RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8862
(265 letters)
>gnl|CDD|236412 PRK09204, secY, preprotein translocase subunit SecY; Reviewed.
Length = 426
Score = 248 bits (637), Expect = 8e-81
Identities = 90/184 (48%), Positives = 132/184 (71%), Gaps = 4/184 (2%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G++IP+P I+ + L +LF++ ILG+FN+FSGGALSR +IF+LGIMPYI++SIIMQLL
Sbjct: 31 GSYIPVPGIDPAALAQLFDQQSGGILGLFNLFSGGALSRFSIFALGIMPYITASIIMQLL 90
Query: 88 SSIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGISLILKSQKN----LVLDTSF 143
+ ++PK E LKKEGE G+ KI QY R+ T++LA +Q GI+ L S + + F
Sbjct: 91 TVVIPKLEELKKEGEAGRRKINQYTRYLTVVLAFVQSIGIAAGLNSMSGGGGLVPIPPGF 150
Query: 144 YFHFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLVKIDL 203
+F+ T V+TL +GT+FLMWL EQITE G+GNG S+II +GI++ P+ + +L +
Sbjct: 151 FFYLTIVITLTAGTMFLMWLGEQITERGIGNGISLIIFAGIVAGLPSAIGQTFELARTGS 210
Query: 204 VNII 207
++I+
Sbjct: 211 LSIL 214
>gnl|CDD|223279 COG0201, SecY, Preprotein translocase subunit SecY [Intracellular
trafficking and secretion].
Length = 436
Score = 187 bits (478), Expect = 5e-57
Identities = 83/174 (47%), Positives = 119/174 (68%), Gaps = 4/174 (2%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G+ IP+P IN + L+ LF N L +FNMFSGGALSR +IF+LGIMPYI++SIIMQLL
Sbjct: 36 GSFIPVPGINPAALSDLF--NSQRFLILFNMFSGGALSRGSIFALGIMPYITASIIMQLL 93
Query: 88 SSIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGISLILKSQ--KNLVLDTSFYF 145
+ P + L KEGE G+ KI QY R+ TL+LA++Q G+ L + + V + +F
Sbjct: 94 TVGSPILKKLDKEGEEGRRKIQQYTRYLTLVLAVIQALGVVLGGNNGGSPSDVGNGGIFF 153
Query: 146 HFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLV 199
+ +L L +GT+FLMWL EQIT+ G+GNG S+II +GI++S P+ + ++ +
Sbjct: 154 YLLIILQLTAGTMFLMWLGEQITKRGIGNGISLIIFAGIVASLPSAIFGIIGAL 207
>gnl|CDD|233214 TIGR00967, 3a0501s007, preprotein translocase, SecY subunit.
Members of this protein family are the SecY component of
the SecYEG translocon, or protein translocation pore,
which is driven by the ATPase SecA. This model does not
discriminate bacterial from archaeal forms [Protein
fate, Protein and peptide secretion and trafficking].
Length = 410
Score = 165 bits (419), Expect = 2e-48
Identities = 81/192 (42%), Positives = 123/192 (64%), Gaps = 8/192 (4%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G IPIP I+ S L + QN I G+ N FSGGAL +++IF+LGI PYI++SII+QLL
Sbjct: 17 GTFIPIPGIDASAFQNLIQ--QNPIFGLLNTFSGGALGQISIFALGISPYITASIIIQLL 74
Query: 88 S-SIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGISLILKSQKNLVLDTSFYFH 146
+ + P + KKEGE+G+ KI Q R+ TLILA +Q GI + V D +F+
Sbjct: 75 TGDVPPLLQLQKKEGEIGRRKINQLTRYLTLILAFIQSLGIVMTGMY--GYVGDPGAFFY 132
Query: 147 FTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLVKI---DL 203
V+ L +G++ +MWL EQIT+YG+GNG S++I +GI ++ P+ L+ ++ + DL
Sbjct: 133 LLIVIQLTTGSMIVMWLGEQITKYGIGNGISLLIFAGIAATIPSGLLQPTEVRQSKVRDL 192
Query: 204 VNIIENLPNATF 215
++ ++NLP +
Sbjct: 193 ISFLQNLPFLLY 204
>gnl|CDD|215869 pfam00344, SecY, SecY translocase.
