RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021869
(306 letters)
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 235 bits (601), Expect = 3e-78
Identities = 88/168 (52%), Positives = 119/168 (70%), Gaps = 1/168 (0%)
Query: 139 GKTKKEKVKDGFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAA 198
+ EK K EE+VV + RVTKVVKGG++ F A+VVVGD KG+VG G KA+EV A
Sbjct: 2 RMMRIEKNKLELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEA 61
Query: 199 VQKSAVDARRNIVTVPMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMA 258
++K+ DA++N++ VP+ T PH G FGAAKV+L+PAS GTGVIAGGAVR VLE+A
Sbjct: 62 IRKAVEDAKKNMIKVPLVG-GTIPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELA 120
Query: 259 GVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEELWK 306
GV++ L K LGSNN +N RAT A+++++ EV+ +RG +EE+
Sbjct: 121 GVKDVLAKSLGSNNPINVVRATFDALKQLRSPEEVAAKRGKSVEEILG 168
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 212 bits (541), Expect = 5e-69
Identities = 82/179 (45%), Positives = 116/179 (64%)
Query: 128 MDSKAKKTSAFGKTKKEKVKDGFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGV 187
A G KE D E+VV + RV+KVVKGG++ +F A+VVVGD+ G+VG
Sbjct: 2 EGKIATIEFKSGLPIKEPEVDELLEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGF 61
Query: 188 GVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVIA 247
G+ KAKEV A++K+ DA++NI+ VP T PH G GA KV+L+PA GTG+IA
Sbjct: 62 GIGKAKEVPEAIRKAIEDAKKNIIEVPRGNGHTIPHEVIGKHGAVKVLLKPAPEGTGIIA 121
Query: 248 GGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEELWK 306
GGAVR VLE+AG+++ L K LGS N +N RAT A++K++ +V+ +RG +E++
Sbjct: 122 GGAVRAVLELAGIKDVLAKSLGSRNPINVVRATFDALKKLRTPEDVAAKRGKKVEDILG 180
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 203 bits (518), Expect = 5e-66
Identities = 88/154 (57%), Positives = 114/154 (74%), Gaps = 1/154 (0%)
Query: 150 FEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRN 209
EER++ V RV+KVVKGG++ F A+VVVGD KG+VG G KAKEV A++K+ AR+N
Sbjct: 2 LEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEAARKN 61
Query: 210 IVTVPMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLG 269
++ VP+TK T PH G GAAKV+L+PASPGTGVIAGGAVR +LE+AGV++ L K LG
Sbjct: 62 LINVPLTKG-TIPHEVIGRSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLG 120
Query: 270 SNNALNNARATVVAVQKMKQWREVSRERGIPMEE 303
SNN +N RAT A+ K+K +V+ RG P+EE
Sbjct: 121 SNNPINVVRATFDALLKLKSPEDVAELRGKPVEE 154
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 187 bits (476), Expect = 9e-60
Identities = 81/143 (56%), Positives = 111/143 (77%), Gaps = 1/143 (0%)
Query: 128 MDSKAKKTSAFGKTKKEKVKD-GFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVG 186
M KK K +K +K+ +EERV+Q++RV+KVVKGGK+L FRAIVV+G++ G VG
Sbjct: 1 MLFLLKKMYNKKKNRKSNIKENKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVG 60
Query: 187 VGVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVI 246
VGV KA +V AV+K+ DA++N++T+P+TK + PH G FGAAKV+LRP++PG+GVI
Sbjct: 61 VGVGKADDVQNAVKKAVTDAKKNLITIPLTKSNSIPHNITGIFGAAKVILRPSAPGSGVI 120
Query: 247 AGGAVRIVLEMAGVENALGKQLG 269
AGG+VRIVLE+AG++N L KQLG
Sbjct: 121 AGGSVRIVLELAGIKNILAKQLG 143
>gnl|CDD|190724 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal domain.
Length = 74
Score = 99.0 bits (248), Expect = 1e-26
Identities = 39/72 (54%), Positives = 53/72 (73%)
Query: 227 GDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQK 286
G FGA KV+L+PA GTG+IAGGAVR VLE+AG+++ L K LGS N +N +AT A++K
Sbjct: 3 GKFGAVKVLLKPAPRGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPINVVKATFDALKK 62
Query: 287 MKQWREVSRERG 298
++ EV+ RG
Sbjct: 63 LRTPEEVAALRG 74
>gnl|CDD|144065 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain.
