RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1174
(182 letters)
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 231 bits (592), Expect = 4e-75
Identities = 92/130 (70%), Positives = 97/130 (74%), Gaps = 12/130 (9%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
GTIGHVAHGKSTVVKA+SGV+TVRFK E RNITIKLGYANAKIYKC KC RP CY S
Sbjct: 38 GTIGHVAHGKSTVVKALSGVKTVRFKREKVRNITIKLGYANAKIYKC--PKCPRPTCYQS 95
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA 140
S+K D+ PC C + L RHVSFVDCPGHDILMATMLNGAAVMDAALLLI A
Sbjct: 96 YGSSKPDNPPC--PGCGHKMTLKRHVSFVDCPGHDILMATMLNGAAVMDAALLLI----A 149
Query: 141 AKTPEIVDCP 150
A CP
Sbjct: 150 ANES----CP 155
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). 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 = 197
Score = 207 bits (528), Expect = 1e-68
Identities = 79/115 (68%), Positives = 87/115 (75%), Gaps = 10/115 (8%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
GTIGHVAHGK+T+VKA+SGV TVR K EL+RNITIKLGYANAKIYKC N C RP
Sbjct: 4 GTIGHVAHGKTTLVKALSGVWTVRHKEELKRNITIKLGYANAKIYKCPNCGCPRP----- 58
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
D+ C C G +LVRHVSFVDCPGH+ILMATML+GAAVMD ALLLI
Sbjct: 59 -----YDTPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLLI 108
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 180 bits (458), Expect = 2e-55
Identities = 70/130 (53%), Positives = 82/130 (63%), Gaps = 19/130 (14%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
G +GHV HGK+T+ KA+SGV T R EL+R ITIKLGYA+AKIYKC C RP CY
Sbjct: 14 GMVGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCPE--CYRPECYT- 70
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA 140
C +C +LVR VSFVD PGH+ LMATML+GAA+MD ALL+I A
Sbjct: 71 ------TEPKC--PNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVI----A 118
Query: 141 AKTPEIVDCP 150
A P CP
Sbjct: 119 ANEP----CP 124
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 148 bits (376), Expect = 2e-43
Identities = 61/130 (46%), Positives = 79/130 (60%), Gaps = 19/130 (14%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
G +GHV HGK+T+V+A++GV T R EL+R ITI+LGYA+A I KC C P Y +
Sbjct: 13 GMVGHVDHGKTTLVQALTGVWTDRHSEELKRGITIRLGYADATIRKC--PDCEEPEAYTT 70
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA 140
+ C +L+R VSFVD PGH+ LMATML+GAA+MD A+L+I A
Sbjct: 71 EPKCPN---------CGSETELLRRVSFVDAPGHETLMATMLSGAALMDGAILVI----A 117
Query: 141 AKTPEIVDCP 150
A P CP
Sbjct: 118 ANEP----CP 123
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 139 bits (352), Expect = 6e-40
Identities = 63/130 (48%), Positives = 82/130 (63%), Gaps = 19/130 (14%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
G +GHV HGK+T+ KA++GV T EL+R I+I+LGYA+A+IYKC +C P CY +
Sbjct: 8 GMVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKC--PECDGPECYTT 65
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA 140
C +C +L+R VSFVD PGH+ LMATML+GAA+MD ALL+I A
Sbjct: 66 EPV-------C--PNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVI----A 112
Query: 141 AKTPEIVDCP 150
A P CP
Sbjct: 113 ANEP----CP 118
>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 = 82.3 bits (204), Expect = 3e-20
Identities = 36/118 (30%), Positives = 54/118 (45%), Gaps = 36/118 (30%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
GT GH+ HGK+T++KA++G++T R E +R ITI LG+A
Sbjct: 3 GTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLD----------------- 45
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCD 138
P + + F+D PGH+ + ML GA +DA LL++ D
Sbjct: 46 --------LPD-----------GKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAAD 84
Score = 38.7 bits (91), Expect = 4e-04
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 142 KTPEIVDCPGHDILMATMLNGAAVMDAALLLI 173
K +D PGH+ + ML GA +DA LL++
Sbjct: 50 KRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVV 81
>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 = 82.2 bits (204), Expect = 5e-20
Identities = 30/131 (22%), Positives = 44/131 (33%), Gaps = 50/131 (38%)
Query: 21 GTIGHVAHGKSTVVKAISGV-------------QTVRFKNELERNITIKLGYANAKIYKC 67
G IGHV HGK+T+ A+ V + K E ER ITIK+
Sbjct: 7 GIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAV------- 59
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
+ R ++ +D PGH M+ GA+
Sbjct: 60 ----------SFETKK--------------------RLINIIDTPGHVDFTKEMIRGASQ 89
Query: 128 MDAALLLIGCD 138
D A+L++
Sbjct: 90 ADGAILVVDAV 100
Score = 47.5 bits (114), Expect = 4e-07
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I+D PGH M+ GA+ D A+L++
Sbjct: 70 IIDTPGHVDFTKEMIRGASQADGAILVV 97
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 70.1 bits (172), Expect = 2e-14
Identities = 42/126 (33%), Positives = 60/126 (47%), Gaps = 38/126 (30%)
Query: 22 TIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYISG 81
T GHV HGK+T+++AI+GV R E +R +TI LGYA Y +P G
