486, KOG2486, Predicted GTPase [General function
prediction only].
Length = 320
Score = 111 bits (278), Expect = 2e-25
Identities = 67/196 (34%), Positives = 88/196 (44%), Gaps = 16/196 (8%)
Query: 24 LPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNA-PGRTQHLNFFVPKDFSNLKNN 82
PK PE+AF GRSNVGKSSL+N LV KN+A TS + G+TQ +N F +
Sbjct: 131 CPKDKRPELAFYGRSNVGKSSLLNDLVRVKNIADTSKSKNGKTQAINHF---------HV 181
Query: 83 LPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVF 142
+ VD+PGYG A + W YL ER L V+LL+D ++ D
Sbjct: 182 GKSWYEVDLPGYGRAGYGFELPADWDKFTKSYLLERENLVRVFLLVDASVPIQPTDNPEI 241
Query: 143 SFLDKKAVSYQIVLTKIDKLS---PTTAQETLEKTKY---LIRNYPTAHPEVIPTSSVKR 196
++L + V V TK DK T + L LIR I SSV
Sbjct: 242 AWLGENNVPMTSVFTKCDKQKKVKRTGKKPGLNIKINFQGLIRGVFLVDLPWIYVSSVTS 301
Query: 197 KGIEVLRKAILETINY 212
G ++L I + Y
Sbjct: 302 LGRDLLLLHIAQLRGY 317
>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This
family includes several distinct subfamilies (TrmE/ThdF,
FeoB, YihA (EngG), 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 = 163
Score = 76.2 bits (188), Expect = 6e-15
Identities = 41/173 (23%), Positives = 70/173 (40%), Gaps = 14/173 (8%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYG 95
GR+N GKSSL+N L+ + +A S PG T +V + + L+D PG
Sbjct: 3 GRTNAGKSSLLNALLG-QEVAIVSPVPGTTTDPVEYVWELGPLGP-----VVLIDTPGID 56
Query: 96 YARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIV 155
A + ++D + ++ + L ++ +V
Sbjct: 57 EAG------GLGREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLV 110
Query: 156 LTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208
L KID L +E LE ++ VI S++ +GI+ LR+A++E
Sbjct: 111 LNKIDLLPEEEEEELLELRLLILLLLLGLP--VIAVSALTGEGIDELREALIE 161
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 72.7 bits (179), Expect = 6e-14
Identities = 30/118 (25%), Positives = 49/118 (41%), Gaps = 12/118 (10%)
Query: 41 GKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAP 100
GKS+LIN L +K A S+ PG T+ N ++ + + LVD PG +
Sbjct: 1 GKSTLINALTGKKR-AIVSDYPGTTRDPNEGR------VELDGKQIILVDTPGIIEGASK 53
Query: 101 KKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTK 158
+ G L R L + ++D G+ + D ++ L + +VL K
Sbjct: 54 GE-----GELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVLNK 106
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 56.0 bits (135), Expect = 7e-09
Identities = 48/183 (26%), Positives = 82/183 (44%), Gaps = 28/183 (15%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH-LNFFVPKDFSNLKNNLPAMALVD 90
+A GR NVGKS+L+N LV +K ++ S P T++ + V D + + VD
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIVTTDNAQI-------IFVD 60
Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSE--RSTLR---CVYLLIDCRHGVKQIDQDVFSFL 145
PG PK + +++ RS L+ + ++D G D+ + L
Sbjct: 61 TPGI---HKPKHALG-------ELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQL 110
Query: 146 DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKA 205
K +V+ KIDK+ P L+ +L + P E++P S++K ++ L +
Sbjct: 111 KKTKTPVILVVNKIDKVKP--KTVLLKLIAFLKKLLP--FKEIVPISALKGDNVDTLLEI 166
Query: 206 ILE 208
I E
Sbjct: 167 IKE 169
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 55.2 bits (133), Expect = 1e-08
Identities = 46/186 (24%), Positives = 71/186 (38%), Gaps = 33/186 (17%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT-----QHLNFFVPKDFSNLKNNLPAM 86
+ GR NVGKSSL+N L+ R + A ++ G T + +N N +P +
Sbjct: 220 VVIIGRPNVGKSSLLNALLGR-DRAIVTDIAGTTRDVIEEDINL----------NGIP-V 267
Query: 87 ALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLD 146
LVD G R V+ G I R V ++D + + D + L
Sbjct: 268 RLVDTAGI---RETDDVVERIG--IERAKKAIEEADLVLFVLDASQPLDKEDLALIELLP 322
Query: 147 KKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAI 206
KK +VL K D +S + I I S+ +G++ LR+AI
Sbjct: 323 KK-KPIIVVLNKADLVSKIELESEKLANGDAI----------ISISAKTGEGLDALREAI 371
Query: 207 LETINY 212
+
Sbjct: 372 KQLFGK 377
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 54.0 bits (130), Expect = 3e-08
Identities = 47/185 (25%), Positives = 75/185 (40%), Gaps = 30/185 (16%)
Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNF----FVPKDFSNLKNNLP 84
P +A GR NVGKS+L N L + +A S+ PG T+ + ++ ++F
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLT-GRRIAIVSDTPGVTRDRIYGDAEWLGREF-------- 53
Query: 85 AMALVDMPGYGYARAPKKNVDSWGGLIVRY-LSERSTLRCVYLLIDCRHGVKQIDQDVFS 143
L+D G + D LI L + ++D R G+ D+++
Sbjct: 54 --ILIDTGGL-----DDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAK 106
Query: 144 FLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLR 203
L + +V+ KID L E+ Y Y E +P S+ +GI L
Sbjct: 107 ILRRSKKPVILVVNKIDNLKA-------EELAYEF--YSLGFGEPVPISAEHGRGIGDLL 157
Query: 204 KAILE 208
A+LE
Sbjct: 158 DAVLE 162
Score = 52.5 bits (126), Expect = 7e-08
Identities = 51/206 (24%), Positives = 85/206 (41%), Gaps = 25/206 (12%)
Query: 14 FLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVP 73
L E + P +IA GR NVGKSSLIN ++ + S+ G T+ +
Sbjct: 163 LLPPDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILG-EERVIVSDIAGTTRDS---ID 218
Query: 74 KDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRC------VYLL 127
+F + + L+D G R K +S V S TL+ V L+
Sbjct: 219 IEF---ERDGRKYVLIDTAG---IRRKGKITES-----VEKYSVARTLKAIERADVVLLV 267
Query: 128 IDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN--YPTAH 185
ID G+ + D + +++ IV+ K D + A T+E+ K +R
Sbjct: 268 IDATEGISEQDLRIAGLIEEAGRGIVIVVNKWDLVEEDEA--TMEEFKKKLRRKLPFLDF 325
Query: 186 PEVIPTSSVKRKGIEVLRKAILETIN 211
++ S++ +G++ L +AI E
Sbjct: 326 APIVFISALTGQGLDKLFEAIKEIYE 351