Length = 67
Score = 94.3 bits (235), Expect = 9e-25
Identities = 35/66 (53%), Positives = 48/66 (72%)
Query: 149 GFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARR 208
EE+V+ + RV KV KGG++ FRA+VVVGDK G VG+G KAKEV A++K+ DA+
Sbjct: 1 DLEEKVLVINRVQKVTKGGRRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKL 60
Query: 209 NIVTVP 214
N++ VP
Sbjct: 61 NLIEVP 66
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 96.5 bits (241), Expect = 5e-24
Identities = 47/148 (31%), Positives = 84/148 (56%), Gaps = 10/148 (6%)
Query: 149 GFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARR 208
E+ V+ + V ++ G++++FR +VVVG++ G VGVG KAK+V A++K+ +A+
Sbjct: 49 DLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKL 108
Query: 209 NIVTVPM---------TKYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAG 259
NI+ V + + P + G G+ +V L+PA G G++AG + VLE+AG
Sbjct: 109 NIIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAG 168
Query: 260 VENALGKQLGSN-NALNNARATVVAVQK 286
+++ + G +N A+AT A++
Sbjct: 169 IKDVWTRTFGETRTTVNFAKATFNALKN 196
>gnl|CDD|233235 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal
type)/S2(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S2 as well as archaeal
ribosomal protein S5 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 212
Score = 89.8 bits (223), Expect = 2e-21
Identities = 50/146 (34%), Positives = 83/146 (56%), Gaps = 10/146 (6%)
Query: 151 EERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210
EE V+ V V ++ G++ +FRA VVVG++ G VG+G+ KAKEV A++K+ ++A+ NI
Sbjct: 51 EEEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRKAIINAKLNI 110
Query: 211 VTV---------PMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVE 261
+ V + + P + G G+ +V L PA G G++AG + VL +AG++
Sbjct: 111 IPVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAGID 170
Query: 262 NALGKQLGSNNALNN-ARATVVAVQK 286
+ + G N A+AT A++K
Sbjct: 171 DVWTQTRGETRTTVNFAKATFDALKK 196
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 76.3 bits (188), Expect = 4e-16
Identities = 52/166 (31%), Positives = 82/166 (49%), Gaps = 15/166 (9%)
Query: 152 ERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIV 211
+ V+++ V K G++ +F+A VVVGD G +G+G AKEV A++ + + A+ N+V
Sbjct: 82 DEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAIIAAKLNLV 141
Query: 212 TVPMTKY-------LTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENAL 264
V + T P + G G+ +V L PA GTG++A + +LE AGVE+
Sbjct: 142 PVRRGYWGNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVF 201
Query: 265 GKQLGSNNALNN-ARATVVAVQKMKQ------WREVSRERGIPMEE 303
G N +AT A++K W+E R P +E
Sbjct: 202 TSSRGKTRTRGNFLKATFYALRKTYGFLTPDLWKETELSR-SPYDE 246
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 33.5 bits (77), Expect = 0.11
Identities = 26/109 (23%), Positives = 37/109 (33%), Gaps = 20/109 (18%)
Query: 14 SLSSLSLSLSL-----HSTPRLSFLSTA---------KLTRLPKLTLSTVLVRASESDKP 59
SL SL +L L P F S+ K + L ++LS VL+ A S +
Sbjct: 236 SLESLIAALGLCKIPGVFVPCFKFYSSGILEVVGAPLKQSSLLDVSLSVVLLNADSSVEA 295
Query: 60 NGIVFDDFNNPDEDAAVFDPPTPPED-YTPPPSFDELPMETEDEIAAAY 107
NG+ + P D PP + TE A+
Sbjct: 296 NGV-----EPEPTGSVSDRPRHLSSDSSPSPPDTSDSDPSTETPPPASL 339
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 29.8 bits (68), Expect = 2.0
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 204 VDARRNIVTVPMTKYLTFPHRSDGDFGAAKV 234
VDAR+ T MT YL + D + A +V
Sbjct: 103 VDARKEPSTPMMTIYLKDEYAYDREK-AEEV 132
>gnl|CDD|204662 pfam11487, RestrictionSfiI, Type II restriction enzyme SfiI. SfiI
is a restriction enzyme that can cleave two DNA sites
simultaneously to leave 3-base 3' overhangs. It acts as
a homo-tetramer and recognises a specific eight
base-paid palindromic DNA sequence. After binding two
copies of its recognition sequence, SfiI becomes
activated leading to cleavage of all four DNA strands.
The structure of SfiI consists of a central twisted
beta-sheet surrounded by alpha-helices.
