RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10355
(156 letters)
>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 = 255 bits (654), Expect = 5e-88
Identities = 83/130 (63%), Positives = 107/130 (82%), Gaps = 1/130 (0%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
RE+G T++VG A FET++ FTI+DAPGH+ FV NMI G +QAD+AVLV+SARKGEFE G
Sbjct: 59 RERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAG 118
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFNAA 131
F++GGQTREHA+LA+T GVK L+V +NKMDD TV WS+ RY+E K K+ P+LKK+G+N
Sbjct: 119 FEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYN-P 177
Query: 132 KDLSFMPCSG 141
KD+ F+P SG
Sbjct: 178 KDVPFIPISG 187
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 198 bits (506), Expect = 7e-63
Identities = 71/134 (52%), Positives = 97/134 (72%), Gaps = 3/134 (2%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
+++RE+G T++V + FETD+ +FTI+DAPGH+ FV NMI G +QAD+AVLV+ AR GE
Sbjct: 63 TKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGE 122
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
FE GF GGQTREHA LA+T G+K L+V +NKMD + W E R+ E ++ LK +G
Sbjct: 123 FEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVS--WDEERFEEIVSEVSKLLKMVG 180
Query: 128 FNAAKDLSFMPCSG 141
+N KD+ F+P SG
Sbjct: 181 YN-PKDVPFIPISG 193
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 168 bits (428), Expect = 3e-51
Identities = 71/134 (52%), Positives = 101/134 (75%), Gaps = 1/134 (0%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+ +RE+G T+++ FET + +FTI+DAPGH+ F+ NMI GT+QAD+A+LV+++ GE
Sbjct: 63 LKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGE 122
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
FE G + GQTREHA+LA T GVK ++V INKMDD TV +S+ RY+E K ++ YLKK+G
Sbjct: 123 FEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVG 182
Query: 128 FNAAKDLSFMPCSG 141
+N K + F+P SG
Sbjct: 183 YNPEK-VPFIPISG 195
>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 = 141 bits (359), Expect = 1e-43
Identities = 52/146 (35%), Positives = 78/146 (53%), Gaps = 16/146 (10%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
L+++RE+G T+++ FET ++ I+D PGH F MI G +QAD A+LV+ A +G
Sbjct: 43 KLKEERERGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEG 102
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKIL-PYLKK 125
QTREH +LAKT GV ++V INK+D +A E ++I L+K
Sbjct: 103 -------VMPQTREHLLLAKTLGVP-IIVFINKIDRVD----DAELEEVVEEISRELLEK 150
Query: 126 LGFNAAKDLSFMPCSGELEKN--PLL 149
GF + + +P S + LL
Sbjct: 151 YGFG-GETVPVVPGSALTGEGIDELL 175
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 147 bits (373), Expect = 3e-43
Identities = 59/134 (44%), Positives = 84/134 (62%), Gaps = 8/134 (5%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+++RE+G T+++ FETD+ +FTI+D PGH+ FV NMI G +QAD AVLV++A
Sbjct: 62 LKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAG 121
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
QTREH LA+T G+ L+V INKMD V + E RY E K+++ LK +G
Sbjct: 122 -----GVMPQTREHVFLARTLGINQLIVAINKMD--AVNYDEKRYEEVKEEVSKLLKMVG 174
Query: 128 FNAAKDLSFMPCSG 141
+ D+ F+P S
Sbjct: 175 YKPD-DIPFIPVSA 187
>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 = 136 bits (345), Expect = 3e-39
Identities = 59/134 (44%), Positives = 85/134 (63%), Gaps = 7/134 (5%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+++RE+G T++V FETD+ TI+D PGH+ F+ NMI G +QAD AVLV++ GE
Sbjct: 63 LKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGE 122
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
FE QTREHA LA+T G+ L+V INKMD +V + E + K ++ +KK+G
Sbjct: 123 FE----VQPQTREHAFLARTLGINQLIVAINKMD--SVNYDEEEFEAIKKEVSNLIKKVG 176
Query: 128 FNAAKDLSFMPCSG 141
+N + F+P S
Sbjct: 177 YN-PDTVPFIPISA 189
>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 = 129 bits (327), Expect = 2e-38
Identities = 52/133 (39%), Positives = 78/133 (58%), Gaps = 12/133 (9%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+ +RE+G T++V YF T ++ F I D PGH+ + NM+ G + ADLA+L++ ARKG
Sbjct: 56 LQAEREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGV 115
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
E QTR H+ +A G++H+VV +NKMD V + E + E K L + LG
Sbjct: 116 LE-------QTRRHSYIASLLGIRHVVVAVNKMD--LVDYDEEVFEEIKADYLAFAASLG 166
Query: 128 FNAAKDLSFMPCS 140
D++F+P S
Sbjct: 167 IE---DITFIPIS 176
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 134 bits (338), Expect = 4e-38
Identities = 65/134 (48%), Positives = 93/134 (69%), Gaps = 1/134 (0%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+ +RE+G T+++ FET + + T++DAPGH+ F+ NMI GT+QAD AVL+I + G
Sbjct: 63 LKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGG 122
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
FE G + GQTREHA+LA T GVK ++ NKMD T +S+ARY+E ++ YLKK+G
Sbjct: 123 FEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVG 182
Query: 128 FNAAKDLSFMPCSG 141
+N K + F+P SG
Sbjct: 183 YNPDK-IPFVPISG 195
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 117 bits (294), Expect = 7e-32
Identities = 52/134 (38%), Positives = 77/134 (57%), Gaps = 12/134 (8%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L +RE+G T++V YF T+++ F I D PGH+ + NM G + ADLA+L++ ARKG
Sbjct: 64 LEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGV 123
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
E QTR H+ +A G++H+VV +NKMD V +SE + L + +LG
Sbjct: 124 LE-------QTRRHSFIASLLGIRHVVVAVNKMD--LVDYSEEVFEAIVADYLAFAAQLG 174
Query: 128 FNAAKDLSFMPCSG 141
KD+ F+P S
Sbjct: 175 L---KDVRFIPISA 185
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 115 bits (291), Expect = 8e-31
Identities = 46/134 (34%), Positives = 77/134 (57%), Gaps = 12/134 (8%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L +RE+G T++V YF T ++ F + D PGH+ + NM+ G + ADLA++++ ARKG
Sbjct: 82 LAAEREQGITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGV 141
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
QTR H+ +A G++H+V+ +NKMD V + + ++E + KLG