Length = 340
Score = 159 bits (406), Expect = 2e-47
Identities = 74/149 (49%), Positives = 99/149 (66%), Gaps = 6/149 (4%)
Query: 68 TIFSLGIMPYISSSIIMQLLSSIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGI 127
+IF+LGI PYI++SIIMQLL+ + PK E L KEGE G+ KI QY R+ TL+LA++Q GI
Sbjct: 1 SIFALGIGPYITASIIMQLLTVVGPKLEKLDKEGEEGRKKIQQYTRYLTLVLALIQAIGI 60
Query: 128 SLILKSQKN----LVLDTSFYFHFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSG 183
L L S +VL F VL L +GT+FLMWL E IT+YG+GNG S+II +G
Sbjct: 61 VLGLGSYGAFSNGIVLGVGFLNLLLIVLQLTAGTMFLMWLGELITKYGIGNGISLIIFAG 120
Query: 184 IISSFPNILINLLKLVKID--LVNIIENL 210
I++S P +INL L+ L++I+ L
Sbjct: 121 IVASIPWAIINLFSLLSSAGGLLSILYLL 149
>gnl|CDD|214379 CHL00161, secY, preprotein translocase subunit SecY; Validated.
Length = 417
Score = 160 bits (406), Expect = 1e-46
Identities = 79/189 (41%), Positives = 116/189 (61%), Gaps = 6/189 (3%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G IP+P I+++QL N +L + N FSGG + +F+LGI+PYI++SII+QLL
Sbjct: 27 GTFIPVPGIDHTQLYPSLS--NNPLLNLLNTFSGGGFFVIGLFALGILPYINASIIIQLL 84
Query: 88 SSIMPKFENLKKE-GELGKYKIAQYIRFSTLILAILQGSGISLILKSQKNLVLDTSFYFH 146
+SI+P E L+KE GE G+ KI QY R+ TL AI+Q GIS LK + + +
Sbjct: 85 TSIIPSLEKLQKEEGEAGRRKINQYTRYLTLGWAIIQSIGISFWLKPY---LFNWNLLLA 141
Query: 147 FTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLVKIDLVNI 206
VL L SG++ ++WLSE ITE GLGNG+S++I I+S+ P +L +LL + ++ +
Sbjct: 142 LEIVLALTSGSMIVLWLSELITEKGLGNGSSLLIFFNIVSNLPKLLQSLLFSLSANITIL 201
Query: 207 IENLPNATF 215
L F
Sbjct: 202 SILLLLFLF 210
>gnl|CDD|178954 PRK00276, infA, translation initiation factor IF-1; Validated.
Length = 72
Score = 131 bits (332), Expect = 2e-39
Identities = 43/60 (71%), Positives = 52/60 (86%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFRTK 265
++E LPNA F+V+LEN H +L HISGKMR NYIRILPGDKVTVEL+PYDL++GRI +R K
Sbjct: 13 VVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72
>gnl|CDD|183828 PRK12907, secY, preprotein translocase subunit SecY; Reviewed.