>gnl|CDD|133363 cd04163, Era, Era subfamily. 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 = 52.4 bits (127), Expect = 8e-08
Identities = 46/183 (25%), Positives = 81/183 (44%), Gaps = 28/183 (15%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH-LNFFVPKDFSNLKNNLPAMALVD 90
+A GR NVGKS+L+N LV +K ++ S P T++ + D + + VD
Sbjct: 6 VAIVGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIYTDDDAQI-------IFVD 57
Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSE--RSTLR---CVYLLIDCRHGVKQIDQDVFSFL 145
PG PKK + + + S L+ V ++D + + D+ + L
Sbjct: 58 TPGI---HKPKKKLG-------ERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELL 107
Query: 146 DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKA 205
K +VL KID + ++ L + L P A E+ P S++K + ++ L +
Sbjct: 108 KKSKTPVILVLNKIDLVKD--KEDLLPLLEKLKELGPFA--EIFPISALKGENVDELLEE 163
Query: 206 ILE 208
I++
Sbjct: 164 IVK 166
>gnl|CDD|133281 cd01881, Obg_like, 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 = 176
Score = 46.7 bits (112), Expect = 4e-06
Identities = 44/197 (22%), Positives = 70/197 (35%), Gaps = 51/197 (25%)
Query: 39 NVGKSSLINILVNRKNLARTSNAPGRTQHLN---FFVPKDFSNLKNNLPAMALVDMPG-- 93
NVGKS+L+N L N K + +N P T N VP + + D+PG
Sbjct: 6 NVGKSTLLNALTNAK--PKVANYPFTTLEPNLGVVEVPDGAR--------IQVADIPGLI 55
Query: 94 YGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDC----RHGVKQI------------ 137
G + GL ++L+ + ++D G
Sbjct: 56 EG----ASEGR----GLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELK 107
Query: 138 ---DQDVFSFL-DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSS 193
+ + L K + VL KID +E L + L EV+P S+
Sbjct: 108 LYDLETILGLLTAKPVI---YVLNKIDLDDAEELEEELVRELALEEG-----AEVVPISA 159
Query: 194 VKRKGIEVLRKAILETI 210
+G++ L +AI E +
Sbjct: 160 KTEEGLDELIRAIYELL 176
>gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 46.2 bits (109), Expect = 7e-06
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 10/59 (16%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGY 94
G NVGKS+LIN L+ +K A+TSN PG T+ + + D L+D PG
Sbjct: 139 GYPNVGKSTLINRLLGKKV-AKTSNRPGTTKGIQWIKLDDGIY---------LLDTPGI 187
>gnl|CDD|133364 cd04164, trmE, 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 = 157
Score = 44.8 bits (107), Expect = 2e-05
Identities = 43/191 (22%), Positives = 69/191 (36%), Gaps = 56/191 (29%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRT-----QHLNFFVPKDFSNLKNNLPAMALVD 90
G+ NVGKSSL+N L R + A S+ G T + ++ +P + L+D
Sbjct: 8 GKPNVGKSSLLNALAGR-DRAIVSDIAGTTRDVIEESIDI----------GGIP-VRLID 55
Query: 91 MPGY----------GYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQD 140
G G RA R E + L +ID G+ + D +
Sbjct: 56 TAGIRETEDEIEKIGIERA-------------REAIEEADLVL--FVIDASRGLDEEDLE 100
Query: 141 VFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIE 200
+ K +VL K D L + L +I S+ +G++
Sbjct: 101 ILELPADK--PIIVVLNKSDLLPDSELLSLLAG------------KPIIAISAKTGEGLD 146
Query: 201 VLRKAILETIN 211
L++A+LE
Sbjct: 147 ELKEALLELAG 157
>gnl|CDD|57928 cd01857, HSR1_MMR1, HSR1/MMR1. 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 = 141
Score = 44.4 bits (105), Expect = 2e-05
Identities = 24/63 (38%), Positives = 29/63 (46%), Gaps = 12/63 (19%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLN-FFVPKDFSNLKNNLPAMALVD 90
I G NVGKSSLIN LV +K S PG+T+H F+ + L D
Sbjct: 86 IGLVGYPNVGKSSLINALVGKK-KVSVSATPGKTKHFQTIFLTPTIT----------LCD 134
Query: 91 MPG 93
PG
Sbjct: 135 CPG 137
>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This 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 = 43.2 bits (103), Expect = 5e-05
Identities = 46/192 (23%), Positives = 79/192 (41%), Gaps = 29/192 (15%)
Query: 28 GPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKD--FSNLKNNLPA 85
P IA GR NVGKSSL+N L+ + S+ G T+ D + +
Sbjct: 1 DPIRIAIIGRPNVGKSSLVNALLG-EERVIVSDIAGTTR--------DSIDVPFEYDGKK 51
Query: 86 MALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLR------CVYLLIDCRHGVKQIDQ 139
L+D G R K + + S TL+ V L+ID G+ + D
Sbjct: 52 YTLIDTAG---IRRKGKVEEG-----IEKYSVLRTLKAIERADVVLLVIDATEGITEQDL 103
Query: 140 DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN--YPTAHPEVIPTSSVKRK 197
+ + ++ + IV+ K D + +T+++ K IR + ++ S++ +
Sbjct: 104 RIAGLILEEGKALVIVVNKWDLVEKD--SKTMKEFKKEIRRKLPFLDYAPIVFISALTGQ 161
Query: 198 GIEVLRKAILET 209
G++ L AI E
Sbjct: 162 GVDKLFDAIDEV 173
>gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1
[General function prediction only].
Length = 562
Score = 41.9 bits (98), Expect = 1e-04
Identities = 19/36 (52%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH 67
+ F G NVGKSS IN LV RK ++ S+ PG+T+H
Sbjct: 317 VGFVGYPNVGKSSTINALVGRKKVS-VSSTPGKTKH 351
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. 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 = 164
Score = 41.4 bits (98), Expect = 2e-04
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 5/91 (5%)
Query: 121 LRCVYLLIDCRHGVKQ--IDQ-DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYL 177
+ V L++ G+ + ++ L K +VLTK D + + E+ + L
Sbjct: 75 IDLVLLVVAADEGIMPQTREHLEILELLGIKRGL--VVLTKADLVDEDWLELVEEEIREL 132
Query: 178 IRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208
+ A + P S+V +GIE L++ + E
Sbjct: 133 LAGTFLADAPIFPVSAVTGEGIEELKEYLDE 163
>gnl|CDD|57927 cd01856, YlqF, YlqF. 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 a
phylogenetically diverse array of bacteria (including
gram-positive bacteria, proteobacteria, Synechocystis,
Borrelia, and Thermotoga) and in all eukaryotes..