Sbjct: 142 LT-------QTRRHSFIASLLGIRHVVLAVNKMD--LVDYDQEVFDEIVADYRAFAAKLG 192
Query: 128 FNAAKDLSFMPCSG 141
+ D++F+P S
Sbjct: 193 LH---DVTFIPISA 203
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 113 bits (284), Expect = 3e-30
Identities = 52/133 (39%), Positives = 79/133 (59%), Gaps = 11/133 (8%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+ +RE+G T++V YF T+++ F I D PGH+ + NM G + DLA+L+I ARKG
Sbjct: 85 LQAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGV 144
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
+ QTR H+ +A G+KHLVV +NKMD V +SE + ++ L + ++L
Sbjct: 145 LD-------QTRRHSFIATLLGIKHLVVAVNKMD--LVDYSEEVFERIREDYLTFAEQLP 195
Query: 128 FNAAKDLSFMPCS 140
N D+ F+P S
Sbjct: 196 GN--LDIRFVPLS 206
>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 = 107 bits (269), Expect = 2e-28
Identities = 52/134 (38%), Positives = 81/134 (60%), Gaps = 12/134 (8%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L+ +RE+G T++V YF TD++ F + D PGH+ + NM G + ADLAVL++ ARKG
Sbjct: 58 LQAEREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGV 117
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
E QTR H+ +A G++H+V+ +NKMD V + E + K L + ++LG
Sbjct: 118 LE-------QTRRHSYIASLLGIRHVVLAVNKMD--LVDYDEEVFENIKKDYLAFAEQLG 168
Query: 128 FNAAKDLSFMPCSG 141
F +D++F+P S
Sbjct: 169 F---RDVTFIPLSA 179
>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 = 100 bits (251), Expect = 2e-27
Identities = 48/148 (32%), Positives = 72/148 (48%), Gaps = 15/148 (10%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
L+++RE+G T++ G FE ++ +D PGH+ F + G AQAD A+LV+ A +G
Sbjct: 39 TLKEERERGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEG 98
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKL 126
QTREH +A AG ++V +NK+D E ++E +I LK +
Sbjct: 99 V-------EPQTREHLNIAL-AGGLPIIVAVNKID----RVGEEDFDEVLREIKELLKLI 146
Query: 127 GFNAAKDL--SFMPCSGEL-EKNPLLLG 151
GF K +P S E LL
Sbjct: 147 GFTFLKGKDVPIIPISALTGEGIEELLD 174
>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 = 87.6 bits (218), Expect = 3e-22
Identities = 36/90 (40%), Positives = 52/90 (57%), Gaps = 7/90 (7%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+ +G T+ +ET +H+ +D PGH ++ NMI G AQ D A+LV+SA G
Sbjct: 47 KARGITINTAHVEYETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMP-- 104
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QTREH +LA+ GV ++VV +NK D
Sbjct: 105 -----QTREHLLLARQVGVPYIVVFLNKAD 129
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 90.4 bits (225), Expect = 4e-22
Identities = 36/90 (40%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+ +G T+ +ET +H+ +D PGH +V NMI G AQ D A+LV++A G
Sbjct: 57 KARGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP-- 114
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QTREH +LA+ GV ++VV +NK+D
Sbjct: 115 -----QTREHILLARQVGVPYIVVFLNKVD 139
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 86.2 bits (214), Expect = 1e-20
Identities = 38/90 (42%), Positives = 56/90 (62%), Gaps = 7/90 (7%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+E+G T+ +ET+++H+ +D PGH +V NMI G AQ D A+LV++A G
Sbjct: 57 KERGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP-- 114
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QTREH +LA+ GV +LVV +NK+D
Sbjct: 115 -----QTREHILLARQVGVPYLVVFLNKVD 139
>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 = 83.3 bits (206), Expect = 2e-19
Identities = 37/92 (40%), Positives = 55/92 (59%), Gaps = 7/92 (7%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFE 69
+++ +G T+ +ET+ +H+ +D PGH +V NMI G AQ D A+LV+SA G
Sbjct: 55 EEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMP 114
Query: 70 TGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QTREH +LA+ GV ++VV +NK D
Sbjct: 115 -------QTREHILLARQVGVPYIVVFLNKCD 139
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 82.5 bits (205), Expect = 2e-19
Identities = 38/95 (40%), Positives = 56/95 (58%), Gaps = 10/95 (10%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+ +G T+ +ET+++H+ +D PGH +V NMI G AQ D A+LV+SA G
Sbjct: 57 KARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-- 114
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINK---MDDP 103
QTREH +LA+ GV ++VV +NK +DD
Sbjct: 115 -----QTREHILLARQVGVPYIVVFLNKCDMVDDE 144
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 81.8 bits (203), Expect = 4e-19
Identities = 38/95 (40%), Positives = 54/95 (56%), Gaps = 10/95 (10%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+ +G T+ +ET +H+ +D PGH +V NMI G AQ D A+LV+SA G
Sbjct: 57 KARGITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-- 114
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINK---MDDP 103
QTREH +LA+ GV ++VV +NK +DD
Sbjct: 115 -----QTREHILLARQVGVPYIVVFLNKCDMVDDE 144
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 81.2 bits (201), Expect = 9e-19
Identities = 37/90 (41%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
+ +G T+ +ET+ +H+ +D PGH +V NMI G AQ D A+LV+SA G
Sbjct: 57 KARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-- 114
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QT+EH +LAK GV ++VV +NK D
Sbjct: 115 -----QTKEHILLAKQVGVPNIVVFLNKED 139
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 79.5 bits (196), Expect = 4e-18
Identities = 36/92 (39%), Positives = 54/92 (58%), Gaps = 7/92 (7%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFE 69
+++ +G T+ +ET ++H+ +D PGH +V NMI G AQ D +LV+SA G
Sbjct: 104 EEKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMP 163
Query: 70 TGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QT+EH +LA+ GV LVV +NK+D
Sbjct: 164 -------QTKEHILLARQVGVPSLVVFLNKVD 188
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 78.5 bits (193), Expect = 9e-18
Identities = 37/92 (40%), Positives = 54/92 (58%), Gaps = 7/92 (7%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFE 69
++R +G T+ +ET+ +H+ +D PGH +V NMI G AQ D A+LV+S G
Sbjct: 124 EERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMP 183