Length = 262
Score = 29.1 bits (64), Expect = 2.4
Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 7/53 (13%)
Query: 46 LSTVLVRASESDKPNGIVFDDFNNPDEDA---AVFDPPTPPEDYTPPPSFDEL 95
L ++ V + P+ + +N + + A P E FD L
Sbjct: 178 LKSIYVLSL----PHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRL 226
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 29.3 bits (66), Expect = 2.9
Identities = 20/85 (23%), Positives = 26/85 (30%), Gaps = 5/85 (5%)
Query: 22 LSLHSTPRLSFLSTAKLTRLPKLTLSTVLVRASESDKPNGIVFDDFNNPDEDAAVFDPPT 81
L + STP L + T T S SD NG + ++ +
Sbjct: 253 LLVVSTPELVLPPEPDEQSSERQTFKTPPQPESSSDAENG-----LVSLVDEDDKEEVSR 307
Query: 82 PPEDYTPPPSFDELPMETEDEIAAA 106
E PP D E E AA
Sbjct: 308 DSESDAPPDDTDLTRALAEYEAAAP 332
>gnl|CDD|215191 PLN02333, PLN02333, glucose-6-phosphate 1-dehydrogenase.
Length = 604
Score = 29.2 bits (65), Expect = 3.3
Identities = 28/123 (22%), Positives = 50/123 (40%), Gaps = 16/123 (13%)
Query: 5 ASATRATLSSLSSLSLSLSLHSTPRLSFLSTAKLTRLPKLTLSTVLVRASESDKPNGIVF 64
A + +LS SS S S + LSFLS L + + VR+ + N ++
Sbjct: 13 ARSYSYSLSPSSSSSHSSVVDPHRSLSFLSAIP----QGLNPAKLCVRSQRNSYQNVVLM 68
Query: 65 DDFNNPDEDAAVFDPPTPPEDYTPPPSFDE-----LPMETEDEIAAAYEELYGPAYAGVS 119
+D AV P P E+ + + +P ED++ A ++ + ++
Sbjct: 69 -------QDGAVATPSNPVENDSSFKKLKDGLLSSIPSSEEDKVVAEFDGNKDESTVSIT 121
Query: 120 VLG 122
V+G
Sbjct: 122 VVG 124
>gnl|CDD|216473 pfam01388, ARID, ARID/BRIGHT DNA binding domain. This domain is
know as ARID for AT-Rich Interaction Domain, and also
known as the BRIGHT domain.
Length = 90
Score = 27.2 bits (61), Expect = 4.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 283 AVQKMKQWREVSRERGIP 300
V K K+WREV+++ GIP
Sbjct: 51 KVTKSKKWREVAQKLGIP 68
>gnl|CDD|113530 pfam04763, DUF562, Protein of unknown function (DUF562). Family of
uncharacterized proteins.
Length = 146
Score = 27.8 bits (62), Expect = 4.3
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 13/53 (24%)
Query: 50 LVRASESDKPNGIVFDDFNNPDEDAAVFDPPTPPEDYTPPPSFDELPMETEDE 102
V E++K +V + TP + PP S L E E+
Sbjct: 8 RVLHDETEKNVVVVCNH-------------STPGPESLPPESVSLLIEELEES 47
>gnl|CDD|239913 cd04467, S1_aIF5A, S1_aIF5A: Archaeal translation Initiation Factor
5A (aIF5A), S1-like RNA-binding domain. aIF5A is a
homolog of eukaryotic eIF5A. IF5A is the only protein
known to have the unusual amino acid hypusine. Hypusine
is a post-translationally modified lysine and is
essential for IF5A function. In yeast, eIF5A interacts
with components of the 80S ribosome and translation
elongation factors 2 (eEF2) in a hypusine-dependent
manner. This C-terminal S1 domain resembles the
cold-shock domain which binds RNA. Moreover, IF5A
prefers binding to the actively translating ribosome.
This evidence suggests that IF5A plays a role in
translation elongation instead of translation initiation
as previously proposed.
Length = 57
Score = 26.1 bits (58), Expect = 4.8
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 118 VSVLGNDVYVMDSKAKKTSAFGKTKKEKVKDGFEE 152
+S++G+ V +MD + +T F E++KD E
Sbjct: 9 LSIMGDVVQLMDLETYET--FEVPIPEEIKDKLEP 41
>gnl|CDD|225852 COG3315, COG3315, O-Methyltransferase involved in polyketide
biosynthesis [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 297
Score = 28.1 bits (63), Expect = 5.3
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 28 PRLSFLSTAKLTRLPKLTLSTVLVRASESDKPNGIVFDDF 67
PR S KL+ + K L RA ES KP+ ++ D F
Sbjct: 1 PRTDDDSWDKLSGVGKTALIVAAARALESRKPDPLIDDPF 40
>gnl|CDD|219916 pfam08580, KAR9, Yeast cortical protein KAR9. The KAR9 protein in
Saccharomyces cerevisiae is a cytoskeletal protein
required for karyogamy, correct positioning of the
mitotic spindle and for orientation of cytoplasmic
microtubules. KAR9 localises at the shmoo tip in mating
cells and at the tip of the growing bud in anaphase.