Length = 434
Score = 135 bits (341), Expect = 4e-37
Identities = 71/167 (42%), Positives = 111/167 (66%), Gaps = 6/167 (3%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G IP+P N +++ K+ ++Q N+LGM N+F GGAL +IF++GI PYI++SII+QLL
Sbjct: 31 GTFIPVPHTN-AEVLKV--QDQANVLGMLNVFGGGALQHFSIFAVGITPYITASIIVQLL 87
Query: 88 S-SIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGISLILK--SQKNLVLDTSFY 144
++PKF K+GE+G+ K AQ+ R+ T+ILA +Q G+S + L+ D S+
Sbjct: 88 QMDVIPKFSEWAKQGEMGRKKSAQFTRYFTIILAFIQAIGMSYGFNNIAGGQLITDQSWT 147
Query: 145 FHFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNI 191
+ L +GT FL+WL EQIT G+GNG S++I +G++++ PN+
Sbjct: 148 TYLFIATVLTAGTAFLLWLGEQITANGVGNGISMLIFAGLVAAIPNV 194
>gnl|CDD|239898 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like
RNA-binding domain. IF1 contains an S1-like RNA-binding
domain, which is found in a wide variety of
RNA-associated proteins. Translation initiation includes
a number of interrelated steps preceding the formation
of the first peptide bond. In Escherichia coli, the
initiation mechanism requires, in addition to mRNA,
fMet-tRNA, and ribosomal subunits, the presence of
three additional proteins (initiation factors IF1, IF2,
and IF3) and at least one GTP molecule. The three
initiation factors influence both the kinetics and the
stability of ternary complex formation. IF1 is the
smallest of the three factors. IF1 enhances the rate of
70S ribosome subunit association and dissociation and
the interaction of 30S ribosomal subunit with IF2 and
IF3. It stimulates 30S complex formation. In addition,
by binding to the A-site of the 30S ribosomal subunit,
IF1 may contribute to the fidelity of the selection of
the initiation site of the mRNA.
Length = 64
Score = 116 bits (292), Expect = 1e-33
Identities = 41/58 (70%), Positives = 51/58 (87%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
+ E LPNA F+V+LEN H +L HISGKMRMNYIRILPGD+V VEL+PYDL++GRI++R
Sbjct: 7 VTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
>gnl|CDD|188015 TIGR00008, infA, translation initiation factor IF-1. This family
consists of translation initiation factor IF-1 as found
in bacteria and chloroplasts. This protein, about 70
residues in length, consists largely of an S1 RNA
binding domain (pfam00575) [Protein synthesis,
Translation factors].
Length = 69
Score = 109 bits (275), Expect = 4e-31
Identities = 40/58 (68%), Positives = 51/58 (87%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
+ E+LPNA F+V+LEN H +L HISGK+RM+YIRILPGD+V VEL+PYDL+RGRI +R
Sbjct: 11 VTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDRVKVELSPYDLTRGRITYR 68
>gnl|CDD|223438 COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation,
ribosomal structure and biogenesis].
Length = 75
Score = 108 bits (273), Expect = 1e-30
Identities = 40/61 (65%), Positives = 48/61 (78%)
Query: 205 NIIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFRT 264
+IE LPN F+V+LEN H L HISGKMR N IRILPGD V VEL+PYDL++GRI++R
Sbjct: 12 TVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRY 71
Query: 265 K 265
K
Sbjct: 72 K 72
>gnl|CDD|214332 CHL00010, infA, translation initiation factor 1.
Length = 78
Score = 104 bits (262), Expect = 6e-29
Identities = 36/58 (62%), Positives = 49/58 (84%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
+ E+LPN F+V+L+N +LG+ISGK+R N IRILPGD+V VEL+PYDL++GRII+R
Sbjct: 13 VTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYR 70
>gnl|CDD|216345 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This
family includes both the eukaryotic translation factor
eIF-1A and the bacterial translation initiation factor
IF-1.
Length = 65
Score = 90.3 bits (225), Expect = 1e-23
Identities = 30/58 (51%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
+ E L N F+V+LE+ H L HI GK R I IL GD V VEL+PYD ++G II+R
Sbjct: 9 VTEMLGNGRFEVELEDGHERLAHIPGKRR-KRIWILRGDFVLVELSPYDKTKGDIIYR 65
>gnl|CDD|237102 PRK12442, PRK12442, translation initiation factor IF-1; Reviewed.
Length = 87
Score = 85.6 bits (212), Expect = 2e-21
Identities = 32/58 (55%), Positives = 44/58 (75%)
Query: 208 ENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFRTK 265
E LP++ F+V LEN + + SG+MR + IRIL GD+VT+EL+PYDL++GRI FR K
Sbjct: 15 EVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72
>gnl|CDD|237095 PRK12417, secY, preprotein translocase subunit SecY; Reviewed.