Length = 171
Score = 41.0 bits (96), Expect = 3e-04
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 10/55 (18%)
Query: 39 NVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPG 93
NVGKS+LIN L K +A+ N PG T+ + + P + L+D PG
Sbjct: 125 NVGKSTLINRLRG-KKVAKVGNKPGVTKGIQWIK---------ISPGIYLLDTPG 169
>gnl|CDD|133298 cd01898, Obg, Obg subfamily. 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 = 40.5 bits (96), Expect = 3e-04
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 144 FLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLR 203
L+K + +VL KID L E L++ + P V P S++ +G++ L
Sbjct: 112 LLEKPRI---VVLNKIDLLDEEELFELLKELLKELWGKP-----VFPISALTGEGLDELL 163
Query: 204 KAILETI 210
+ + E +
Sbjct: 164 RKLAELL 170
>gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 39.9 bits (93), Expect = 5e-04
Identities = 37/179 (20%), Positives = 68/179 (37%), Gaps = 24/179 (13%)
Query: 32 IAFSGRSNVGKSSLINILVN-RKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90
I +G + GK++L+ L + G T L F K M +D
Sbjct: 3 IGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGF------YYRKLEDGVMGFID 56
Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAV 150
+PG+ P I L+ + L++ G+ + LD +
Sbjct: 57 VPGH-----PDF--------ISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGI 103
Query: 151 SYQI-VLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208
I VLTK D++ +K K ++ + A+ ++ TS+ +GIE L+ +++
Sbjct: 104 KNGIIVLTKADRVDE---ARIEQKIKQILADLSLANAKIFKTSAKTGRGIEELKNELID 159
>gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This 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 = 39.3 bits (93), Expect = 9e-04
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRT 65
GR NVGKS+L N L + A + PG T
Sbjct: 4 GRPNVGKSTLFNRLT-GRRDAIVEDTPGVT 32
>gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 366
Score = 39.2 bits (91), Expect = 9e-04
Identities = 46/207 (22%), Positives = 76/207 (36%), Gaps = 52/207 (25%)
Query: 15 LRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRK----NLARTSNAPGRTQHLNF 70
L+ + ++GL+ G N GKS+L+N L K + A T+ P H+
Sbjct: 193 LKSIADVGLV-----------GFPNAGKSTLLNALSRAKPKVAHYAFTTLRP----HIGT 237
Query: 71 FVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLS--ERSTLRCVYLLI 128
DFS + + D+PG K GL ++L ER ++
Sbjct: 238 VNYDDFSQ-------ITVADIPGIIEGAHMNK------GLGYKFLRHIERCKGLL--FVV 282
Query: 129 DCRHGVKQIDQDVFSFLDKKAVSYQ---------IVLTKIDKLSPTTAQETLEKTKYLIR 179
D + L ++ Y+ IV KID A++ L + L +
Sbjct: 283 DLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLPE---AEKNLLSS--LAK 337
Query: 180 NYPTAHPEVIPTSSVKRKGIEVLRKAI 206
H V+P S+ +G+E L +
Sbjct: 338 RLQNPH--VVPVSAKSGEGLEELLNGL 362
>gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 38.3 bits (89), Expect = 0.001
Identities = 40/195 (20%), Positives = 72/195 (36%), Gaps = 36/195 (18%)
Query: 31 EIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90
++ G N GKS+L++ + K + ++ P T N V + + + D
Sbjct: 161 DVGLVGLPNAGKSTLLSAVSAAK--PKIADYPFTTLVPNLGVVRVDGG-----ESFVVAD 213
Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLL----------IDCRHGVKQIDQD 140
+PG + GL +R+L R R LL D + I +
Sbjct: 214 IPGL------IEGASEGVGLGLRFL--RHIERTRVLLHVIDLSPIDGRDPIEDYQTIRNE 265
Query: 141 VFSF----LDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196
+ + +K + +VL KID +E E K L S++ R
Sbjct: 266 LEKYSPKLAEKPRI---VVLNKIDLPLD--EEELEELKKALAEALGW--EVFYLISALTR 318
Query: 197 KGIEVLRKAILETIN 211
+G++ L +A+ E +
Sbjct: 319 EGLDELLRALAELLE 333
>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
ribosomal structure and biogenesis].
Length = 531
Score = 38.0 bits (88), Expect = 0.002
Identities = 42/194 (21%), Positives = 70/194 (36%), Gaps = 24/194 (12%)
Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMAL 88
+IA GR NVGKSSL+N L + + S PG T+ + + + L
Sbjct: 268 GLQIAIVGRPNVGKSSLLNALSRE-DRSIVSPVPGTTRDA-IEAQVTVNGVP-----VRL 320
Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFL--D 146
D G +++ G R ER+ + L++D + D + L +
Sbjct: 321 SDTAGIREESN--DGIEALGIERARKRIERADVIL--LVVDAEESDTESDLKIARILETE 376
Query: 147 KKAVSYQ----------IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196
+ +V K D +S + T Y + P V+ S +
Sbjct: 377 GVGLVVIVNKMEKQRIILVANKSDLVSKIP-EMTKIPVVYPSAEGRSVFPIVVEVSCTTK 435
Query: 197 KGIEVLRKAILETI 210
+G E L A+L +
Sbjct: 436 EGCERLSTALLNIV 449
>gnl|CDD|133279 cd01878, HflX, 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 = 37.4 bits (88), Expect = 0.003
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
+VL KID L +E LE P+ + S+ +G++ L +AI E +
Sbjct: 158 LVLNKIDLLDDEELEERLEAG----------RPDAVFISAKTGEGLDELLEAIEELL 204
Score = 29.3 bits (67), Expect = 0.89
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 26 KAGPPEIAFSGRSNVGKSSLINILVN 51
++G P +A G +N GKS+L N L
Sbjct: 38 RSGIPTVALVGYTNAGKSTLFNALTG 63
>gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family.
