RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045123
(219 letters)
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 1, represents the clamp domain, which a
mobile domain involved in positioning the DNA,
maintenance of the transcription bubble and positioning
of the nascent RNA strand.
Length = 330
Score = 170 bits (434), Expect = 3e-52
Identities = 77/178 (43%), Positives = 101/178 (56%), Gaps = 17/178 (9%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTERGM--PMAGGLSDLRLGTIDKRFKCETCSS 71
K++ +QF I SP+EIRK SV E+ +T G P GGL D R+GTI K+ CETC
Sbjct: 3 KIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTIKKKSICETCGV 62
Query: 72 NMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED----DKFKLALKI 127
+ ECPGHFGH+ELAKP+FHIGF K +L+I+RCVC CS +L +E K + K
Sbjct: 63 EVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFFLKVVIDPKG 122
Query: 128 RHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDG 185
++ K RL++I CK K+ C E K GCG QP ++ DG
Sbjct: 123 KNSKKRLKKINNLCKKKSICSKCGED-----------NGGLKAFEGCGKYQPKISKDG 169
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 138 bits (351), Expect = 9e-38
Identities = 53/141 (37%), Positives = 81/141 (57%), Gaps = 7/141 (4%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
++ ++F +LSP+EIRKMSVT+I T + G P+ GGL D RLG ID +C+TC
Sbjct: 8 RIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGR 67
Query: 73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED-----DKFKLALKI 127
GECPGHFGH+ELA+P+ H+GF K + ++R C C ++ EE+ +K + +
Sbjct: 68 AGECPGHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEW 127
Query: 128 RHPKSRL-EQILCACKTKNKC 147
L +++ + C
Sbjct: 128 GSLADDLIKEVKKEAAKRMVC 148
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 128 bits (324), Expect = 3e-34
Identities = 37/97 (38%), Positives = 56/97 (57%), Gaps = 3/97 (3%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
++F + SP+EIR E+ +T R P GGL D R+ DK ++C TC C
Sbjct: 7 IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRIC 64
Query: 77 PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKIL 113
PG FGH+ELA P+ HI F K++ +++ C +C ++L
Sbjct: 65 PGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVL 101
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 127 bits (321), Expect = 7e-34
Identities = 51/106 (48%), Positives = 71/106 (66%), Gaps = 1/106 (0%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSN 72
K+ ++F +LSP+EIRKMSV E+ T + G P+ GGL D RLG I+ +C+TC
Sbjct: 3 KIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGK 62
Query: 73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED 118
+GECPGHFGH+ELA+P+ H+GF K + I+R C C +I EE+
Sbjct: 63 VGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTEEE 108
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 111 bits (279), Expect = 2e-28
Identities = 44/117 (37%), Positives = 67/117 (57%), Gaps = 1/117 (0%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
+ F ++SP + RK+ EI + E G+P+ GGL D RLGTI+ KC TC + C
Sbjct: 12 IIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANC 71
Query: 77 PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSR 133
PGHFGH+ELA+P+ HI F+ + ++ C C+K+ +ED ++ H +R
Sbjct: 72 PGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAAR 128
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 34.2 bits (78), Expect = 0.047
Identities = 32/101 (31%), Positives = 43/101 (42%), Gaps = 20/101 (19%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKTTE-RGMPM-AGGL-----------SDLRLGTIDKRF 64
V SI SP+ I++MS EI+ T R + GGL + G KR
Sbjct: 1451 VSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRR 1510
Query: 65 K----CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
CE C + GH+ELA P+ HI F+K+L
Sbjct: 1511 HRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFLKSL 1551
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 32.7 bits (75), Expect = 0.15
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 8/34 (23%)
Query: 17 MVQFSI-------LSPDEIRKMSV-TEIDHGKTT 42
MV F++ +PD+IR MSV +DHGK+T
Sbjct: 1 MVNFTVDQIREIMDNPDQIRNMSVIAHVDHGKST 34
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 30.8 bits (70), Expect = 0.71
Identities = 30/98 (30%), Positives = 41/98 (41%), Gaps = 20/98 (20%)
Query: 21 SILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID---------KRFK--- 65
SI SPD IR S E+ +T R + P GL ++ G K+ +
Sbjct: 5 SIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKG 64
Query: 66 --CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
CE C + E GH+ELA P+ HI + K L
Sbjct: 65 VVCERCGVEVTESKVRRERMGHIELAAPVAHIWYFKGL 102
>gnl|CDD|139168 PRK12708, flgJ, peptidoglycan hydrolase; Reviewed.