Sbjct: 5 TAGHVDHGKTTLLQAITGVNADRLPEEKKRGMTIDLGYA----Y------WPQP----DG 50
Query: 82 RSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA- 140
R + F+D PGH+ ++ ML G +D ALL++ CD+
Sbjct: 51 RV----------------------LGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGV 88
Query: 141 -AKTPE 145
A+T E
Sbjct: 89 MAQTRE 94
Score = 30.0 bits (68), Expect = 0.67
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
+D PGH+ ++ ML G +D ALL++
Sbjct: 56 IDVPGHEKFLSNMLAGVGGIDHALLVV 82
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 68.9 bits (169), Expect = 3e-14
Identities = 36/128 (28%), Positives = 48/128 (37%), Gaps = 50/128 (39%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKN-------------ELERNITIKLGYANAKIYKC 67
GTIGHV HGK+T+ AI+ V + E R ITI + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVE---YET 72
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
N RH + VDCPGH + M+ GAA
Sbjct: 73 AN----------------------------------RHYAHVDCPGHADYVKNMITGAAQ 98
Query: 128 MDAALLLI 135
MD A+L++
Sbjct: 99 MDGAILVV 106
Score = 38.0 bits (89), Expect = 0.001
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVV 106
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 68.6 bits (168), Expect = 6e-14
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 37/119 (31%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
GT GH+ HGK+T++KA++G T R E +R ITI LG+ K
Sbjct: 4 GTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGFYYRK----------------- 46
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDN 139
+D + F+D PGH ++ +L G +D ALL++ D
Sbjct: 47 ----LED----------------GVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADE 85
Score = 32.8 bits (75), Expect = 0.087
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 142 KTPEIVDCPGHDILMATMLNGAAVMDAALLLI 173
+D PGH ++ +L G +D ALL++
Sbjct: 50 GVMGFIDVPGHPDFISNLLAGLGGIDYALLVV 81
>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 = 65.4 bits (160), Expect = 9e-14
Identities = 31/131 (23%), Positives = 44/131 (33%), Gaps = 50/131 (38%)
Query: 21 GTIGHVAHGKSTVVKAISGV-------------QTVRFKNELERNITIKLGYANAKIYKC 67
G IGHV HGK+T+ ++ K E ER ITIK G + K
Sbjct: 3 GVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK- 61
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
R ++F+D PGH+ + G A
Sbjct: 62 ------------------------------------RRINFIDTPGHEDFSKETVRGLAQ 85
Query: 128 MDAALLLIGCD 138
D ALL++ +
Sbjct: 86 ADGALLVVDAN 96
Score = 37.3 bits (87), Expect = 0.002
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
+D PGH+ + G A D ALL++
Sbjct: 66 FIDTPGHEDFSKETVRGLAQADGALLVV 93
>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 = 68.0 bits (166), Expect = 1e-13
Identities = 34/123 (27%), Positives = 52/123 (42%), Gaps = 37/123 (30%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
T GHV HGK+T++KA++G+ R E +R +TI LG+A
Sbjct: 4 ATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFA-------------------- 43
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNA 140
FP + F+D PGH+ ++ + G +DAALL++ D
Sbjct: 44 -------YFPLPD----------YRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEG 86
Query: 141 AKT 143
T
Sbjct: 87 VMT 89
Score = 35.6 bits (82), Expect = 0.010
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 142 KTPEIVDCPGHDILMATMLNGAAVMDAALLLI 173
+D PGH+ ++ + G +DAALL++
Sbjct: 50 YRLGFIDVPGHEKFISNAIAGGGGIDAALLVV 81
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 60.1 bits (146), Expect = 1e-11
Identities = 34/119 (28%), Positives = 57/119 (47%), Gaps = 27/119 (22%)
Query: 21 GTIGHVAHGKSTVVKAISGV-QTVRF-KN--ELERNITIKLGYANAKIYKCDNEKCSRPA 76
G +GHV GK+++ KA+S + T F KN ER IT+ LG++ +
Sbjct: 4 GLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFS---------------S 48
Query: 77 CYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
+ +K + +Q ++ VDCPGH L+ T++ GA ++D LL++
Sbjct: 49 FEV----DKPKHLEDNENPQIENYQ----ITLVDCPGHASLIRTIIGGAQIIDLMLLVV 99
Score = 38.1 bits (89), Expect = 9e-04
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH L+ T++ GA ++D LL++
Sbjct: 73 VDCPGHASLIRTIIGGAQIIDLMLLVV 99
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 59.8 bits (146), Expect = 5e-11
Identities = 36/127 (28%), Positives = 47/127 (37%), Gaps = 52/127 (40%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKN-------------ELERNITIKLGYANAKI-YK 66
GTIGHV HGK+T+ AI+ V + E R ITI A + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARGITI----NTAHVEYE 71
Query: 67 CDNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAA 126
+ RH + VDCPGH + M+ GAA
Sbjct: 72 TEK----------------------------------RHYAHVDCPGHADYVKNMITGAA 97
Query: 127 VMDAALL 133
MD A+L
Sbjct: 98 QMDGAIL 104
Score = 37.5 bits (88), Expect = 0.002
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALL 171
VDCPGH + M+ GAA MD A+L
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAIL 104