This 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 = 189
Score = 37.3 bits (87), Expect = 0.003
Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 24/134 (17%)
Query: 88 LVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDK 147
+D PG+ D + ++R LS L++D GV+ ++ +
Sbjct: 66 FIDTPGH---------ED-FSSEVIRGLS---VSDGAILVVDANEGVQPQTREHLRIARE 112
Query: 148 KAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE-----------VIPTSSVKR 196
+ + + KID++ +E L + K L+ + ++P S++
Sbjct: 113 GGLPIIVAINKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTG 172
Query: 197 KGIEVLRKAILETI 210
G+E L +AI+E +
Sbjct: 173 IGVEELLEAIVEHL 186
>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 37.2 bits (86), Expect = 0.003
Identities = 39/195 (20%), Positives = 74/195 (37%), Gaps = 36/195 (18%)
Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRKNLAR-----TSNAPGRTQHLNFFVPKDFSNLK 80
++G P +A G +N GKS+L N L T + R L
Sbjct: 189 RSGIPLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELG----------- 237
Query: 81 NNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHG--VKQID 138
+ + L D G+ P V+++ L E + ++D +++++
Sbjct: 238 DGRKVL-LTDTVGF-IRDLPHPLVEAFK----STLEEVKEADLLLHVVDASDPEILEKLE 291
Query: 139 Q--DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196
DV + + + +VL KID L LE+ P + S+
Sbjct: 292 AVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELER----------GSPNPVFISAKTG 341
Query: 197 KGIEVLRKAILETIN 211
+G+++LR+ I+E ++
Sbjct: 342 EGLDLLRERIIELLS 356
>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 37.1 bits (86), Expect = 0.004
Identities = 41/187 (21%), Positives = 70/187 (37%), Gaps = 33/187 (17%)
Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLN-FFVPKDFSNLKNNLPAMA 87
PP + G + GK++L++ + RK A G TQH+ + VP D +P +
Sbjct: 5 PPVVTIMGHVDHGKTTLLDKI--RKTNVAAGEAGGITQHIGAYQVPLD----VIKIPGIT 58
Query: 88 LVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDK 147
+D PG+ + + G S L++ GV + +
Sbjct: 59 FIDTPGH----EAFTAMRARGA---------SVTDIAILVVAADDGVMPQTIEAINHAKA 105
Query: 148 KAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE-------VIPTSSVKRKGIE 200
V + + KIDK + E +Y + PE +P S+ +GI+
Sbjct: 106 AGVPIVVAINKIDKPEANPDKVKQELQEYGLV------PEEWGGDVIFVPVSAKTGEGID 159
Query: 201 VLRKAIL 207
L + IL
Sbjct: 160 ELLELIL 166
>gnl|CDD|143801 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 = 185
Score = 36.7 bits (86), Expect = 0.005
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 126 LLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLI---RNYP 182
L++D GV ++ + V + + K+D++ E +E+ + +
Sbjct: 96 LVVDAVEGVMPQTREHLLLAKQLGVPIIVFINKMDRVDDAELDEVVEEISRELLEKYGFG 155
Query: 183 TAHPEVIPTSSVKRKGIEVLRKAILETI 210
VIP S++ +GI+ L +A+ +
Sbjct: 156 GETIPVIPGSALTGEGIDTLLEALDLYL 183
>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis)
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. This domain architecture suggests a role for
YjeQ as a regulator of translation..
Length = 287
Score = 35.5 bits (82), Expect = 0.010
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 33 AFSGRSNVGKSSLINILVNRKNLA--RTSNAPGRTQH 67
G+S VGKS+LIN L+ +LA S GR +H
Sbjct: 165 VLVGQSGVGKSTLINALLPDLDLATGEISEKLGRGRH 201
Score = 33.6 bits (77), Expect = 0.046
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAI 206
IVLTK D L +E LE + L YP V+ S+ +G++ LR+ +
Sbjct: 114 IVLTKADLLDD--EEEELELVEALALGYP-----VLAVSAKTGEGLDELREYL 159
>gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 35.2 bits (82), Expect = 0.011
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLART---SNAPGRTQH 67
+G+S VGKS+L+N L+ +L RT S GR +H
Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDL-RTGEISEKLGRGRH 75
>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 35.3 bits (81), Expect = 0.013
Identities = 43/197 (21%), Positives = 67/197 (34%), Gaps = 29/197 (14%)
Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMAL 88
P + G + GKSSLIN L + S T L + + L
Sbjct: 39 PVNVLLMGATGAGKSSLINALFQG-EVKEVSKVGVGTDITTRLR------LSYDGENLVL 91
Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKK 148
D PG G + L YL + L V LI D+D +
Sbjct: 92 WDTPGLGDGKDKDAEHRQ---LYRDYLPK---LDLVLWLIKADDRALGTDEDFLRDVIIL 145
Query: 149 AVSYQI--VLTKIDKL-------------SPTTAQETLEKTKYLIRNYPTAHPEVIPTSS 193
+ ++ V+T+ D+ SP Q EK + L R + P V+ S
Sbjct: 146 GLDKRVLFVVTQADRAEPGREWDSAGHQPSPAIKQFIEEKAEALGRLFQEVKP-VVAVSG 204
Query: 194 VKRKGIEVLRKAILETI 210
G++ L +A++ +
Sbjct: 205 RLPWGLKELVRALITAL 221
>gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control,
cell division, chromosome partitioning, Signal
transduction mechanisms].
Length = 379
Score = 34.6 bits (79), Expect = 0.022
Identities = 37/208 (17%), Positives = 70/208 (33%), Gaps = 47/208 (22%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDM 91
+A G NVGKS+L N ++ +K ++ S T+H + + + + D
Sbjct: 75 VAVIGAPNVGKSTLTNQMIGQK-VSAVSRKVHTTRHRILGI------ITSGETQLVFYDT 127
Query: 92 PG-------YGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSF 144
PG + + CV +++D + V
Sbjct: 128 PGLVSKKMHRRHHLMMSVLQNPRDAAQ--------NADCVVVVVDASATRTPLHPRVLHM 179
Query: 145 LDK-KAVSYQIVLTKIDKLSP---------TTAQETLEKTKYLIRNYPTAHP-------- 186
L++ + +V+ KIDKL L K K ++ T P
Sbjct: 180 LEEYSKIPSILVMNKIDKLKQKRLLLNLKDLLTNGELAKLKLEVQEKFTDVPSDEKWRTI 239
Query: 187 -------EVIPTSSVKRKGIEVLRKAIL 207
V S++ +GI+ L++ ++
Sbjct: 240 CGWSHFERVFMVSALYGEGIKDLKQYLM 267
>gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerize to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 34.6 bits (80), Expect = 0.022
Identities = 46/171 (26%), Positives = 69/171 (40%), Gaps = 39/171 (22%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFS-------NLKNNLPAMAL 88
G S +GK++LIN L +L PG ++ + V + +K NL +
Sbjct: 11 GESGLGKTTLINTLFLT-DLYPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLNL---TV 66
Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSER--STLR-----------------CVYLLID 129
+D PG+G A N + W IV Y+ E+ LR C+Y +
Sbjct: 67 IDTPGFGDA---IDNSNCW-KPIVEYIDEQFEQYLRDESRLNRTSIVDNRVHCCLYFISP 122
Query: 130 CRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN 180
HG+K +D + L +K V+ V+ K D L T E K IR
Sbjct: 123 TGHGLKPLDVEFMKKLHEK-VNIIPVIAKADTL---TPDELQR-FKKRIRA 168
>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 34.4 bits (79), Expect = 0.023
Identities = 41/181 (22%), Positives = 74/181 (40%), Gaps = 25/181 (13%)
Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALV 89
+A G NVGK++L N L + N PG T V K LK + +V
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGAN--QKVGNWPGVT------VEKKEGKLKYKGHEIEIV 55
Query: 90 DMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKA 149
D+PG Y+ S + R + ++D ++++++ L
Sbjct: 56 DLPGT-YSLTAY----SEDEKVARDFLLEGKPDLIVNVVD----ATNLERNLYLTLQLLE 106
Query: 150 VSYQIV--LTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAIL 207
+ ++ L ID+ + +EK L+ V+PT + + +G+E L++AI+
Sbjct: 107 LGIPMILALNMIDEAKKRGIRIDIEKLSKLLG------VPVVPTVAKRGEGLEELKRAII 160
Query: 208 E 208
E
Sbjct: 161 E 161
>gnl|CDD|57926 cd01855, YqeH, YqeH. 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 = 190
Score = 33.7 bits (77), Expect = 0.039
Identities = 24/68 (35%), Positives = 28/68 (41%), Gaps = 16/68 (23%)
Query: 34 FSGRSNVGKSSLINILVNRKN-------LARTSNAPGRTQHLNFFVPKDFSNLKNNLPAM 86
G +NVGKS+LIN L+ + N L TS PG T L L N
Sbjct: 132 VVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKI------PLGNGK--- 182
Query: 87 ALVDMPGY 94
L D PG
Sbjct: 183 KLYDTPGI 190
>gnl|CDD|57930 cd01859, MJ1464, MJ1464. 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 = 156
Score = 33.7 bits (77), Expect = 0.041
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFF 71
++ G NVGKSS+IN L R + A TS +PG T+
Sbjct: 98 DGKEGKVGVVGYPNVGKSSIINALKGRHS-ASTSPSPGYTKGEQLV 142
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP
is released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma
is a member of the same family as eubacterial IF2, but
the two proteins are only distantly related. This
family includes translation initiation, elongation, and
release factors.