Length = 134
Score = 29.4 bits (66), Expect = 0.72
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 77 PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKF 121
G L+LA F F++T+L MR + S ++AD EDD F
Sbjct: 22 NLEQGALKLAAQQFEAQFLQTVLKQMR----SASDVMAD-EDDPF 61
>gnl|CDD|181845 PRK09425, prpD, 2-methylcitrate dehydratase; Provisional.
Length = 480
Score = 29.8 bits (68), Expect = 1.2
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 119 DKFKLALKIRHPKSRLEQILCACKTKNKCE 148
+KFK L R P + ++IL C + + E
Sbjct: 438 EKFKANLATRFPAKQQQRILDLCLDQERLE 467
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 28.5 bits (64), Expect = 3.0
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 17 MVQFSILS-------PDEIRKMSV-TEIDHGKTT 42
MV+F+ IR MSV +DHGK+T
Sbjct: 1 MVKFTAEELRRIMDKKHNIRNMSVIAHVDHGKST 34
>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 = 28.0 bits (63), Expect = 3.3
Identities = 23/98 (23%), Positives = 35/98 (35%), Gaps = 43/98 (43%)
Query: 36 IDHGKTT-----------------ERGMPMAGGLSDLRLGTID-KRFKCETCSSNM---- 73
+ HGKTT +R + ++LG + K +KC C
Sbjct: 9 VAHGKTTLVKALSGVWTVRHKEELKRNI-------TIKLGYANAKIYKCPNCGCPRPYDT 61
Query: 74 --GECPGHFGHLELAKPMFHIGF---------MKTLLT 100
ECPG G +L + H+ F M T+L+
Sbjct: 62 PECECPGCGGETKL---VRHVSFVDCPGHEILMATMLS 96
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 28.3 bits (64), Expect = 4.1
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 25 PDEIRKMSVT-EIDHGKTT 42
P++IR + + IDHGKTT
Sbjct: 17 PEQIRNIGIIAHIDHGKTT 35
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 27.9 bits (63), Expect = 4.7
Identities = 19/73 (26%), Positives = 24/73 (32%), Gaps = 30/73 (41%)
Query: 36 IDHGKTT-----------------ERGMPMAGGLSDLRLGTIDKRF-KCETCSSNMG--- 74
+DHGKTT +RG+ +RLG D KC C
Sbjct: 18 VDHGKTTLVQALTGVWTDRHSEELKRGI-------TIRLGYADATIRKCPDCEEPEAYTT 70
Query: 75 --ECPGHFGHLEL 85
+CP EL
Sbjct: 71 EPKCPNCGSETEL 83
>gnl|CDD|187765 cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the
Tellurite-resistance/Dicarboxylate Transporter (TDT)
family. This subfamily contains bacterial
C4-dicarboxylate transporters, which is part of the
Tellurite-resistance/Dicarboxylate Transporter (TDT)
family. It includes Tellurite resistance protein tehA;
the tehA gene encodes an integral membrane protein that
has been shown to have efflux activity of quaternary
ammonium compounds. TehA protein of Escherichia coli
functions as a tellurite-resistance uptake permease.
Length = 293
Score = 27.5 bits (62), Expect = 4.9
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 80 FGHLELAKPMFHIGFMKT--LLTIM 102
FG L + F GF+ LL ++
Sbjct: 141 FGQPLLGQIAFWFGFVAYLILLPLV 165
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4).