Query: 70 TGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QT+EH +LAK GV ++VV +NK D
Sbjct: 184 -------QTKEHILLAKQVGVPNMVVFLNKQD 208
>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 = 74.2 bits (183), Expect = 2e-17
Identities = 38/126 (30%), Positives = 64/126 (50%), Gaps = 12/126 (9%)
Query: 8 LRQKREKGKTVEVGRAYFE-TDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
L +++++G T+++G AY + D K +D PGH+ FV NM+ G D +LV++A +G
Sbjct: 27 LPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEG 86
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKL 126
QTREH + + G+K +V++ K D + E R +++IL L
Sbjct: 87 IMP-------QTREHLEILELLGIKKGLVVLTKAD----LVDEDRLELVEEEILELLAGT 135
Query: 127 GFNAAK 132
A
Sbjct: 136 FLADAP 141
>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 = 77.2 bits (190), Expect = 3e-17
Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 11/122 (9%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L +++++G T+++G AYF +D PGH+ F+ N I G D A+LV+ A +G
Sbjct: 28 LPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGV 87
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLG 127
QT EH + G+ H +V+I K D +E + + L
Sbjct: 88 MT-------QTGEHLAVLDLLGIPHTIVVITKAD----RVNEEEIKRTEMFMKQILNSYI 136
Query: 128 FN 129
F
Sbjct: 137 FL 138
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 66.7 bits (163), Expect = 1e-13
Identities = 31/113 (27%), Positives = 59/113 (52%), Gaps = 11/113 (9%)
Query: 8 LRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGE 67
L +++++G T+++G Y + + +D PGH F+ N++ G D A+LV++A +G
Sbjct: 28 LPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEG- 86
Query: 68 FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKIL 120
QT EH ++ G+K+ ++++ K D EAR + +IL
Sbjct: 87 ------LMAQTGEHLLILDLLGIKNGIIVLTKADRVD----EARIEQKIKQIL 129
>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 = 59.6 bits (145), Expect = 1e-11
Identities = 35/118 (29%), Positives = 60/118 (50%), Gaps = 15/118 (12%)
Query: 30 KHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAG 89
+H + +D PGH+ + M+ G A D A+L+I+A + QT EH + G
Sbjct: 77 RHVSFVDCPGHEILMATMLSGAAVMDGALLLIAA-----NEPCPQ-PQTSEHLAALEIMG 130
Query: 90 VKHLVVLINKMDDPTVMWSEARYNECKDKILPYLK-KLGFNAAKDLSFMPCSGELEKN 146
+KH+++L NK+D V +A N ++I ++K + NA +P S +L+ N
Sbjct: 131 LKHIIILQNKID--LVKEEQALEN--YEQIKEFVKGTIAENAP----IIPISAQLKYN 180
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 60.4 bits (147), Expect = 2e-11
Identities = 39/125 (31%), Positives = 65/125 (52%), Gaps = 12/125 (9%)
Query: 8 LRQKREKGKTVEVGRAYF-ETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
L +++++G T+++G AY+ + D + +D PGH+ F+ NM+ G D A+LV++ G
Sbjct: 28 LPEEKKRGMTIDLGYAYWPQPDGRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDG 87
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKL 126
QTREH + + G L V + K D V EAR E + ++ L++
Sbjct: 88 VM-------AQTREHLAILQLTGNPMLTVALTKAD--RV--DEARIAEVRRQVKAVLREY 136
Query: 127 GFNAA 131
GF A
Sbjct: 137 GFAEA 141
>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 = 58.1 bits (141), Expect = 1e-10
Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 6/69 (8%)
Query: 33 TILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKH 92
+ +DAPGH++ + M+ G A D A+LVI+A + + QTREH M + G+K+
Sbjct: 83 SFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQP------QTREHLMALEIIGIKN 136
Query: 93 LVVLINKMD 101
+V++ NK+D
Sbjct: 137 IVIVQNKID 145
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 56.4 bits (137), Expect = 4e-10
Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 10/86 (11%)
Query: 34 ILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHL 93
+DAPGH++ + M+ G A D A+LVI+A + + QT+EH M G+K++
Sbjct: 89 FVDAPGHETLMATMLSGAALMDGAILVIAANEPCPQP------QTKEHLMALDIIGIKNI 142
Query: 94 VVLINKMDDPTVMWSEAR--YNECKD 117
V++ NK+D V A Y + K+
Sbjct: 143 VIVQNKID--LVSKERALENYEQIKE 166
>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 = 55.1 bits (133), Expect = 5e-10
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 22/107 (20%)
Query: 9 RQKREKGKTVEVGRAYFETDRK--------------HFTILDAPGHKSFVPNMIGGTAQA 54
Q +E+G T+++G + FE D+ T++D PGH S + +IGG
Sbjct: 33 PQSQERGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQII 92
Query: 55 DLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
DL +LV+ A+KG +T QT E ++ + L+V++NK+D
Sbjct: 93 DLMLLVVDAKKG-IQT------QTAECLVIGELLCKP-LIVVLNKID 131
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 54.7 bits (132), Expect = 2e-09
Identities = 30/96 (31%), Positives = 54/96 (56%), Gaps = 10/96 (10%)
Query: 29 RKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTA 88
+ + +DAPGH++ + M+ G A D A+LVI+A + + QTREH M +
Sbjct: 85 VRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQP------QTREHLMALEII 138
Query: 89 GVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLK 124
G+K+++++ NK+D + S R E ++I ++K
Sbjct: 139 GIKNIIIVQNKID----LVSRERALENYEQIKEFVK 170
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 52.1 bits (126), Expect = 4e-09
Identities = 36/126 (28%), Positives = 54/126 (42%), Gaps = 22/126 (17%)
Query: 22 RAYF---ETDRKHFTILDAPGHKSFVPNM-IGGTAQADLAVLVISARKGEFETGFDRG-- 75
AY + T +D PGH++F NM G + D+A+LV++A D G
Sbjct: 38 GAYQVPIDVKIPGITFIDTPGHEAFT-NMRARGASVTDIAILVVAA---------DDGVM 87
Query: 76 GQTREHAMLAKTAGVKHLVVLINKMD-DPTVMWSEARYNECKDKILPYLKKLGFNAAKDL 134
QT E AK A V ++V INK+D R ++ ++ G D+
Sbjct: 88 PQTIEAINHAKAANVP-IIVAINKIDKPYGTEADPERVKNELSELGLVGEEWG----GDV 142
Query: 135 SFMPCS 140
S +P S
Sbjct: 143 SIVPIS 148
>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 = 52.8 bits (127), Expect = 9e-09
Identities = 41/135 (30%), Positives = 55/135 (40%), Gaps = 21/135 (15%)
Query: 10 QKREKGKTVEVGRAYFET-DRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEF 68
Q G T +G + E D K T LD PGH++F G D+ VLV++A G
Sbjct: 114 QGEAGGITQHIGAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVM 173
Query: 69 ETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGF 128
QT E AK A V ++V INK+D P D++ L + G