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 59.9 bits (146), Expect = 6e-11
Identities = 36/129 (27%), Positives = 49/129 (37%), Gaps = 52/129 (40%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNEL-------------ERNITIKLGYANAKI-YK 66
GTIGHV HGK+T+ AI+ V + E R ITI + + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARGITI----NTSHVEYE 71
Query: 67 CDNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAA 126
N RH + VDCPGH + M+ GAA
Sbjct: 72 TAN----------------------------------RHYAHVDCPGHADYVKNMITGAA 97
Query: 127 VMDAALLLI 135
MD A+L++
Sbjct: 98 QMDGAILVV 106
Score = 37.1 bits (87), Expect = 0.003
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVV 106
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 57.3 bits (139), Expect = 4e-10
Identities = 38/128 (29%), Positives = 50/128 (39%), Gaps = 50/128 (39%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKN-------------ELERNITIKLGYANAKIYKC 67
GTIGHV HGK+T+ AI+ V R N E ER ITI + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERGITINTAHVE---YET 72
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
+ RH + VDCPGH + M+ GAA
Sbjct: 73 EK----------------------------------RHYAHVDCPGHADYVKNMITGAAQ 98
Query: 128 MDAALLLI 135
MD A+L++
Sbjct: 99 MDGAILVV 106
Score = 37.2 bits (87), Expect = 0.002
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVV 106
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 54.5 bits (132), Expect = 2e-09
Identities = 38/119 (31%), Positives = 50/119 (42%), Gaps = 32/119 (26%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAK----IYKCDNEKCSRPA 76
GTIGHV HGK+T+ AI+ V K G A AK I K EK
Sbjct: 6 GTIGHVDHGKTTLTAAITKVLA-------------KKGGAKAKKYDEIDKAPEEKARGIT 52
Query: 77 CYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
+ + + RH + VDCPGH + M+ GAA MD A+L++
Sbjct: 53 INTAHVEYETAN---------------RHYAHVDCPGHADYIKNMITGAAQMDGAILVV 96
Score = 34.9 bits (81), Expect = 0.009
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 70 VDCPGHADYIKNMITGAAQMDGAILVV 96
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 55.2 bits (133), Expect = 2e-09
Identities = 36/128 (28%), Positives = 49/128 (38%), Gaps = 50/128 (39%)
Query: 21 GTIGHVAHGKSTVVKAISGV-------QTVRFKN------ELERNITIKLGYANAKIYKC 67
GTIGHV HGK+T+ AI+ V + E R ITI + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARGITINTAHVE---YET 72
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
+N RH + VDCPGH + M+ GAA
Sbjct: 73 EN----------------------------------RHYAHVDCPGHADYVKNMITGAAQ 98
Query: 128 MDAALLLI 135
MD A+L++
Sbjct: 99 MDGAILVV 106
Score = 38.2 bits (89), Expect = 0.001
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVV 106
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 53.8 bits (130), Expect = 6e-09
Identities = 35/128 (27%), Positives = 48/128 (37%), Gaps = 50/128 (39%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKN-------------ELERNITIKLGYANAKIYKC 67
GTIGHV HGK+T+ AI+ + E R ITI + Y+
Sbjct: 16 GTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHVE---YET 72
Query: 68 DNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAV 127
+N RH + VDCPGH + M+ GAA
Sbjct: 73 EN----------------------------------RHYAHVDCPGHADYVKNMITGAAQ 98
Query: 128 MDAALLLI 135
MD A+L++
Sbjct: 99 MDGAILVV 106
Score = 37.2 bits (87), Expect = 0.002
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVV 106
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 53.3 bits (128), Expect = 1e-08
Identities = 38/129 (29%), Positives = 50/129 (38%), Gaps = 52/129 (40%)
Query: 21 GTIGHVAHGKSTVVKAISGV-------QTVRFKN------ELERNITIKLGYANAKI-YK 66
GTIGHV HGK+T+ AI+ V + V F E R ITI A A + Y+
Sbjct: 65 GTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITI----ATAHVEYE 120
Query: 67 CDNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAA 126
RH + VDCPGH + M+ GAA
Sbjct: 121 TAK----------------------------------RHYAHVDCPGHADYVKNMITGAA 146
Query: 127 VMDAALLLI 135
MD +L++
Sbjct: 147 QMDGGILVV 155
Score = 36.3 bits (84), Expect = 0.005
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD +L++
Sbjct: 129 VDCPGHADYVKNMITGAAQMDGGILVV 155
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 48.5 bits (115), Expect = 5e-07
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 25/119 (21%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYIS 80
GTIGHV HGK+T+ A++ +G + K Y +E + P
Sbjct: 85 GTIGHVDHGKTTLTAALTMA-------------LASMGGSAPKKY---DEIDAAPEERAR 128
Query: 81 GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI-GCD 138
G + + ++ RH + VDCPGH + M+ GAA MD A+L++ G D
Sbjct: 129 GIT--------INTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGAD 179
Score = 37.3 bits (86), Expect = 0.003
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 147 VDCPGHDILMATMLNGAAVMDAALLLI 173
VDCPGH + M+ GAA MD A+L++
Sbjct: 149 VDCPGHADYVKNMITGAAQMDGAILVV 175