LepA (also known as elongation factor 4, EF4) belongs
to the GTPase family and exhibits significant homology
to the translation factors EF-G and EF-Tu, indicating
its possible involvement in translation and association
with the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G
gene in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 27.1 bits (61), Expect = 5.8
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 14/42 (33%)
Query: 36 IDHGKTTERGMPMAGGLSDLRL----GTIDKRFKCETCSSNM 73
IDHGK+T L+D RL GT+ +R E +M
Sbjct: 9 IDHGKST---------LAD-RLLELTGTVSEREMKEQVLDSM 40
>gnl|CDD|239149 cd02698, Peptidase_C1A_CathepsinX, Cathepsin X; the only
papain-like lysosomal cysteine peptidase exhibiting
carboxymonopeptidase activity. It can also act as a
carboxydipeptidase, like cathepsin B, but has been shown
to preferentially cleave substrates through a
monopeptidyl carboxypeptidase pathway. The propeptide
region of cathepsin X, the shortest among papain-like
peptidases, is covalently attached to the active site
cysteine in the inactive form of the enzyme. Little is
known about the biological function of cathepsin X. Some
studies point to a role in early tumorigenesis. A more
recent study indicates that cathepsin X expression is
restricted to immune cells suggesting a role in
phagocytosis and the regulation of the immune response.
Length = 239
Score = 27.4 bits (61), Expect = 6.3
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 119 DKFKLALKIRHPKSRLE-QILCACKTKNKCEGGDEIDVL 156
D+ +A K P L Q++ C C GGD V
Sbjct: 42 DRINIARKGAWPSVYLSVQVVIDCAGGGSCHGGDPGGVY 80
>gnl|CDD|216415 pfam01291, LIF_OSM, LIF / OSM family.
Length = 162
Score = 26.7 bits (59), Expect = 6.4
Identities = 21/122 (17%), Positives = 42/122 (34%), Gaps = 20/122 (16%)
Query: 67 ETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEED-------D 119
+ C N + P EL++ F+ TL + V +N + A ++
Sbjct: 36 KLCRPNPTDFPSEDTLRELSRL----VFLYTLNATLGAVLYN---LTALQQVLNKTAHFL 88
Query: 120 KFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLG----HDGEEPLRKRKSGCG 175
+ KL + + +LC + + G ++ +++K GCG
Sbjct: 89 QVKLQSARDNIRGLRNNVLCMACLLYHS--SEHEPTQTGSGPSPDTSTKDVFQRKKLGCG 146
Query: 176 AL 177
L
Sbjct: 147 FL 148
>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 = 27.3 bits (61), Expect = 6.6
Identities = 16/60 (26%), Positives = 20/60 (33%), Gaps = 25/60 (41%)
Query: 33 VTEIDHGKTT-----------------ERGMPMAGGLSDLRLGTIDKRF-KCETCSSNMG 74
V +DHGKTT +RG+ +RLG D KC C
Sbjct: 10 VGHVDHGKTTLTKALTGVWTDTHSEELKRGI-------SIRLGYADAEIYKCPECDGPEC 62
>gnl|CDD|204007 pfam08625, Utp13, Utp13 specific WD40 associated domain. Utp13 is
a component of the five protein Pwp2 complex that forms
part of a stable particle subunit independent of the U3
small nucleolar ribonucleoprotein that is essential for
the initial assembly steps of the 90S pre-ribosome. Pwp2
is capable of interacting directly with the 35 S
pre-rRNA 5' end.
Length = 138
Score = 26.4 bits (59), Expect = 7.6
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 121 FKLALKIRHPKSRLEQILCACKTKNKCEGGDEID-VLSLLGHDGEEPLRKR 170
LAL + HP L + + ++ G DE++ + L D E L K
Sbjct: 17 LLLALTLDHPHRLLNVLKSVIEDEDSI-GSDELEETIGRLRKDQLERLLKF 66
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 27.3 bits (62), Expect = 8.2
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 14/32 (43%)
Query: 36 IDHGKTTERGMPMAGGLSDLRL----GTIDKR 63
IDHGK+T L+D RL GT+ +R
Sbjct: 16 IDHGKST---------LAD-RLIELTGTLSER 37
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 27.1 bits (61), Expect = 9.1
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 15/44 (34%)
Query: 25 PDEIRKMS-VTEIDHGKTTERGMPMAGGLSDLRL----GTIDKR 63
IR S + IDHGK+T L+D RL G + +R
Sbjct: 6 QKNIRNFSIIAHIDHGKST---------LAD-RLLELTGGLSER 39
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.137 0.414
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,854,144
Number of extensions: 988020
Number of successful extensions: 780
Number of sequences better than 10.0: 1
Number of HSP's gapped: 770
Number of HSP's successfully gapped: 31
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.6 bits)