Length = 626
Score = 27.9 bits (62), Expect = 8.3
Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 10/89 (11%)
Query: 13 SSLSSLSLSLSLHSTPRLSFLSTAKLTRLPKLTLSTVLVRASESDKPNGIVFDDFNNPDE 72
S++SS + + R+ + ++ P L S + S D +P+
Sbjct: 416 SNVSSRRVGTPGSKSDRVGAVLLRRMNIKPTLA-SIPDEKPSNISVFE----DSETSPNS 470
Query: 73 DAAVFDPPTPPEDYTP-----PPSFDELP 96
+ DPP P F++L
Sbjct: 471 STLLRDPPPKKCGEESGHLPNNPFFNKLK 499
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 27.6 bits (62), Expect = 8.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 204 VDARRNIVTVPMTKYLTFPHRSDGDFGAAKV 234
VDAR+ T MT YL ++ D + A +V
Sbjct: 84 VDARKEPSTPTMTIYLEEEYKYDREK-AEEV 113
>gnl|CDD|240517 cd13153, KOW_GPKOW_B, KOW motif of the "G-patch domain and KOW
motifs-containing protein" (GPKOW) repeat B. GPKOW
contains one G-patch domain and two KOW motifs. GPKOW is
a nuclear protein that regulated by catalytic (C)
subunit of Protein Kinase A (PKA) and bind RNA in vivo.
PKA may be involved in regulating multiple steps in
post-transcriptional processing of pre-mRNAs. KOW domain
is known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. GPKOW is also known
as the T54 protein or MOS2 homolog.
Length = 51
Score = 25.2 bits (56), Expect = 8.3
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 173 RAIVVVGDKKGQVGVGVAKAKE-VIAAVQKSAVDARRNIVTVPM 215
+VV G +GQVG + + K+ A VQ + ++VT+
Sbjct: 3 YVMVVRGKHRGQVGKLLERDKKKETAVVQ---LLDDFSVVTLSY 43
>gnl|CDD|215591 PLN03124, PLN03124, poly [ADP-ribose] polymerase; Provisional.
Length = 643
Score = 27.5 bits (61), Expect = 9.7
Identities = 17/42 (40%), Positives = 21/42 (50%)
Query: 129 DSKAKKTSAFGKTKKEKVKDGFEERVVQVRRVTKVVKGGKQL 170
+S K SA G + EK K G EER + + VT KG L
Sbjct: 114 ESDVKVGSANGTGEDEKEKGGDEEREKEEKIVTATKKGRAVL 155
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 27.2 bits (61), Expect = 9.7
Identities = 11/30 (36%), Positives = 22/30 (73%)
Query: 272 NALNNARATVVAVQKMKQWREVSRERGIPM 301
N N+A VV+++++++ R ++RE GIP+
Sbjct: 136 NTHNSAGGQVVSLEELREIRAIAREHGIPL 165
>gnl|CDD|239199 cd02800, tRNA_bind_EcMetRS_like, tRNA-binding-domain-containing
Escherichia coli methionyl-tRNA synthetase
(EcMetRS)-like proteins. This family includes EcMetRS
and Aquifex aeolicus Trbp111 (AaTrbp111). This domain
has general tRNA binding properties. MetRS
aminoacylates methionine transfer RNAs (tRNAmet).
AaTrbp111 is structure-specific molecular chaperone
recognizing the L-shape of the tRNA fold. AaTrbp111
plays a role in nuclear trafficking of tRNAs. The
functional unit of EcMetRs and AaTrbp111 is a homodimer,
this domain acts as the dimerization domain.
Length = 105
Score = 26.3 bits (59), Expect = 9.9
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 150 FEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKA 192
+ RV +V +V K LK V +G+++ Q+ G+AK
Sbjct: 9 VDLRVGKVLEAERVEGSDKLLKL--TVDLGEEERQIVSGIAKF 49
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
0.313 0.129 0.359
Gapped
Lambda K H
0.267 0.0462 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,687,857
Number of extensions: 1575616
Number of successful extensions: 1497
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1491
Number of HSP's successfully gapped: 44
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (27.2 bits)