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 43.4 bits (103), Expect = 2e-05
Identities = 27/133 (20%), Positives = 47/133 (35%), Gaps = 41/133 (30%)
Query: 23 IGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAK-IYKCDNEKCSRPACYISG 81
IGHV GKST+V + LG + + + K + E +
Sbjct: 13 IGHVDAGKSTLVG----------------RLLYDLGEIDKRTMEKLEKE---------AK 47
Query: 82 RSNKD--------DSFPCLR------SSCTGRFQL-VRHVSFVDCPGHDILMATMLNGAA 126
K+ D R +F+ + + +D PGH + M+ GA+
Sbjct: 48 ELGKESFKFAWVLDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGAS 107
Query: 127 VMDAALLLIGCDN 139
D A+L++ +
Sbjct: 108 QADVAVLVVDARD 120
Score = 37.7 bits (88), Expect = 0.002
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 145 EIVDCPGHDILMATMLNGAAVMDAALLLI 173
I+D PGH + M+ GA+ D A+L++
Sbjct: 88 TIIDAPGHRDFVKNMITGASQADVAVLVV 116
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 42.9 bits (101), Expect = 3e-05
Identities = 35/125 (28%), Positives = 51/125 (40%), Gaps = 23/125 (18%)
Query: 23 IGHVAHGKSTVVK-------AISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRP 75
IGHV HGKST V AI +F+ E + +A + D K R
Sbjct: 13 IGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFA----WVMDRLKEERE 68
Query: 76 ACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
R D T +++ V+ VDCPGH + M+ GA+ DAA+L++
Sbjct: 69 ------RGVTIDV--AHWKFETDKYE----VTIVDCPGHRDFIKNMITGASQADAAVLVV 116
Query: 136 GCDNA 140
+
Sbjct: 117 AVGDG 121
Score = 38.3 bits (89), Expect = 0.001
Identities = 18/38 (47%), Positives = 26/38 (68%), Gaps = 4/38 (10%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI----GKFKVQ 179
IVDCPGH + M+ GA+ DAA+L++ G+F+VQ
Sbjct: 89 IVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQ 126
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 41.1 bits (97), Expect = 1e-04
Identities = 47/184 (25%), Positives = 67/184 (36%), Gaps = 80/184 (43%)
Query: 23 IGHVAHGKSTVV------------KAIS---------GVQTVRF-------KNELERNIT 54
IGHV HGKST+V I G ++ +F K E ER +T
Sbjct: 12 IGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERERGVT 71
Query: 55 IKLGYANAKIYKCDNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGH 114
I L + K + +K + + VDCPGH
Sbjct: 72 IDLAH-----KKFETDK--------------------------------YYFTIVDCPGH 94
Query: 115 DILMATMLNGAAVMDAALLLIGCDNA----AKTPEIVDCPGHDILMATM-LNGAAV---- 165
+ M+ GA+ DAA+L++ D+A +T E H L T+ +N V
Sbjct: 95 RDFVKNMITGASQADAAVLVVAADDAGGVMPQTRE------HVFLARTLGINQLIVAINK 148
Query: 166 MDAA 169
MDA
Sbjct: 149 MDAV 152
Score = 35.7 bits (83), Expect = 0.010
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
IVDCPGH + M+ GA+ DAA+L++
Sbjct: 88 IVDCPGHRDFVKNMITGASQADAAVLVV 115
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 39.4 bits (92), Expect = 6e-04
Identities = 32/132 (24%), Positives = 56/132 (42%), Gaps = 27/132 (20%)
Query: 21 GTIGHVAHGKSTVVKAI--------SGVQTV---RFKNELERNITIKLGYANAKIYKCDN 69
G GHV HGKST+V + G K+E+ER ++ + +Y D+
Sbjct: 121 GVAGHVDHGKSTLVGVLVTGRLDDGDGATRSYLDVQKHEVERGLSADISLR---VYGFDD 177
Query: 70 EKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNG--AAV 127
K R + ++ + ++ + + VSFVD GH+ + T + G
Sbjct: 178 GKVVR----LKNPLDEAEKAAVVKRA-------DKLVSFVDTVGHEPWLRTTIRGLLGQK 226
Query: 128 MDAALLLIGCDN 139
+D LL++ D+
Sbjct: 227 VDYGLLVVAADD 238
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 39.0 bits (91), Expect = 8e-04
Identities = 33/125 (26%), Positives = 48/125 (38%), Gaps = 38/125 (30%)
Query: 23 IGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLG-YANAKIYKCDNEKCSRPACYISG 81
+GHV HGK+T++ I Q + IT K+G Y YK +N+K
Sbjct: 250 LGHVDHGKTTLLDKIRKTQIA---QKEAGGITQKIGAYEVEFEYKDENQK---------- 296
Query: 82 RSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCDNAA 141
+ F+D PGH+ + GA V D A+L+I D+
Sbjct: 297 ------------------------IVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGV 332
Query: 142 KTPEI 146
K I
Sbjct: 333 KPQTI 337
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 35.2 bits (82), Expect = 0.009
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 104 RHVSFVDCPGHDILMATMLNGAAVMDAALLLIGCD 138
+ +D PGH + M+ GA+ D A+L++
Sbjct: 77 YRFTIIDAPGHRDFVKNMITGASQADVAVLVVSAR 111
Score = 34.0 bits (79), Expect = 0.027
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I+D PGH + M+ GA+ D A+L++
Sbjct: 81 IIDAPGHRDFVKNMITGASQADVAVLVV 108
Score = 27.8 bits (63), Expect = 2.9
Identities = 8/10 (80%), Positives = 8/10 (80%)
Query: 23 IGHVAHGKST 32
IGHV GKST
Sbjct: 5 IGHVDAGKST 14
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 33.4 bits (77), Expect = 0.057
Identities = 22/130 (16%), Positives = 39/130 (30%), Gaps = 51/130 (39%)
Query: 21 GTIGHVAHGKST-------VVKAISGVQTVRFKN--------ELERNITIKLGYANAKIY 65
G + H+ GK+T IS + V E ER ITI A ++
Sbjct: 14 GIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITS--AATTLF 71
Query: 66 KCDNEKCSRPACYISGRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGA 125