Sbjct: 174 P-------QTIEAISHAKAANVP-IIVAINKIDKPEAN---------PDRVKQELSEYGL 216
Query: 129 NAAK---DLSFMPCS 140
D F+P S
Sbjct: 217 VPEDWGGDTIFVPVS 231
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 51.5 bits (124), Expect = 3e-08
Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 15/99 (15%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKH-FTILDAPGHKSFVPNMIGGTAQADLAVLVISARK 65
W+ Q++E+G T+ + ++D PGH F + D AV+V+ A +
Sbjct: 52 WMEQEQERGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVE 111
Query: 66 GE---FETGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
G ET + A GV ++ +NKMD
Sbjct: 112 GVEPQTETVWR----------QADKYGVPRILF-VNKMD 139
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 51.0 bits (123), Expect = 3e-08
Identities = 46/150 (30%), Positives = 64/150 (42%), Gaps = 32/150 (21%)
Query: 15 GKTVEVGRAYFETD---RKHFTILDAPGHKSFVPNM-IGGTAQADLAVLVISARKGEFET 70
G T +G D T +D PGH++F M G + D+A+LV++A G
Sbjct: 37 GITQHIGAYQVPLDVIKIPGITFIDTPGHEAFT-AMRARGASVTDIAILVVAADDG---- 91
Query: 71 GFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFNA 130
QT E AK AGV +VV INK+D P DK+ L++ G
Sbjct: 92 ---VMPQTIEAINHAKAAGVP-IVVAINKIDKPEAN---------PDKVKQELQEYGLVP 138
Query: 131 AK---DLSFMPCSG-------ELEKNPLLL 150
+ D+ F+P S EL + LLL
Sbjct: 139 EEWGGDVIFVPVSAKTGEGIDELLELILLL 168
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 51.2 bits (123), Expect = 3e-08
Identities = 32/117 (27%), Positives = 59/117 (50%), Gaps = 13/117 (11%)
Query: 30 KHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAG 89
+H + +D PGH + M+ G A D A+L+I+A + + QT EH +
Sbjct: 117 RHVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQP------QTSEHLAAVEIMK 170
Query: 90 VKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFNAAKDLSFMPCSGELEKN 146
+KH+++L NK+D + EA+ + ++I ++K A + +P S +L+ N
Sbjct: 171 LKHIIILQNKID----LVKEAQAQDQYEEIRNFVKG---TIADNAPIIPISAQLKYN 220
>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 = 49.5 bits (119), Expect = 9e-08
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 8/92 (8%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFE 69
+++++ ++E A E + ++D PG+ FV + D A++V+ A+ G
Sbjct: 44 EEKKRKMSIETSVAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSG--- 100
Query: 70 TGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
T + A + ++ INKMD
Sbjct: 101 ----VEVGTEKVWEFLDDAKLPRIIF-INKMD 127
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 48.6 bits (117), Expect = 2e-07
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFE 69
++RE+G ++ E ++D PGH F + D AV+V+ A G
Sbjct: 40 EERERGISITSAATTCEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGG--- 96
Query: 70 TGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QT A+ GV ++ +NKMD
Sbjct: 97 ----VEPQTETVWRQAEKYGVPRIIF-VNKMD 123
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 46.4 bits (111), Expect = 1e-06
Identities = 36/95 (37%), Positives = 45/95 (47%), Gaps = 33/95 (34%)
Query: 23 AY-FETDRKHFTILDAPGHKSFVPNMIGGT------AQA-DLAVLVISARKGEFETGFDR 74
AY ET+ T LD PGH++F T AQ D+ VLV++A D
Sbjct: 288 AYQVETNGGKITFLDTPGHEAF-------TAMRARGAQVTDIVVLVVAA---------DD 331
Query: 75 G--GQTRE---HAMLAKTAGVKHLVVLINKMDDPT 104
G QT E H AK AGV ++V INK+D P
Sbjct: 332 GVMPQTIEAINH---AKAAGVP-IIVAINKIDKPG 362
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 43.4 bits (103), Expect = 1e-05
Identities = 28/95 (29%), Positives = 40/95 (42%), Gaps = 8/95 (8%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
W+ Q++E+G T+E + D ++D PGH F + D AV+V A G
Sbjct: 50 WMPQEQERGITIESAATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTG 109
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QT A G+ L+ INKMD
Sbjct: 110 -------VQPQTETVWRQADRYGIPRLIF-INKMD 136
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 41.1 bits (97), Expect = 6e-05
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 8/90 (8%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETG 71
R++G T+ A F+ + I+D PGH F+ + + D A+LVISA +G
Sbjct: 46 RQRGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGV---- 101
Query: 72 FDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
QTR L + + ++ +NK+D
Sbjct: 102 ---QAQTRILFRLLRKLNIP-TIIFVNKID 127
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 38.7 bits (91), Expect = 5e-04
Identities = 28/98 (28%), Positives = 45/98 (45%), Gaps = 8/98 (8%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
W+ ++++G +V FE +LD PGH+ F + D AV+VI A KG
Sbjct: 48 WMEIEKQRGISVTSSVMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG 107
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPT 104
E QTR+ + + G+ ++ INK+D
Sbjct: 108 -VEP------QTRKLFEVCRLRGIP-IITFINKLDREG 137
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 38.7 bits (90), Expect = 6e-04
Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 12/99 (12%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
W+ ++++G ++ F +LD PGH+ F + D ++VI A KG
Sbjct: 57 WMEMEKQRGISITTSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKG 116
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVL--INKMDDP 103
ET +TR+ L + ++ + +NK+D
Sbjct: 117 -VET------RTRK---LMEVTRLRDTPIFTFMNKLDRD 145
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 37.2 bits (87), Expect = 0.001
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 18/82 (21%)
Query: 27 TDRKH----FTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTRE-- 80
D K I+D PGH +F+ + D VLV+ +G T
Sbjct: 64 EDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTS-------VTERLI 116
Query: 81 -HAMLAKTAGVKHLVVLINKMD 101
HA+ +V++INK+D
Sbjct: 117 RHAIQEG----LPMVLVINKID 134
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 36.5 bits (85), Expect = 0.003
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 12/97 (12%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
W+ ++++G +V F+ +LD PGH+ F + D AV+VI A KG
Sbjct: 58 WMEIEKQRGISVTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG 117
Query: 67 EFETGFDRGGQTREHAMLAKTAGVKHLVVL--INKMD 101
E QT + L + ++ + + INK+D