Length = 203
Score = 32.6 bits (75), Expect = 0.078
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
IV KID + A E E+ K ++ + +IP S+ + I+VL + I++ I
Sbjct: 142 IVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPIIPISAQLKYNIDVLLEYIVKKI 198
>gnl|CDD|30869 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 32.6 bits (74), Expect = 0.079
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 115 LSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKT 174
L++ L V ++D H ++ +D D+ A + IVL K D + E LE
Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIVLNKTDLVDA----EELEAL 166
Query: 175 KYLIR 179
+ +R
Sbjct: 167 EARLR 171
>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 32.5 bits (74), Expect = 0.084
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
IV KID +S A E E+ K ++ + +IP S+ + I+ L +AI + I
Sbjct: 145 IVQNKIDLVSRERALENYEQIKEFVKGTVAENAPIIPISAQHKANIDALIEAIEKYI 201
>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 32.6 bits (74), Expect = 0.084
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 33 AFSGRSNVGKSSLINILVNRKNLA--RTSNAPGRTQH 67
G+S VGKS+LIN L+ N S GR +H
Sbjct: 168 VLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRH 204
>gnl|CDD|57924 cd01849, YlqF_related_GTPase, 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 = 155
Score = 32.3 bits (73), Expect = 0.094
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65
+ G NVGKSS+IN L+N+ L + N PG T
Sbjct: 103 VGVIGYPNVGKSSVINALLNKLKL-KVGNVPGTT 135
>gnl|CDD|145523 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 = 188
Score = 32.1 bits (74), Expect = 0.12
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 188 VIPTSSVKRKGIEVLRKAILETIN 211
V+PTS+ K +GI+ L+ AI+E
Sbjct: 137 VVPTSARKGEGIDELKDAIIEVAE 160
Score = 32.1 bits (74), Expect = 0.13
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDM 91
IA G NVGK++L N L + N PG T V K K + +VD+
Sbjct: 2 IALVGNPNVGKTTLFNALTGAR--QHVGNWPGVT------VEKKEGTFKYKGYEIEIVDL 53
Query: 92 PG 93
PG
Sbjct: 54 PG 55
>gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function
prediction only].
Length = 572
Score = 31.9 bits (72), Expect = 0.14
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQ 66
+ F G NVGKSS+IN L +K + + + PG T+
Sbjct: 310 VGFIGYPNVGKSSIINTL-RKKKVCKVAPIPGETK 343
>gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 31.6 bits (72), Expect = 0.17
Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 10/91 (10%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT--------QHLNFFVPKDFSNL--KN 81
I SG S VGKS+L+ L+ L + +A R F ++F L ++
Sbjct: 7 IVLSGPSGVGKSTLVKALLEDDKLRFSVSATTRKPRPGEVDGVDYFFVTEEEFEELIERD 66
Query: 82 NLPAMALVDMPGYGYARAPKKNVDSWGGLIV 112
A YG +R P + + G ++
Sbjct: 67 EFLEWAEYHGNYYGTSREPVEQALAEGKDVI 97
>gnl|CDD|57929 cd01858, NGP_1, NGP-1. 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 = 31.4 bits (71), Expect = 0.20
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQ 66
+ F G NVGKSS+IN L K + + + PG T+
Sbjct: 105 VGFIGYPNVGKSSIINTL-RSKKVCKVAPIPGETK 138
>gnl|CDD|39846 KOG4647, KOG4647, KOG4647, Uncharacterized membrane protein
[Function unknown].
Length = 263
Score = 30.8 bits (69), Expect = 0.31
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 165 TTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIE 200
Q + EK + N AH E + V+R+ E
Sbjct: 10 VYGQRSEEKDYGSMENLANAHREYL--KVVRRQNRE 43
>gnl|CDD|133265 cd01862, 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 = 30.7 bits (70), Expect = 0.32
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 36 GRSNVGKSSLINILVNRK 53
G S VGK+SL+N VN+K
Sbjct: 7 GDSGVGKTSLMNQYVNKK 24
>gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein
[General function prediction only].
Length = 335
Score = 30.7 bits (69), Expect = 0.33
Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 6 IFTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVN----RKNLARTSNA 61
+ + V I L + G NVGKSSLIN L N +K AR
Sbjct: 122 LLKILTILSEELVRFIRTLN--SEYNVMVVGVPNVGKSSLINALRNVHLRKKKAARVGAE 179
Query: 62 PGRTQ 66
PG T+
Sbjct: 180 PGVTR 184
>gnl|CDD|35669 KOG0448, KOG0448, KOG0448, Mitofusin 1 GTPase, involved in
mitochondrila biogenesis [Posttranslational
modification, protein turnover, chaperones].
Length = 749
Score = 30.4 bits (68), Expect = 0.36
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68
+A GR++ GKS++IN ++++K L P H
Sbjct: 112 VAIFGRTSAGKSTVINAMLHKKLL------PSGIGHT 142
>gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B
(eIF-5B) [Translation, ribosomal structure and
biogenesis].