Length = 404
Score = 75.4 bits (186), Expect = 1e-15
Identities = 56/180 (31%), Positives = 93/180 (51%), Gaps = 14/180 (7%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G++I IP ++Y+ + L + +GG L L IFSLG+ P+++S II+QL
Sbjct: 29 GSNISIPFVSYND----MLGGHESFLKIAAANTGGDLRTLNIFSLGLGPWMTSMIILQLF 84
Query: 88 SSIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGSGISLILKSQKNLVLDTSFYFHF 147
S K + L K+ ++ + + TLI+A++Q + L L S K + T+
Sbjct: 85 SYR--KRDGLMKQTIEEQHYRERIL---TLIIAVIQSLAVILSLPS-KERISQTNIL--- 135
Query: 148 TTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLVKIDLVNII 207
L LV+GT+FL+WLS+ YG+G G I+ +I S P +I + I ++ +I
Sbjct: 136 LNTLILVTGTMFLVWLSDLNARYGIG-GPMPIVLVSMIKSIPQDVIEYIDASHIVIILLI 194
>gnl|CDD|131966 TIGR02920, acc_sec_Y2, accessory Sec system translocase SecY2.
Members of this family are restricted to the Firmicutes
lineage (low-GC Gram-positive bacteria) and appear to be
paralogous to, and much more divergent than, the
preprotein translocase SecY. Members include the SecY2
protein of the accessory Sec system in Streptococcus
gordonii, involved in export of the highly glycosylated
platelet-binding protein GspB [Protein fate, Protein and
peptide secretion and trafficking].
Length = 395
Score = 72.1 bits (177), Expect = 2e-14
Identities = 58/182 (31%), Positives = 98/182 (53%), Gaps = 16/182 (8%)
Query: 28 GAHIPIPSINYSQLTKLFEKNQNNILGMFNMFSGGALSRLTIFSLGIMPYISSSIIMQLL 87
G++IPIP + S + E +N+ + +GG L+ L+IFSLG+ P+++S II+QL
Sbjct: 19 GSYIPIPFVEVS--KQDMEGVKNSFFKIAIANTGGNLTTLSIFSLGLGPWMTSMIILQLF 76
Query: 88 S-SIMPKFENLKKEGELGKYKIAQYI-RFSTLILAILQGSGISLILKSQKNLVLDTSFYF 145
S + F+ K QY RF TLI+AI+QG I + KN + D +
Sbjct: 77 SFTKSDGFDAQSP-------KEQQYRERFLTLIIAIIQGLAIIHSFTN-KNGLSDFNMLL 128
Query: 146 HFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGIISSFPNILINLLKLVKIDLVN 205
L LV+GT L+WL++ +YG+G G+ I+ ++ + P+ + L ++ I L+
Sbjct: 129 ---ATLILVTGTCLLVWLADLNAKYGIG-GSMPIVLVSMLKNIPSNVFELFQMSYIWLIA 184
Query: 206 II 207
++
Sbjct: 185 LL 186
>gnl|CDD|235523 PRK05592, rplO, 50S ribosomal protein L15; Reviewed.
Length = 146
Score = 48.9 bits (118), Expect = 2e-07
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 1 MRLNNILPNKDAKHYKKRLGRGIGSGSG 28
M+LN + P ++ +KR+GRGIGSG G
Sbjct: 1 MKLNELKPAPGSRKARKRVGRGIGSGLG 28
>gnl|CDD|240219 cd05793, S1_IF1A, S1_IF1A: Translation initiation factor IF1A, also
referred to as eIF1A in eukaryotes and aIF1A in archaea,
S1-like RNA-binding domain. S1-like RNA-binding domains
are found in a wide variety of RNA-associated proteins.
IF1A is essential for translation initiation. eIF1A acts
synergistically with eIF1 to mediate assembly of
ribosomal initiation complexes at the initiation codon
and maintain the accuracy of this process by recognizing
and destabilizing aberrant preinitiation complexes from
the mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors. This protein family is only found in
eukaryotes and archaea.