+ + ++ +D PGH +
Sbjct: 72 WKGDYR----------------------------------INLIDTPGHVDFTIEVERSL 97
Query: 126 AVMDAALLLI 135
V+D A++++
Sbjct: 98 RVLDGAVVVV 107
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 32.5 bits (75), Expect = 0.066
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I D PGH+ M+ GA+ D A+LL+
Sbjct: 82 IADTPGHEQYTRNMVTGASTADLAILLV 109
Score = 30.2 bits (69), Expect = 0.48
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 109 VDCPGHDILMATMLNGAAVMDAALLLI 135
D PGH+ M+ GA+ D A+LL+
Sbjct: 83 ADTPGHEQYTRNMVTGASTADLAILLV 109
Score = 26.4 bits (59), Expect = 7.9
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 22 TIGHVAHGKSTVV 34
T G V GKST++
Sbjct: 4 TCGSVDDGKSTLI 16
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 31.9 bits (73), Expect = 0.16
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I D PGH+ M GA+ D A+LL+
Sbjct: 90 IADTPGHEQYTRNMATGASTADLAILLV 117
Score = 30.0 bits (68), Expect = 0.62
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 110 DCPGHDILMATMLNGAAVMDAALLLI 135
D PGH+ M GA+ D A+LL+
Sbjct: 92 DTPGHEQYTRNMATGASTADLAILLV 117
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 31.8 bits (73), Expect = 0.18
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 12/47 (25%)
Query: 23 IGHVAHGKSTVVKAI----SGVQTVRFKN--------ELERNITIKL 57
I H+ HGKST+ + G+ + E ER ITIK
Sbjct: 15 IAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGITIKA 61
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 31.7 bits (72), Expect = 0.22
Identities = 30/125 (24%), Positives = 45/125 (36%), Gaps = 21/125 (16%)
Query: 16 ISSYPGTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRP 75
++ PGT GK+T+ +AI + EL + + L + K E
Sbjct: 343 LTGGPGT------GKTTITRAI-----IELAEELGGLLPVGLAAPTGRAAKRLGEVTGLT 391
Query: 76 ACYIS---GRSNKDDSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMD-AA 131
A I G L +V S +D L ++L AA+ D A
Sbjct: 392 ASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMD----TWLALSLL--AALPDHAR 445
Query: 132 LLLIG 136
LLL+G
Sbjct: 446 LLLVG 450
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4).
LepA (also known as elongation factor 4, EF4) belongs
to the GTPase family and exhibits significant homology
to the translation factors EF-G and EF-Tu, indicating
its possible involvement in translation and association
with the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G
gene in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 30.6 bits (70), Expect = 0.29
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 12/47 (25%)
Query: 23 IGHVAHGKSTVVKAI---SGVQTVRFKN---------ELERNITIKL 57
I H+ HGKST+ + +G + R E ER ITIK
Sbjct: 6 IAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGITIKA 52
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The
properties thus far described for BipA are related to
its role in the process of pathogenesis by
enteropathogenic E. coli. It appears to be involved in
the regulation of several processes important for
infection, including rearrangements of the cytoskeleton
of the host, bacterial resistance to host defense
peptides, flagellum-mediated cell motility, and
expression of K5 capsular genes. It has been proposed
that BipA may utilize a novel mechanism to regulate the
expression of target genes. In addition, BipA from
enteropathogenic E. coli has been shown to be
phosphorylated on a tyrosine residue, while BipA from
Salmonella and from E. coli K12 strains is not
phosphorylated under the conditions assayed. The
phosphorylation apparently modifies the rate of
nucleotide hydrolysis, with the phosphorylated form
showing greatly increased GTPase activity.
Length = 194
Score = 30.3 bits (69), Expect = 0.39
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 13/46 (28%)
Query: 23 IGHVAHGKSTVVKAI---SGV----QTVRFK----NEL--ERNITI 55
I HV HGK+T+V A+ SG + V + N+L ER ITI
Sbjct: 8 IAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITI 53
>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 = 0.44
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 18/68 (26%)
Query: 98 GRFQLVRH----VSFVDCPGHDILMATMLNGAAVMDAALLLIGCDN-------------- 139
G + + ++F+D PGH+ + GA V D +L++ D+
Sbjct: 125 GAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAK 184
Query: 140 AAKTPEIV 147
AA P IV
Sbjct: 185 AANVPIIV 192
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast)
originated within the bacterial LepA family. The
function is unknown [Unknown function, General].
Length = 595
Score = 30.4 bits (69), Expect = 0.48
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 23 IGHVAHGKSTVVKAI----SGVQTVRFKN--------ELERNITIKL 57
I H+ HGKST+ + + + E ER ITIK
Sbjct: 9 IAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKA 55
>gnl|CDD|223837 COG0766, MurA, UDP-N-acetylglucosamine enolpyruvyl transferase
[Cell envelope biogenesis, outer membrane].