Length = 1064
Score = 30.4 bits (68), Expect = 0.36
Identities = 30/145 (20%), Positives = 57/145 (39%), Gaps = 27/145 (18%)
Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL--NFF----------VPKDFS 77
P G + GK+ L++ + R + A G TQ + +F K +
Sbjct: 476 PICCILGHVDTGKTKLLDKI--RGTNVQEGEAGGITQQIGATYFPAENIREKTKELKKDA 533
Query: 78 NLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQI 137
+ +P + ++D PG+ +S+ L R S L++D HG++
Sbjct: 534 KKRLKVPGLLVIDTPGH----------ESFTNLRSRGSS---LCDLAILVVDIMHGLEPQ 580
Query: 138 DQDVFSFLDKKAVSYQIVLTKIDKL 162
+ + L + + + L KID+L
Sbjct: 581 TIESINLLRMRKTPFIVALNKIDRL 605
>gnl|CDD|29456 cd02760, MopB_Phenylacetyl-CoA-OR, The MopB_Phenylacetyl-CoA-OR CD
contains the phenylacetyl-CoA:acceptor oxidoreductase,
large subunit (PadB2), and other related proteins. The
phenylacetyl-CoA:acceptor oxidoreductase has been
characterized as a membrane-bound molybdenum-iron-sulfur
enzyme involved in anaerobic metabolism of phenylalanine
in the denitrifying bacterium Thauera aromatica. Members
of this CD belong to the molybdopterin_binding (MopB)
superfamily of proteins..
Length = 760
Score = 30.4 bits (68), Expect = 0.38
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 8 TKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKS 43
T+ AW+FLR VP P++ F+ R+N S
Sbjct: 492 TQLAWMFLREVPLDWKFELPTLPDVWFNYRTNPAIS 527
>gnl|CDD|57931 cd04178, Nucleostemin_like, Nucleostemin-like. 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 = 172
Score = 29.8 bits (67), Expect = 0.58
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68
G NVGKSSLIN L R PG T+ +
Sbjct: 124 GFPNVGKSSLINSL-KRSRACNVGATPGVTKSM 155
>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction
only].
Length = 365
Score = 29.4 bits (66), Expect = 0.79
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 24 LPKAGPPEIAFSGRSNVGKSSLINILVNRK 53
+ K+G +A G +VGKS+L+N L N K
Sbjct: 58 VKKSGDATVALVGFPSVGKSTLLNKLTNTK 87
>gnl|CDD|133297 cd01897, 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 = 168
Score = 29.1 bits (66), Expect = 0.83
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 8/27 (29%)
Query: 27 AGPPEIAFSGRSNVGKSSLINILVNRK 53
AG P NVGKSSL+N L K
Sbjct: 6 AGYP--------NVGKSSLVNKLTRAK 24
>gnl|CDD|133280 cd01879, FeoB, 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 = 158
Score = 29.3 bits (67), Expect = 0.88
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 188 VIPTSSVKRKGIEVLRKAILET 209
V+PTS+ K +GI+ L+ AI E
Sbjct: 134 VVPTSARKGEGIDELKDAIAEL 155
Score = 28.9 bits (66), Expect = 1.0
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPG 93
G NVGK++L N L + + N PG T V K K + +VD+PG
Sbjct: 3 GNPNVGKTTLFNALTGAR--QKVGNWPGVT------VEKKEGRFKLGGKEIEIVDLPG 52
>gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction
only].
Length = 435
Score = 29.2 bits (65), Expect = 0.93
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 35 SGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68
G NVGKSS+IN L RK N PG T+ +
Sbjct: 258 IGYPNVGKSSVINSLKRRKACN-VGNVPGVTRSM 290
>gnl|CDD|72972 cd03213, ABCG_EPDR, 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 = 28.6 bits (64), Expect = 1.3
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTS 59
A G S GKS+L+N L R+ S
Sbjct: 38 TAIMGPSGAGKSTLLNALAGRRTGLGVS 65
>gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 122
Score = 28.5 bits (64), Expect = 1.3
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 30 PEIAFSGRSNVGKSSLINILVN 51
P + G + GK++LI L+N
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLN 22
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.4 bits (63), Expect = 1.5
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRN---YPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
IV+ K D+ A L L+R P V+ TS+++ +GI+ L AI +
Sbjct: 194 IVINKADRKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHR 253
Query: 211 NY 212
+
Sbjct: 254 KF 255
>gnl|CDD|133304 cd04104, p47_IIGP_like, p47 (47-kDa) family. 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 = 28.1 bits (63), Expect = 1.7
Identities = 12/21 (57%), Positives = 13/21 (61%)
Query: 29 PPEIAFSGRSNVGKSSLINIL 49
P IA +G S GKSS IN L
Sbjct: 1 PLNIAVTGESGAGKSSFINAL 21
>gnl|CDD|133258 cd00882, Ras_like_GTPase, 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 regulate
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 = 157
Score = 28.2 bits (63), Expect = 1.8
Identities = 32/175 (18%), Positives = 62/175 (35%), Gaps = 22/175 (12%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYG 95
G S VGK+SL+N L+ + + F K + + + D G
Sbjct: 3 GDSGVGKTSLLNRLLGGEFVPEEYETTIID-----FYSKTIEVDGKKVK-LQIWDTAGQE 56
Query: 96 YARAPKKNVDSWG-GLIVRY-LSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQ 153
R+ ++ G+I+ Y +++R + VK+ + + + +
Sbjct: 57 RFRSLRRLYYRGADGIILVYDVTDRESFEN----------VKEWLLLILINKEGENIPII 106
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208
+V KID L E + L + TS+ + +E L + + E
Sbjct: 107 LVGNKID-LPEERVVSEEELAEQLAKEL---GVPYFETSAKTGENVEELFEELAE 157
>gnl|CDD|99853 cd06099, CS_ACL-C_CCL, Citrate synthase (CS), citryl-CoA lyase
(CCL), the C-terminal portion of the single-subunit type
ATP-citrate lyase (ACL) and the C-terminal portion of
the large subunit of the two-subunit type ACL. CS
catalyzes the condensation of acetyl coenzyme A (AcCoA)
and oxalacetate (OAA) from citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. Some CS proteins function as a
2-methylcitrate synthase (2MCS). 2MCS catalyzes the
condensation of propionyl-CoA (PrCoA) and OAA to form
2-methylcitrate and CoA during propionate metabolism.
CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs
catalyze an ATP- and a CoA- dependant cleavage of
citrate to form AcCoA and OAA; they do this in a
multistep reaction, the final step of which is likely to
involve the cleavage of CiCoA to generate AcCoA and OAA.
The overall CS reaction is thought to proceed through
three partial reactions and involves both closed and
open conformational forms of the enzyme: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate CiCoA, and c) the
hydrolysis of CiCoA to produce citrate and CoA. This
group contains proteins which functions exclusively as
either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS. There are two types of CSs: type I CS and type II
CSs. Type I CSs are found in eukarya, gram-positive
bacteria, archaea, and in some gram-negative bacteria
and are homodimers with both subunits participating in
the active site. Type II CSs are unique to
gram-negative bacteria and are homohexamers of identical
subunits (approximated as a trimer of dimers). Some type
II CSs are strongly and specifically inhibited by NADH
through an allosteric mechanism. In fungi, yeast,
plants, and animals ACL is cytosolic and generates AcCoA
for lipogenesis. In several groups of autotrophic
prokaryotes and archaea, ACL carries out the
citrate-cleavage reaction of the reductive tricarboxylic
acid (rTCA) cycle. In the family Aquificaceae this
latter reaction in the rTCA cycle is carried out via a
two enzyme system the second enzyme of which is CCL..