Sbjct: 118 -IEP------QTLK---LFEVCRLRDIPIFTFINKLD 144
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 35.5 bits (82), Expect = 0.003
Identities = 19/99 (19%), Positives = 33/99 (33%), Gaps = 13/99 (13%)
Query: 12 REKGKTVE--VGRAYFETDRKHFTILDAPGHKSFVPNMIGGTA-----QADLAVLVISAR 64
G T + V + + ++D PG F A ADL +LV+ +
Sbjct: 27 DVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDST 86
Query: 65 KGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDP 103
E + + G+ ++V NK+D
Sbjct: 87 DRES---EED--AKLLILRRLRKEGIPIILV-GNKIDLL 119
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 35.2 bits (81), Expect = 0.010
Identities = 31/99 (31%), Positives = 47/99 (47%), Gaps = 18/99 (18%)
Query: 10 QKREKGKTVEVGRAY-----FETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISAR 64
QK G T ++G AY ++ + + LD PGH++F G D+A+L+I+A
Sbjct: 271 QKEAGGITQKIG-AYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAA- 328
Query: 65 KGEFETGFDRG--GQTREHAMLAKTAGVKHLVVLINKMD 101
D G QT E + A V ++V INK+D
Sbjct: 329 --------DDGVKPQTIEAINYIQAANVP-IIVAINKID 358
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 33.6 bits (77), Expect = 0.032
Identities = 9/32 (28%), Positives = 11/32 (34%)
Query: 15 GKTVEVGRAYFETDRKHFTILDAPGHKSFVPN 46
G TVE + I+D PG S
Sbjct: 26 GVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTF 57
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 33.0 bits (76), Expect = 0.033
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 52 AQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEAR 111
+ADL +LV+ + E + + +L + G L+V +NK+D E
Sbjct: 75 DRADLVLLVVDSDLTPVE-------EEAKLGLLRER-GKPVLLV-LNKIDLVPESEEEEL 125
Query: 112 YNECKDKILPYLKKLGFNAAK 132
E K ++LP L + +A
Sbjct: 126 LRERKLELLPDLPVIAVSALP 146
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 32.2 bits (73), Expect = 0.063
Identities = 15/146 (10%), Positives = 38/146 (26%), Gaps = 8/146 (5%)
Query: 7 WLRQKREKGKTVEVGRAYFETDRK--HFTILDAPGHKSFVPNMIGGTAQADLAVLVISAR 64
+ E R+ + D G + + A+ ++V +
Sbjct: 29 EFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDST 88
Query: 65 KGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLK 124
E D + + ++++ NK+D S ++ + L
Sbjct: 89 LRE---SSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLV 145
Query: 125 KLGF---NAAKDLSFMPCSGELEKNP 147
+ + + S + P
Sbjct: 146 LAPKAVLPEVANPALLETSAKSLTGP 171
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 32.8 bits (74), Expect = 0.068
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 11 KREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFET 70
++E+G T+ + + I+D PGH F + + D +LV+ A G
Sbjct: 49 EKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMP- 107
Query: 71 GFDRGGQTREHAMLAKTAGVKHLVVLINKMDDP 103
QTR A G+K +VV INK+D P
Sbjct: 108 ------QTRFVTKKAFAYGLKPIVV-INKVDRP 133
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 31.2 bits (71), Expect = 0.12
Identities = 30/152 (19%), Positives = 48/152 (31%), Gaps = 41/152 (26%)
Query: 2 TGQGLWLRQKREKGKTVEVGRAYFETDRKHFTILDAPGHKSFVPNMIGGTAQA------- 54
T + E GKT + F +LD G + +
Sbjct: 35 TTRNYVTTVIEEDGKTYK------------FNLLDTAGQEDYDAIRRLYYRAVESSLRVF 82
Query: 55 DLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNE 114
D+ +LV+ + + QT+E A+ +GV ++V NK+D
Sbjct: 83 DIVILVLDVEEILEK-------QTKEIIHHAE-SGVPIILV-GNKID------------- 120
Query: 115 CKDKILPYLKKLGFNAAKDLSFMPCSGELEKN 146
+D L F +P S E KN
Sbjct: 121 LRDAKLKTHVAFLFAKLNGEPIIPLSAETGKN 152
>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 = 31.3 bits (71), Expect = 0.21
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 34 ILDAPGHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHL 93
+D PGH++F G A ADLA+L++ + GF QT+E + +
Sbjct: 73 FIDTPGHEAFTNLRKRGGALADLAILIV-----DINEGFKP--QTQEALNILRMYKTP-F 124
Query: 94 VVLINKMD 101
VV NK+D
Sbjct: 125 VVAANKID 132
>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 = 30.6 bits (70), Expect = 0.21
Identities = 31/102 (30%), Positives = 44/102 (43%), Gaps = 24/102 (23%)
Query: 10 QKREKGKTVEVGRAYFETDRKHFTILDAPGHKSF------VPNMIGGTAQADLAVLVISA 63
+RE+G T+ I+D PGH F V +M D +L++ A
Sbjct: 45 LERERGITILAKNTAITYKDTKINIIDTPGHADFGGEVERVLSM------VDGVLLLVDA 98
Query: 64 RKGEFETGFDRGGQTREHAMLAKT--AGVKHLVVLINKMDDP 103
+G QTR +L K AG+K +VV INK+D P
Sbjct: 99 SEGPMP-------QTR--FVLKKALEAGLKPIVV-INKIDRP 130
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 30.9 bits (71), Expect = 0.22
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 82 AMLAKTAGVKHLVVLINKMD 101
++LAK G K ++ L+N+
Sbjct: 315 SLLAKRLGAKKVIALVNRPA 334
>gnl|CDD|200460 cd11321, AmyAc_bac_euk_BE, Alpha amylase catalytic domain found in
bacterial and eukaryotic branching enzymes. Branching
enzymes (BEs) catalyze the formation of alpha-1,6 branch
points in either glycogen or starch by cleavage of the
alpha-1,4 glucosidic linkage yielding a non-reducing end
oligosaccharide chain, and subsequent attachment to the
alpha-1,6 position. By increasing the number of
non-reducing ends, glycogen is more reactive to
synthesis and digestion as well as being more soluble.
This group includes bacterial and eukaryotic proteins.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 406
Score = 31.0 bits (71), Expect = 0.22
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 110 ARYNECKDKILPYLKKLGFNA 130
A Y E D +LP +KKLG+NA
Sbjct: 35 ASYREFTDNVLPRIKKLGYNA 55
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 31.0 bits (70), Expect = 0.22
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 34 ILDAPGHKSFVPNMIGGTAQADLAVLVISARKG 66
+D PGH++F G + ADLAVLV+ +G
Sbjct: 530 FIDTPGHEAFTSLRKRGGSLADLAVLVVDINEG 562
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 31.1 bits (71), Expect = 0.23
Identities = 9/31 (29%), Positives = 11/31 (35%)
Query: 15 GKTVEVGRAYFETDRKHFTILDAPGHKSFVP 45
G TVE + I+D PG S
Sbjct: 35 GVTVEKKEGKLKYKGHEIEIVDLPGTYSLTA 65
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane
protein. The N terminus contains a P-loop motif
suggesting that iron transport may be ATP dependent.