Length = 421
Score = 29.8 bits (68), Expect = 0.70
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 19/53 (35%)
Query: 114 HDILMA-TMLNGAAVMDAALLLIGCDNAAKTPEIVDCPGHDILMATMLN--GA 163
+I+MA + G V++ NAA+ PEIVD +A LN GA
Sbjct: 169 ENIMMAAVLAEGTTVIE---------NAAREPEIVD-------LANFLNKMGA 205
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 29.6 bits (67), Expect = 0.77
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
+ D PGH+ M GA+ D A+LL+
Sbjct: 84 VADTPGHEQYTRNMATGASTADLAVLLV 111
Score = 28.5 bits (64), Expect = 1.9
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 110 DCPGHDILMATMLNGAAVMDAALLLI 135
D PGH+ M GA+ D A+LL+
Sbjct: 86 DTPGHEQYTRNMATGASTADLAVLLV 111
>gnl|CDD|183779 PRK12830, PRK12830, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Reviewed.
Length = 417
Score = 29.8 bits (68), Expect = 0.81
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 13/46 (28%)
Query: 120 TMLNGAAVMDAALLLIGCDNAAKTPEIVDCPGHDILMATMLN--GA 163
ML AAV +I +NAAK PEI+D +AT+LN GA
Sbjct: 169 IML--AAVKAKGRTVI--ENAAKEPEIID-------VATLLNNMGA 203
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated
eEF2 reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation
rates by activating the kinase responsible for
phosphorylating eEF2. In contrast, treatment of cells
with insulin increases elongation rates by promoting
eEF2 dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins,
it is presumed that modification by the endogenous
enzyme also inhibits eEF2 activity.
Length = 218
Score = 29.1 bits (66), Expect = 0.90
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 17/51 (33%)
Query: 21 GTIGHVAHGKST-----VVKA--IS----GVQTVRF----KNELERNITIK 56
I HV HGK+T + A IS G R+ ++E ER ITIK
Sbjct: 4 CIIAHVDHGKTTLSDSLLASAGIISEKLAG--KARYLDTREDEQERGITIK 52
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 29.5 bits (67), Expect = 0.90
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
+ D PGH+ M+ GA+ D A++L+
Sbjct: 108 VADTPGHEQYTRNMVTGASTADLAIILV 135
Score = 28.4 bits (64), Expect = 2.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 110 DCPGHDILMATMLNGAAVMDAALLLI 135
D PGH+ M+ GA+ D A++L+
Sbjct: 110 DTPGHEQYTRNMVTGASTADLAIILV 135
>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 = 28.7 bits (65), Expect = 1.1
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 3 WKGTLQSNWVSNEISSYP--GTIGHVAH---GKSTVVKAISGVQTVR 44
W + + S TIG V + GKS+++ A+ G + V
Sbjct: 63 WARYFKKEGIVVLFFSALNEATIGLVGYPNVGKSSLINALVGSKKVS 109
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 29.3 bits (66), Expect = 1.4
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 13/47 (27%)
Query: 23 IGHVAHGKSTVVK---AISGVQT------VRF----KNELERNITIK 56
I HV HGKST+ A +G+ VR +E ER ITIK
Sbjct: 25 IAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIK 71
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 29.2 bits (66), Expect = 1.4
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 8/43 (18%)
Query: 33 VVKAI----SGVQTVRFKNELERNITIKLGYANAKIYKCDNEK 71
VVK I SGV V KN++ R I IK G +++ CD+ +
Sbjct: 651 VVKDIFCQTSGVVEVTQKNDILREIIIKPG----ELHLCDDPE 689
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 29.1 bits (66), Expect = 1.4
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 13/46 (28%)
Query: 23 IGHVAHGKSTVVKAI---SGV--------QTVRFKNEL--ERNITI 55
I HV HGK+T+V A+ SG + V N+L ER ITI
Sbjct: 11 IAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITI 56
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions.
Mutants show altered regulation of some pathways, but
the precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 29.2 bits (66), Expect = 1.4
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 13/46 (28%)
Query: 23 IGHVAHGKSTVVKAI---SGV--------QTVRFKNEL--ERNITI 55
I HV HGK+T+V A+ SG + V N+L ER ITI
Sbjct: 7 IAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITI 52
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 28.9 bits (65), Expect = 1.7
Identities = 22/47 (46%), Positives = 23/47 (48%), Gaps = 13/47 (27%)
Query: 23 IGHVAHGKST-----VVKA--ISGVQT--VRF----KNELERNITIK 56
I HV HGKST V KA IS RF +E ER ITIK
Sbjct: 25 IAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIK 71
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 28.4 bits (64), Expect = 1.7
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 23 IGHVAHGKSTVVKAISGVQ 41
+G + GKS+V+ A+ G
Sbjct: 4 VGDQSAGKSSVLNALLGRD 22
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 28.6 bits (64), Expect = 1.9
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I+D PGH + M+ G + D A+L++
Sbjct: 89 IIDAPGHRDFIKNMITGTSQADVAILVV 116
Score = 28.2 bits (63), Expect = 2.6
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 105 HVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
+ + +D PGH + M+ G + D A+L++
Sbjct: 86 YFTIIDAPGHRDFIKNMITGTSQADVAILVV 116
>gnl|CDD|184208 PRK13649, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 28.2 bits (63), Expect = 2.1
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 18 SYPGTIGHVAHGKSTVVKAISGVQT 42
SY IGH GKST+++ ++G+
Sbjct: 34 SYTAFIGHTGSGKSTIMQLLNGLHV 58
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 28.5 bits (63), Expect = 2.1
Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 99 RFQLVRH-VSFVDCPGHDILMATMLNGAAVMDAALLLI 135
+F+ ++ + +D PGH + M+ G + D A+L+I
Sbjct: 79 KFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLII 116
Score = 28.1 bits (62), Expect = 3.0
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
++D PGH + M+ G + D A+L+I
Sbjct: 89 VIDAPGHRDFIKNMITGTSQADCAVLII 116
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 28.7 bits (64), Expect = 2.2
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 33 VVKAI----SGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSR 74
VVK I SG+ V KN++ R I +K + ++ D+ +
Sbjct: 651 VVKDIFCQNSGIVEVTQKNDILREIIVK----PGEFHEVDDPEAVS 692
>gnl|CDD|224053 COG1129, MglA, ABC-type sugar transport system, ATPase component
[Carbohydrate transport and metabolism].