Length = 213
Score = 28.1 bits (63), Expect = 1.9
Identities = 10/57 (17%), Positives = 18/57 (31%), Gaps = 6/57 (10%)
Query: 64 RTQHLNFFVPKDFSNLKNNLPAMALVD-----MPGYGYARAPKKNVDSWGGLIVRYL 115
R L F + + P L Y + NVD + G++ + +
Sbjct: 118 RATVLKKFAEELLKE-DGDDPMFELAAELEKIAEEVLYEKKLYPNVDFYSGVLYKAM 173
>gnl|CDD|34624 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 27.9 bits (62), Expect = 1.9
Identities = 37/174 (21%), Positives = 65/174 (37%), Gaps = 43/174 (24%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNL-------KNNLPAMAL 88
G S +GK++ IN L + T R + + + + NL +
Sbjct: 30 GESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNL---TV 86
Query: 89 VDMPGYGYARAPKKNVD---SWGGLIV-------RYLSERSTLR------------CVYL 126
+D PG+G +D W ++ +YL E ++ C+Y
Sbjct: 87 IDTPGFG------DFIDNSKCWEPIVDYIDDQFDQYLDEEQKIKRNPKFKDTRVHACLYF 140
Query: 127 LIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN 180
+ HG+K +D + L K+ V+ V+ K D L+ + L + K IR
Sbjct: 141 IRPTGHGLKPLDIEAMKRLSKR-VNLIPVIAKADTLTD----DELAEFKERIRE 189
>gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function
prediction only].
Length = 210
Score = 27.6 bits (61), Expect = 2.4
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRK 53
K ++ G S VGK+SL+N VN+K
Sbjct: 6 KRTLLKVIILGDSGVGKTSLMNQYVNKK 33
>gnl|CDD|48380 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 = 27.5 bits (61), Expect = 2.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 29 PPEIAFSGRSNVGKSSLINILV 50
I F G S GK++L+ L+
Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLI 22
>gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic
initiation factor 5B) subfamily. 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 = 168
Score = 27.5 bits (62), Expect = 2.9
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 14/63 (22%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE--------VIPTSSVKRKGIEVLRKA 205
+ L KIDK E+ K + E ++PTS+ +GI+ L +A
Sbjct: 107 VALNKIDKP-----NANPERVKNELSEL-GLQGEDEWGGDVQIVPTSAKTGEGIDDLLEA 160
Query: 206 ILE 208
IL
Sbjct: 161 ILL 163
>gnl|CDD|145920 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesized ATP binding
activity.
Length = 234
Score = 27.3 bits (61), Expect = 2.9
Identities = 15/76 (19%), Positives = 22/76 (28%), Gaps = 17/76 (22%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYL--------------IRNY---PTAHPEVIPTSSVKR 196
+ L K D LS A + L IR P + +
Sbjct: 159 VALNKFDLLSLEFALKWFTDPDDLQLLLELDYRYLNEAIRLALDLFYLVPRFLCDARETG 218
Query: 197 KGIEVLRKAILETINY 212
+ +E L I E + Y
Sbjct: 219 ESMEDLLTLIDEALQY 234
>gnl|CDD|34592 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 = 27.5 bits (61), Expect = 3.0
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 32 IAFSGRSNVGKSSLINILV 50
+A GRS GKS+L+ +L
Sbjct: 367 VAILGRSGSGKSTLLQLLA 385
>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 27.5 bits (61), Expect = 3.1
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 7 FTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRK 53
F + A L+ +P I P I +G NVGKSSL+ L K
Sbjct: 150 FLRKARDHLKKLPAI----DPDLPTIVVAGYPNVGKSSLVRKLTTAK 192
>gnl|CDD|133252 cd00876, Ras, Ras family. 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 = 27.1 bits (61), Expect = 3.4
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 32 IAFSGRSNVGKSSLINILVN 51
+ G VGKS++ V
Sbjct: 2 VVVLGAGGVGKSAITIQFVK 21
>gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma
subunit (eIF-2gamma; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 466
Score = 27.2 bits (60), Expect = 3.6
Identities = 15/57 (26%), Positives = 29/57 (50%)
Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210
I+ KID + + A E E+ + I+ +IP S+ + I+V+ + I++ I
Sbjct: 184 ILQNKIDLIKESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNIDVVCEYIVKKI 240
>gnl|CDD|37302 KOG2091, KOG2091, KOG2091, Predicted member of glycosyl hydrolase
family 18 [Carbohydrate transport and metabolism].
Length = 392
Score = 26.9 bits (59), Expect = 4.0
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 65 TQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNV-DSWGGLIVRYLSERSTLRC 123
L FF P++FS L +L+ Y + P N W + +L S R
Sbjct: 235 NGQLKFFTPEEFSKLVAVYDGFSLMTY-DYSLVQGPGPNAPLEWIRHCLHHLGGSSAKRP 293
Query: 124 VYLL 127
LL
Sbjct: 294 KILL 297
>gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein
[General function prediction only].
Length = 398
Score = 26.8 bits (59), Expect = 4.4
Identities = 8/38 (21%), Positives = 13/38 (34%)
Query: 15 LRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNR 52
+ E + G + GKS+L L N+
Sbjct: 59 IADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANK 96
>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
cancer resistance protein) [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 613
Score = 26.9 bits (59), Expect = 4.5
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 26 KAGPPEI-AFSGRSNVGKSSLINILVNRKN 54
A P E+ A G S GK++L+N L R N
Sbjct: 52 TAKPGELLAIMGPSGSGKTTLLNALAGRLN 81
>gnl|CDD|35667 KOG0446, KOG0446, KOG0446, Vacuolar sorting protein VPS1,
dynamin, and related proteins [Intracellular
trafficking, secretion, and vesicular transport,
General function prediction only].
Length = 657
Score = 26.9 bits (59), Expect = 4.7
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65
P+I G + GKSS++ LV L R R
Sbjct: 30 PQIVVVGGQSSGKSSVLESLVGFVFLPRGVGIVTRR 65
>gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like
(PDR) family of ATP-binding cassette (ABC)
transporters. PDR is a well-described phenomenon
occurring in fungi and shares several similarities with
processes in bacteria and higher eukaryotes. This PDR
subfamily represents domain I of its (ABC-IM)2
organization. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds including 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 = 192
Score = 26.3 bits (58), Expect = 5.6
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 33 AFSGRSNVGKSSLINILVNRKN 54
A G S GK++L+++L RK
Sbjct: 37 ALMGESGAGKTTLLDVLAGRKT 58
>gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN
superfamily) [General function prediction only].