Length = 159
Score = 30.1 bits (69), Expect = 0.27
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 15 GKTVEVGRAYFETDRKHFTILDAPG 39
G TVE F+ K I+D PG
Sbjct: 29 GVTVEKKEGEFKLGGKEIEIVDLPG 53
>gnl|CDD|129369 TIGR00268, TIGR00268, TIGR00268 family protein. The N-terminal
region of the model shows similarity to
Argininosuccinate synthase proteins using PSI-blast and
using the recognize protein identification server
[Hypothetical proteins, Conserved].
Length = 252
Score = 30.5 bits (69), Expect = 0.32
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 80 EHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYL----KKLGFNAAKD 133
+ ++AK GV H V I+KM +P E R CK +L L +K G++ D
Sbjct: 56 DAIIIAKEIGVNHEFVKIDKMINPFRANVEERCYFCKKMVLSILVKEAEKRGYDVVVD 113
>gnl|CDD|224522 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
[General function prediction only].
Length = 269
Score = 30.4 bits (69), Expect = 0.32
Identities = 13/51 (25%), Positives = 22/51 (43%)
Query: 76 GQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKL 126
+ E +AK G++H + +N+MD E R CK + L +
Sbjct: 58 REIEEAKNIAKEIGIRHEFIKMNRMDPEFKENPENRCYLCKRAVYSTLVEE 108
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 29.8 bits (68), Expect = 0.34
Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 33/88 (37%)
Query: 29 RKHFTILDAPG-------H----KSFVPNMIGGTAQADLAVLVISA----RKGEFETGFD 73
K ++D PG H +SF+P +AD + V+SA + E E
Sbjct: 45 LKGVVLVDTPGLNSTIEHHTEITESFLP-------RADAVIFVLSADQPLTESEREF--- 94
Query: 74 RGGQTREHAMLAKTAGVKHLVVLINKMD 101
K + ++NK+D
Sbjct: 95 --------LKEILKWSGKKIFFVLNKID 114
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 30.0 bits (68), Expect = 0.35
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 82 AMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFN 129
A LAK AGV+H +++ + DP S Y + K ++ L+KLGF
Sbjct: 98 AKLAKAAGVQHFLLVSSLGADPK---SSFLYLKVKGEVERDLQKLGFE 142
>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 = 30.3 bits (69), Expect = 0.38
Identities = 36/124 (29%), Positives = 53/124 (42%), Gaps = 29/124 (23%)
Query: 12 REKGKTVEVGRAYFETDRKHFTILDAPGHKSF------VPNMIGGTAQADLAVLVISARK 65
RE+G T+ + I+D PGH F V M+ G +L++ A +
Sbjct: 46 RERGITILAKNTAIRYNGTKINIVDTPGHADFGGEVERVLGMVDG------VLLLVDASE 99
Query: 66 GEFETGFDRGGQTREHAMLAKT--AGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYL 123
G QTR +L K G+K +VV INK+D P AR +E D++
Sbjct: 100 GPMP-------QTR--FVLKKALELGLKPIVV-INKIDRP-----SARPDEVVDEVFDLF 144
Query: 124 KKLG 127
+LG
Sbjct: 145 AELG 148
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of
the cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 29.4 bits (67), Expect = 0.61
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 15 GKTVEVGRAYFETDRKHFTILDAPG 39
G TVE F+ I+D PG
Sbjct: 32 GVTVEKKEGTFKYKGYEIEIVDLPG 56
>gnl|CDD|180517 PRK06293, PRK06293, single-stranded DNA-binding protein;
Provisional.
Length = 161
Score = 28.7 bits (64), Expect = 0.80
Identities = 15/39 (38%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 87 TAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKK 125
GVK V D TV + DK+LPYLKK
Sbjct: 29 RLGVKSRV----GSKDETVWCRCNIWGNRYDKMLPYLKK 63
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 29.4 bits (67), Expect = 0.81
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 12/68 (17%)
Query: 36 DAPGHKSFVPNM--IGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHL 93
D PGH++F N+ GG A AD+A+LV+ +G F+ QT E + K +
Sbjct: 77 DTPGHEAFT-NLRKRGG-ALADIAILVVDINEG-FQP------QTIEAINILKRRKTPFV 127
Query: 94 VVLINKMD 101
V NK+D
Sbjct: 128 VAA-NKID 134
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 29.1 bits (66), Expect = 0.98
Identities = 31/101 (30%), Positives = 45/101 (44%), Gaps = 23/101 (22%)
Query: 34 ILDAPGHKSFVPNMIGGTAQ-----ADLAVLVISARKGEFETGFDRGGQTREHAMLAKTA 88
I+D PGH F GG + D +L++ A +G QTR A
Sbjct: 72 IVDTPGHADF-----GGEVERVLSMVDGVLLLVDASEGPMP-------QTRFVLKKALAL 119
Query: 89 GVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFN 129
G+K +VV INK+D P +AR +E D++ +LG
Sbjct: 120 GLKPIVV-INKIDRP-----DARPDEVVDEVFDLFVELGAT 154
>gnl|CDD|191424 pfam06001, DUF902, Domain of Unknown Function (DUF902). This
domain of unknown function is found in several
transcriptional co-activators including the CREB-binding
protein, which is an acetyltransferase that acetylates
histones, giving a specific tag for transcriptional
activation. This short domain is found to the C-terminus
of bromodomains. The 40 residue domain contains four
conserved cysteines suggesting that it may be stabilised
by a zinc ion. In CREB this domain is to the N-terminus
of another zinc binding PHD domain.