Length = 500
Score = 28.2 bits (64), Expect = 2.4
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 19 YPGTI----GHVAHGKSTVVKAISGVQT 42
PG + G GKST++K +SGV
Sbjct: 32 RPGEVHALLGENGAGKSTLMKILSGVYP 59
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 28.1 bits (64), Expect = 2.7
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 16/49 (32%)
Query: 23 IGHVAHGKSTVVKA-----ISGVQTVR-FKN--------ELERNITIKL 57
I H+ HGKST+ A ++G + R K E ER ITIK
Sbjct: 13 IAHIDHGKSTL--ADRLIELTGTLSEREMKAQVLDSMDLERERGITIKA 59
>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 = 3.0
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 23 IGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGY 59
+G GKST++K I+G + + + T+K+GY
Sbjct: 32 VGRNGAGKSTLLKLIAG-ELEPDEGIVTWGSTVKIGY 67
>gnl|CDD|238796 cd01555, UdpNAET, UDP-N-acetylglucosamine enolpyruvyl transferase
catalyzes enolpyruvyl transfer as part of the first step
in the biosynthesis of peptidoglycan, a component of the
bacterial cell wall. The reaction is phosphoenolpyruvate
+ UDP-N-acetyl-D-glucosamine = phosphate +
UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine. This
enzyme is of interest as a potential target for
anti-bacterial agents. The only other known enolpyruvyl
transferase is the related
5-enolpyruvylshikimate-3-phosphate synthase.
Length = 400
Score = 27.4 bits (62), Expect = 4.2
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 9/28 (32%)
Query: 138 DNAAKTPEIVDCPGHDILMATMLN--GA 163
+NAA+ PEIVD +A LN GA
Sbjct: 174 ENAAREPEIVD-------LANFLNKMGA 194
>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 = 27.4 bits (62), Expect = 4.2
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 29 GKSTVVKAISGVQTVR 44
GK+T++K I G+ R
Sbjct: 38 GKTTLLKTIMGLLPPR 53
>gnl|CDD|213183 cd03216, ABC_Carb_Monos_I, First domain of the ATP-binding
cassette component of monosaccharide transport system.
This family represents the domain I of the carbohydrate
uptake proteins that transport only monosaccharides
(Monos). The Carb_Monos family is involved in the
uptake of monosaccharides, such as pentoses (such as
xylose, arabinose, and ribose) and hexoses (such as
xylose, arabinose, and ribose), that cannot be broken
down to simple sugars by hydrolysis. Pentoses include
xylose, arabinose, and ribose. Important hexoses
include glucose, galactose, and fructose. In members of
the Carb_monos family, the single hydrophobic gene
product forms a homodimer while the ABC protein
represents a fusion of two nucleotide-binding domains.
However, it is assumed that two copies of the ABC
domains are present in the assembled transporter.
Length = 163
Score = 27.0 bits (61), Expect = 4.3
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 29 GKSTVVKAISGVQT 42
GKST++K +SG+
Sbjct: 38 GKSTLMKILSGLYK 51
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 27.4 bits (61), Expect = 4.3
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 138 DNAAKTPEIVDCPGHDILMATML 160
+N KT +V+ HDI+M L
Sbjct: 163 ENNEKTAFVVE---HDIIMIDYL 182
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 27.4 bits (61), Expect = 4.5
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 21 GTIGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGY 59
G +G GKST++K ++G + E+ IKLGY
Sbjct: 342 GLLGRNGAGKSTLIKLLAG-ELAPVSGEIGLAKGIKLGY 379
>gnl|CDD|238879 cd01841, NnaC_like, NnaC (CMP-NeuNAc synthetase) _like subfamily
of SGNH_hydrolases, a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles two of the three
components of typical Ser-His-Asp(Glu) triad from other
serine hydrolases. E. coli NnaC appears to be involved
in polysaccharide synthesis.
Length = 174
Score = 26.9 bits (60), Expect = 4.7
Identities = 7/42 (16%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 24 GHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIY 65
GK+ I+G+ + ++ +E + K +K++
Sbjct: 18 EAEGKGKTVNNLGIAGISSRQYLEHIEPQLIQKNP---SKVF 56
>gnl|CDD|236486 PRK09369, PRK09369, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Validated.