Length = 391
Score = 26.4 bits (58), Expect = 5.8
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAP 62
+I G NVGKS+ N L K A +N P
Sbjct: 21 LKIGIVGLPNVGKSTFFNALTKSK--AGAANFP 51
>gnl|CDD|34593 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 = 26.3 bits (58), Expect = 5.9
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 32 IAFSGRSNVGKSSLINIL 49
A G S GKS+L+N+L
Sbjct: 350 TALVGASGAGKSTLLNLL 367
>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 26.0 bits (57), Expect = 7.4
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 32 IAFSGRSNVGKSSLINILVN 51
IA G + GKS+L+ +L
Sbjct: 351 IAIVGPNGAGKSTLLKLLAG 370
>gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. 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 = 276
Score = 26.0 bits (58), Expect = 7.7
Identities = 30/135 (22%), Positives = 44/135 (32%), Gaps = 44/135 (32%)
Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQ-----------HLNFFVPKDFS-NLKNNL 83
G S +GKS+ IN L N L + P + L
Sbjct: 11 GESGLGKSTFINTLFN-TKLIPSDYPPDPAEEHIDKTVEIKSSKAEIEENGVKLKLT--- 66
Query: 84 PAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSER--STLR------------------C 123
++D PG+G N D W IV Y+ ++ LR C
Sbjct: 67 ----VIDTPGFGDN---INNSDCWK-PIVDYIDDQFDQYLREESRIKRNPRIPDTRVHAC 118
Query: 124 VYLLIDCRHGVKQID 138
+Y + HG+K +D
Sbjct: 119 LYFIEPTGHGLKPLD 133
>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP)..
Length = 200
Score = 26.0 bits (57), Expect = 7.9
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 32 IAFSGRSNVGKSSLINILVNR 52
I F G GK++LI +L R
Sbjct: 3 IVFEGIDGAGKTTLIELLAER 23
>gnl|CDD|113806 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 localizes
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 25.9 bits (57), Expect = 7.9
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 29 PPEIAFSGRSNVGKSSLINIL 49
P +IA +G S GKSS IN L
Sbjct: 35 PLKIAVTGDSGNGKSSFINAL 55
>gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily
conserved, nucleolar protein. Its depletion interferes
with processing of the 35S pre-rRNA at sites A0, A1,
and A2, and the formation of 40S subunits. Bms1, the
putative endonuclease Rc11, and the essential U3 small
nucleolar RNA form a stable subcomplex that is believed
to control an early step in the formation of the 40S
subumit. The C-terminal domain of Bms1 contains a
GTPase-activating protein (GAP) that functions
intramolecularly. It is believed that Rc11 activates
Bms1 by acting as a guanine-nucleotide exchange factor
(GEF) to promote GDP/GTP exchange, and that activated
(GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Length = 225
Score = 26.1 bits (58), Expect = 8.4
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 18 VPEIGLLPKAGPPEI-AFSGRSNVGKSSLINILVNR 52
VP + P+ PP + A G VGK++LI LV
Sbjct: 27 VPVVDRTPEEPPPLVVAVVGPPGVGKTTLIKSLVKN 62
>gnl|CDD|111954 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 25.9 bits (57), Expect = 8.4
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 64 RTQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPK 101
RT +F+V + + +N PA+ +P R P
Sbjct: 361 RTGARSFYVYASYQDALSNKPALCTGGVPAGARVREPV 398
>gnl|CDD|37866 KOG2655, KOG2655, KOG2655, Septin family protein (P-loop GTPase)
[Cell cycle control, cell division, chromosome
partitioning, Nuclear structure, Intracellular
trafficking, secretion, and vesicular transport].
Length = 366
Score = 26.1 bits (57), Expect = 8.4
Identities = 39/174 (22%), Positives = 59/174 (33%), Gaps = 45/174 (25%)
Query: 36 GRSNVGKSSLIN-----ILVNRKNLARTSNAPGRT----QHLNFFVPKDFSNLKNNLPAM 86
G S +GKS+ IN L + + S T
Sbjct: 28 GESGLGKSTFINSLFLTDLSGNREVPGASERIKETVEIESTKVEIEENGVKLNLT----- 82
Query: 87 ALVDMPGYGYA-------RAPKKNVDSWGGLIVRYLSERSTLR-----------CVYLLI 128
++D PG+G A R +DS +YL E S L C+Y +
Sbjct: 83 -VIDTPGFGDAVDNSNCWRPIVNYIDS---QFDQYLDEESRLNRSKIKDNRVHCCLYFIS 138
Query: 129 DCRHGVKQIDQDVFSFLDKKAVSYQI--VLTKIDKLSPTTAQETLEKTKYLIRN 180
HG+K +D F+ K + + V+ K D L+ + L + K IR
Sbjct: 139 PTGHGLKPLD---IEFMKKLSKKVNLIPVIAKADTLTK----DELNQFKKRIRQ 185
>gnl|CDD|31858 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 359
Score = 25.9 bits (56), Expect = 8.8
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 18 VPEIGLLPKAGPPEIAF-SGRSNVGKSSLINILVNRKNL 55
+ E+ + ++ PP I F GR VGK+SL+ + K
Sbjct: 11 LEELLKIIESEPPSIVFIYGRRRVGKTSLLKEFIKEKLG 49
>gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 25.9 bits (57), Expect = 9.1
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAP 62
+I G NVGKS+L N L K A +N P
Sbjct: 3 LKIGIVGLPNVGKSTLFNALT--KAGAEIANYP 33
>gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 25.7 bits (56), Expect = 9.2
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 11/59 (18%)
Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90
+ +G S +GKS+L+N + R + F + N+P LV
Sbjct: 27 VLVAGESGIGKSALVNEVHKP-------ITQQRGYFIKGK----FDQFERNIPLSPLVQ 74
>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3 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 = 25.8 bits (57), Expect = 9.2
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 32 IAFSGRSNVGKSSLINILVNR 52
I GR+ GKS+L+ ++
Sbjct: 29 IGLVGRNGAGKSTLLKLIAGE 49
>gnl|CDD|133302 cd04102, RabL3, RabL3 (Rab-like3) subfamily. RabL3s are novel
proteins that have high sequence similarity with Rab
family members, but display features that are distinct
from Rabs, and have been termed Rab-like. As in other
Rab-like proteins, RabL3 lacks a prenylation site at
the C-terminus. The specific function of RabL3 remains
unknown.
Length = 202
Score = 25.5 bits (56), Expect = 9.9
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 36 GRSNVGKSSLINILVNRKNLARTS 59
G S VGKSSL++++ + L R S
Sbjct: 7 GDSGVGKSSLVHLICKNQVLGRPS 30
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.136 0.399
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,532,246
Number of extensions: 127256
Number of successful extensions: 562
Number of sequences better than 10.0: 1
Number of HSP's gapped: 535
Number of HSP's successfully gapped: 128
Length of query: 212
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 122
Effective length of database: 4,318,927
Effective search space: 526909094
Effective search space used: 526909094
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: 55 (25.1 bits)