Length = 42
Score = 26.6 bits (59), Expect = 0.99
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 4/25 (16%)
Query: 121 PYLKKLGFNAAKDLSFMP----CSG 141
P ++ LG+ + F P C G
Sbjct: 1 PVMQSLGYCCGRKYEFQPQVLCCYG 25
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 28.9 bits (66), Expect = 1.1
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 13/77 (16%)
Query: 53 QADLAVLVISARKGEFETGFDRGGQTREH-AMLAKTAGVKHLVVLINKMDDPTVMWSEAR 111
+AD+ +LV+ A +G T D A LA AG K LV+++NK D ++ E
Sbjct: 254 RADVVLLVLDATEG--ITEQD------LRIAGLALEAG-KALVIVVNKWD---LVKDEKT 301
Query: 112 YNECKDKILPYLKKLGF 128
E K ++ L L F
Sbjct: 302 REEFKKELRRKLPFLDF 318
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 28.7 bits (65), Expect = 1.5
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 54 ADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYN 113
AD+ +LVI A +G E Q A L + AG + +V+++NK D V EA
Sbjct: 261 ADVVLLVIDATEGISE-------QDLRIAGLIEEAG-RGIVIVVNKWD--LVEEDEATME 310
Query: 114 ECKDKILPYLKKLGF 128
E K K+ L L F
Sbjct: 311 EFKKKLRRKLPFLDF 325
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.1 bits (64), Expect = 1.7
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 12/53 (22%)
Query: 52 AQADLAVLVISARKGEFETGF-DRGGQTREHAML--AKTAGVKHLVVLINKMD 101
A D ++V S ++ F DR L A+ +G++ V+++NK D
Sbjct: 1 ANVDQVLIVFSLKEPFFNLRLLDR--------YLVAAEASGIE-PVIVLNKAD 44
>gnl|CDD|223100 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 28.3 bits (64), Expect = 2.1
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 15/66 (22%)
Query: 29 RKHF-TILDAPGHKSFVPNMIGGTAQADLAV---LVISARKGEFETGFDRGGQT-----R 79
RK L+A K +P +IGG+ ADLA IS G+F + G+ R
Sbjct: 357 RKASGKALNALAKK--LPELIGGS--ADLAPSNLTKISG-SGDFSPE-NYAGRYIHFGVR 410
Query: 80 EHAMLA 85
E AM A
Sbjct: 411 EFAMAA 416
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 28.0 bits (63), Expect = 2.3
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 112 YNECKDKILPYLKKLGFNAAKDLSFMP 138
Y E ++LPYLK+LG + MP
Sbjct: 163 YFELAIELLPYLKELGITH---IELMP 186
>gnl|CDD|232999 TIGR00506, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Several members of the family are bifunctional,
involving both ribA and ribB function. In these cases,
ribA tends to be on the C-terminal end of the protein
and ribB tends to be on the N-terminal [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 199
Score = 27.7 bits (62), Expect = 2.4
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 74 RGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSEARYNECKD 117
RGG T LA+ AG+K V+ M+D M AR E +
Sbjct: 140 RGGHTEASVDLAELAGLKPAGVICEMMNDDGTM---ARKPELME 180
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 27.8 bits (63), Expect = 2.7
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 10/50 (20%)
Query: 52 AQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
+ADL +LV+ A + E + +L + +VVL NK D
Sbjct: 293 EEADLVLLVLDASEPLTEE---------DDEILEELKDKPVIVVL-NKAD 332
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 27.4 bits (62), Expect = 3.4
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 47 MIGGTAQADLAVLVISARKGEFETGFD 73
+ GGT+Q +V + R +TG D
Sbjct: 228 LSGGTSQPSTESMVAALRGTGRDTGLD 254
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 27.0 bits (61), Expect = 3.5
Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 18/90 (20%)
Query: 23 AYFETDRKHFTILDAPG----HKSFVPNMIGGT----AQADLAVLVISARKGEFETGFDR 74
E + F ++D G + + +AD+ + V+ R+G T D
Sbjct: 38 GEAEWGGREFILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREG--LTPAD- 94
Query: 75 GGQTREHA-MLAKTAGVKHLVVLINKMDDP 103
E A L K+ K +++++NK+D+
Sbjct: 95 ----EEIAKYLRKSK--KPVILVVNKIDNI 118
>gnl|CDD|200461 cd11322, AmyAc_Glg_BE, Alpha amylase catalytic domain found in the
Glycogen branching enzyme (also called 1,4-alpha-glucan
branching enzyme). The glycogen branching enzyme
catalyzes the third step of glycogen biosynthesis by the
cleavage of an alpha-(1,4)-glucosidic linkage and the
formation a new alpha-(1,6)-branch by subsequent
transfer of cleaved oligosaccharide. They are part of a
group called branching enzymes which catalyze the
formation of alpha-1,6 branch points in either glycogen
or starch. This group includes proteins from bacteria,
eukaryotes, and archaea. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 402
Score = 27.1 bits (61), Expect = 4.5
Identities = 9/27 (33%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 112 YNECKDKILPYLKKLGFNAAKDLSFMP 138
Y E D+++PY+K++G+ + MP
Sbjct: 57 YRELADELIPYVKEMGYT---HVELMP 80
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 27.1 bits (61), Expect = 4.8
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 12/67 (17%)
Query: 52 AQADLAVLVISARKG--EFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMDDPTVMWSE 109
+ DLA+LV+ A G E+E E K + ++VV INK+D
Sbjct: 84 DKTDLALLVVDAGVGPGEYE---------LELIEELKERKIPYIVV-INKIDLGEESAEL 133
Query: 110 ARYNECK 116
+ +
Sbjct: 134 EKLEKKF 140
>gnl|CDD|235744 PRK06213, PRK06213, enoyl-CoA hydratase; Provisional.
Length = 229
Score = 26.9 bits (60), Expect = 5.2
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 15/49 (30%)
Query: 52 AQADLAVLVISARKGEFETGFD---------------RGGQTREHAMLA 85
A+ D AV+VI+ + G F GFD G T +L+
Sbjct: 41 AEDDRAVVVITGQPGIFSGGFDLKVMTSGAQAAIALLTAGSTLARRLLS 89
>gnl|CDD|200465 cd11326, AmyAc_Glg_debranch, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities: 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. In Escherichia coli, GlgX is
the debranching enzyme and malQ is the
4-alpha-glucanotransferase. TreX, an archaeal
glycogen-debranching enzyme has dual activities like
mammals and yeast, but is structurally similar to GlgX.
TreX exists in two oligomeric states, a dimer and
tetramer. Isoamylase (EC 3.2.1.68) is one of the
starch-debranching enzymes that catalyzes the hydrolysis
of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen and their
beta-limit dextrins. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 433
Score = 27.0 bits (61), Expect = 5.2
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 119 ILPYLKKLGFNAAKDLSFMPC 139
+PYLK+LG A + +P
Sbjct: 49 KIPYLKELGVTA---VELLPV 66
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 27.1 bits (60), Expect = 5.4
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 50 GTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAG 89
AQAD + + R E FDR G RE A LA T G
Sbjct: 749 SRAQADRLPIPSTLR-DSLELRFDRLGPARETAQLAATIG 787
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 26.9 bits (60), Expect = 5.9
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 112 YNECKDKILPYLKKLGFNA 130
Y E D +LP +K LG+NA
Sbjct: 249 YREFADDVLPRIKALGYNA 267
>gnl|CDD|214582 smart00245, TSPc, tail specific protease. tail specific protease.
Length = 192
Score = 26.4 bits (59), Expect = 6.5
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 15/78 (19%)
Query: 26 ETDRKHFTILDAP----GHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREH 81
+T+ + ILD G S ++ + V + R GE T G+
Sbjct: 55 KTNVEGL-ILDLRNNPGGLLSAAIDVSSLFLDKGVIVYTVYRRTGELWTYPANLGR---- 109
Query: 82 AMLAKTAGVKHLVVLINK 99
K + K LVVL+NK
Sbjct: 110 ----KYS--KPLVVLVNK 121
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 25.9 bits (58), Expect = 6.8
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 52 AQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLINKMD 101
+ADL +LV+ A + G E + + K ++V++NK D
Sbjct: 81 EEADLVLLVVDASE----------GLDEEDLEILELPAKKPVIVVLNKSD 120
>gnl|CDD|173383 PTZ00089, PTZ00089, transketolase; Provisional.