Length = 417
Score = 27.3 bits (62), Expect = 4.7
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 19/51 (37%)
Query: 116 ILMA-TMLNGAAVMDAALLLIGCDNAAKTPEIVDCPGHDILMATMLN--GA 163
ILMA + G V++ NAA+ PEIVD +A LN GA
Sbjct: 171 ILMAAVLAEGTTVIE---------NAAREPEIVD-------LANFLNKMGA 205
>gnl|CDD|184203 PRK13643, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 288
Score = 27.0 bits (59), Expect = 5.3
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 18 SYPGTIGHVAHGKSTVVKAISGV 40
SY IGH GKST+++ ++G+
Sbjct: 33 SYTALIGHTGSGKSTLLQHLNGL 55
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 26.8 bits (60), Expect = 6.0
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 105 HVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
++ +D PG+ + L+ +DAAL+++
Sbjct: 65 KINLIDTPGYADFVGETLSALRAVDAALIVV 95
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 27.1 bits (60), Expect = 6.1
Identities = 31/115 (26%), Positives = 43/115 (37%), Gaps = 26/115 (22%)
Query: 23 IGHVAHGKSTVVKAISGVQTVRFKNELERNITIKLGYANAKIYKCDNEKCSRPACYISGR 82
+GHV HGK+T++ I G K E IT +G P I G
Sbjct: 10 LGHVDHGKTTLLDKIRGSAVA--KRE-AGGITQHIGATEI------------PMDVIEGI 54
Query: 83 SNKD--DSFPCLRSSCTGRFQLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
D F +R G F+D PGH+ G A+ D A+L++
Sbjct: 55 C-GDLLKKFK-IRLKIPGLL-------FIDTPGHEAFTNLRKRGGALADLAILIV 100
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 27.2 bits (61), Expect = 6.5
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
I D PGH+ M GA+ D A+LLI
Sbjct: 111 IADTPGHEQYTRNMATGASTCDLAILLI 138
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 27.0 bits (61), Expect = 6.6
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 105 HVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
++ +D PGH + V+D A++++
Sbjct: 61 KINLIDTPGHVDFTGEVERALRVLDGAVVVV 91
Score = 26.6 bits (60), Expect = 8.5
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 146 IVDCPGHDILMATMLNGAAVMDAALLLI 173
++D PGH + V+D A++++
Sbjct: 64 LIDTPGHVDFTGEVERALRVLDGAVVVV 91
>gnl|CDD|226586 COG4101, COG4101, Predicted mannose-6-phosphate isomerase
[Carbohydrate transport and metabolism].
Length = 142
Score = 26.4 bits (58), Expect = 7.2
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 25 HVAHGKSTVVKAISGVQTVRFKNELERNITIKLG 58
H+ T + +SG + N LE + + G
Sbjct: 62 HLHEEHETAIYVLSGEAHTWYGNRLEEHAEVGPG 95
>gnl|CDD|184209 PRK13650, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 279
Score = 26.6 bits (59), Expect = 7.3
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 8/33 (24%)
Query: 8 QSNWVSNEISSYPGTIGHVAHGKSTVVKAISGV 40
Q W+S IGH GKST V+ I G+
Sbjct: 32 QGEWLS--------IIGHNGSGKSTTVRLIDGL 56
>gnl|CDD|237452 PRK13632, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 271
Score = 26.5 bits (59), Expect = 8.5
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 6/41 (14%)
Query: 6 TLQSNWVSNEIS------SYPGTIGHVAHGKSTVVKAISGV 40
N +S Y +GH GKST+ K ++G+
Sbjct: 18 PNSENNALKNVSFEINEGEYVAILGHNGSGKSTISKILTGL 58
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 26.4 bits (59), Expect = 8.7
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 21 GTIGHVAHGKSTVVKAISGV 40
G IGH GKST++K I+G+
Sbjct: 57 GIIGHNGAGKSTLLKLIAGI 76
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. 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 = 231
Score = 26.5 bits (59), Expect = 8.8
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 104 RHVSFVDCPGHDILMATMLNGAAVMDAALLLI 135
R ++F++CP +DI M++ A + D LLLI
Sbjct: 83 RRLTFIECP-NDINS--MIDVAKIADLVLLLI 111
>gnl|CDD|237455 PRK13637, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 26.5 bits (59), Expect = 9.4
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 21 GTIGHVAHGKSTVVKAISG 39
G IGH GKST+++ ++G
Sbjct: 37 GLIGHTGSGKSTLIQHLNG 55
>gnl|CDD|216192 pfam00920, ILVD_EDD, Dehydratase family.
Length = 521
Score = 26.7 bits (60), Expect = 9.6
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 11/39 (28%)
Query: 119 ATMLNGAAVMDAALLLIGCDNAAKTPEIVDCPGHDILMA 157
++ A D +LL GCD KT PG LMA
Sbjct: 72 EVVVR-AHPFDGLVLLGGCD---KTV-----PGM--LMA 99
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.134 0.412
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,799,866
Number of extensions: 769539
Number of successful extensions: 910
Number of sequences better than 10.0: 1
Number of HSP's gapped: 883
Number of HSP's successfully gapped: 140
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
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 (21.9 bits)
S2: 56 (25.5 bits)