Length = 661
Score = 26.6 bits (59), Expect = 7.3
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 8/58 (13%)
Query: 41 KSFVPNMIGGTAQADLAVLVISARKGE--FETGFDRGGQ----TREHAMLAKTAGVKH 92
+P +IGG+A DL ++ K F G REHAM A G+
Sbjct: 369 FQILPELIGGSA--DLTPSNLTRPKEANDFTKASPEGRYIRFGVREHAMCAIMNGIAA 424
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 25.9 bits (58), Expect = 7.9
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 54 ADLAVLVISARKGEFETGFDRGGQTREH-AMLAKTAGVKHLVVLINKMDDPTVMWSEARY 112
AD+ +LV+ A +G T D A L G K L++++NK D V E
Sbjct: 85 ADVVLLVLDASEG--ITEQD------LRIAGLILEEG-KALIIVVNKWD--LVEKDEKTM 133
Query: 113 NECKDKI---LPYLK 124
E + ++ LP+L
Sbjct: 134 KEFEKELRRKLPFLD 148
>gnl|CDD|237052 PRK12313, PRK12313, glycogen branching enzyme; Provisional.
Length = 633
Score = 26.4 bits (59), Expect = 8.1
Identities = 10/27 (37%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 112 YNECKDKILPYLKKLGFNAAKDLSFMP 138
Y E D+++PY+K++G+ + FMP
Sbjct: 169 YRELADELIPYVKEMGYT---HVEFMP 192
>gnl|CDD|234602 PRK00055, PRK00055, ribonuclease Z; Reviewed.
Length = 270
Score = 25.9 bits (58), Expect = 8.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 78 TREHAMLAKTAGVKHLV 94
R+ A +AK AGVK L+
Sbjct: 213 ARQAAEIAKEAGVKRLI 229
>gnl|CDD|200464 cd11325, AmyAc_GTHase, Alpha amylase catalytic domain found in
Glycosyltrehalose trehalohydrolase (also called
Maltooligosyl trehalose Trehalohydrolase).
Glycosyltrehalose trehalohydrolase (GTHase) was
discovered as part of a coupled system for the
production of trehalose from soluble starch. In the
first half of the reaction, glycosyltrehalose synthase
(GTSase), an intramolecular glycosyl transferase,
converts the glycosidic bond between the last two
glucose residues of amylose from an alpha-1,4 bond to an
alpha-1,1 bond, making a non-reducing glycosyl
trehaloside. In the second half of the reaction, GTHase
cleaves the alpha-1,4 glycosidic bond adjacent to the
trehalose moiety to release trehalose and
malto-oligosaccharide. Like isoamylase and other
glycosidases that recognize branched oligosaccharides,
GTHase contains an N-terminal extension and does not
have the conserved calcium ion present in other alpha
amylase family enzymes. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Glycosyltrehalose Trehalohydrolase
Maltooligosyltrehalose Trehalohydrolase.
Length = 436
Score = 26.4 bits (59), Expect = 8.7
Identities = 8/19 (42%), Positives = 9/19 (47%), Gaps = 3/19 (15%)
Query: 120 LPYLKKLGFNAAKDLSFMP 138
L YL LG A + MP
Sbjct: 61 LDYLADLGVTA---IELMP 76
>gnl|CDD|211630 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.
This model describes bacterial (and chloroplast)
ribosomal protein L1. The apparent mitochondrial L1 is
sufficiently diverged to be the subject of a separate
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 227
Score = 26.1 bits (58), Expect = 9.1
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 39 GHKSFVPNMIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKT--------AGV 90
G + +PN GT D+A V +A+KG+ E D+ G HA + K +
Sbjct: 130 GPRGLMPNPKTGTVTTDVAKAVKNAKKGQVEFRADKAGNI--HAPIGKVSFDSEKLKENL 187
Query: 91 KHLVVLINKMDDPTV 105
+ L+ I K
Sbjct: 188 EALLDAIKKAKPSGA 202
>gnl|CDD|232943 TIGR00367, TIGR00367, K+-dependent Na+/Ca+ exchanger
related-protein. This model models a family of
bacterial and archaeal proteins that is homologous,
except for lacking a central region of ~ 250 amino acids
and an N-terminal region of > 100 residues, to a
functionally proven potassium-dependent sodium-calcium
exchanger of the rat [Unknown function, General].
Length = 307
Score = 26.1 bits (58), Expect = 9.1
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 50 GTAQADLAVLVISARKGE 67
GT+ +L V + +ARKG
Sbjct: 215 GTSLPELVVSLAAARKGL 232
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 25.3 bits (56), Expect = 9.3
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 17/94 (18%)
Query: 15 GKTVEVGRAYFETDRKHFTILDAPG--HKSFVPNMIGGTAQ-------ADLAVLVISARK 65
G T + R+ ++D PG + + G + ADL +LV+ A +
Sbjct: 32 GTTRDPILGVLGLGRQ-IILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASE 90
Query: 66 GEFETGFDRGGQTREHAMLAKTAGVKHLVVLINK 99
G E E + K +++++NK
Sbjct: 91 GLTE-------DDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 389
Score = 25.9 bits (58), Expect = 9.6
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 120 LPYLKKLGFNA 130
L YLK LG NA
Sbjct: 62 LDYLKDLGVNA 72
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 26.0 bits (58), Expect = 9.6
Identities = 25/118 (21%), Positives = 42/118 (35%), Gaps = 16/118 (13%)
Query: 31 HFTILDAPGHKSFVPN-------MIGGTAQADLAVLVISARKGEFETGFDRGGQTREHAM 83
+ D PG F+ N I + V E+E + E
Sbjct: 49 TLNLWDCPGQDDFMENYLTRQKEHIFSNVGV--LIYVFDVESREYEEDLATLVKIIEALY 106
Query: 84 L-AKTAGVKHLVVLINKMDDPTVMWSEARYNECKDKILPYLKKLGFNAAKDLSFMPCS 140
+ A V VLI+KMD + + + + K++I+ ++ G DL+F S
Sbjct: 107 QYSPNAKVF---VLIHKMDLLSEDERKEIFEDRKEEIIEEIEDFGIE---DLTFFLTS 158
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
0.319 0.136 0.408
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,062,827
Number of extensions: 728778
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 796
Number of HSP's successfully gapped: 120
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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 (21.7 bits)
S2: 55 (24.9 bits)