Length = 77
Score = 40.2 bits (95), Expect = 6e-05
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
+ + L N +V+ + L I GKMR + I GD V V + + II++
Sbjct: 6 VEKMLGNGRLEVRCFDGKKRLCRIRGKMR-KRVWINEGDIVLVAPWDFQDDKADIIYK 62
>gnl|CDD|185519 PTZ00219, PTZ00219, Sec61 alpha subunit; Provisional.
Length = 474
Score = 43.1 bits (102), Expect = 9e-05
Identities = 39/140 (27%), Positives = 69/140 (49%), Gaps = 14/140 (10%)
Query: 63 ALSRLTIFSLGIMPYISSSIIMQLLSS--IMPKFENLKKEGELGKYKIAQYIRFSTLILA 120
A +R T+ LGI P ++SS++MQLL+ I+ +N K++ L ++ AQ + L++
Sbjct: 72 ASNRGTLMELGISPIVTSSMVMQLLAGSKIIDVDQNNKEDRAL--FEGAQ--KLLGLLIT 127
Query: 121 ILQGSGISLILKSQKNLVLDTSFYFHFTTVLTLVSGTIFLMWLSEQITE-YGLGNGTSII 179
+ G ++ + + + +L L I ++ L E + + YGLG+G S+
Sbjct: 128 L--GEAVAYVWSGMYGDISEIGAGNAILIILQLFFAGIVVILLDELLQKGYGLGSGISLF 185
Query: 180 I----CSGII-SSFPNILIN 194
I C II +F IN
Sbjct: 186 IATNICETIIWKAFSPTTIN 205
>gnl|CDD|233260 TIGR01071, rplO_bact, ribosomal protein L15, bacterial/organelle.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 145
Score = 40.8 bits (96), Expect = 1e-04
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 2 RLNNILPNKDAKHYKKRLGRGIGSGSGA 29
+LN + P K AK +KR+GRGIGSG G
Sbjct: 1 KLNELKPAKGAKKRRKRVGRGIGSGLGK 28
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 39.1 bits (92), Expect = 1e-04
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 215 FKVKLENDHVILGHISGKMRM----NYIRILPGDKVTVELTPYDLSRGRIIFRTK 265
V L N L IS + GD+V V++ D +GRII K
Sbjct: 18 AFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
>gnl|CDD|223278 COG0200, RplO, Ribosomal protein L15 [Translation, ribosomal
structure and biogenesis].
Length = 152
Score = 39.2 bits (92), Expect = 5e-04
Identities = 16/28 (57%), Positives = 22/28 (78%)
Query: 1 MRLNNILPNKDAKHYKKRLGRGIGSGSG 28
MRLN++ P + +K +KR+GRGIGSG G
Sbjct: 1 MRLNDLKPARGSKKTRKRVGRGIGSGLG 28
>gnl|CDD|236293 PRK08568, PRK08568, preprotein translocase subunit SecY; Reviewed.
Length = 462
Score = 39.8 bits (94), Expect = 8e-04
Identities = 28/119 (23%), Positives = 58/119 (48%), Gaps = 6/119 (5%)
Query: 68 TIFSLGIMPYISSSIIMQLL--SSIMPKFENLKKEGELGKYKIAQYIRFSTLILAILQGS 125
T+ LGI P +++ II+QLL S ++ +L + ++ Q + +++ L+ +
Sbjct: 72 TLLQLGIGPIVTAGIILQLLVGSKLINL--DLSDPEDRALFQGLQ--KLLAIVMIALEAA 127
Query: 126 GISLILKSQKNLVLDTSFYFHFTTVLTLVSGTIFLMWLSEQITEYGLGNGTSIIICSGI 184
L L ++ L L G I ++ L E ++++G+G+G S+ I +G+
Sbjct: 128 PFVLAGAFGPATGLASTPLLALLIFLQLFLGGILIILLDELVSKWGIGSGISLFILAGV 186
>gnl|CDD|128900 smart00652, eIF1a, eukaryotic translation initiation factor 1A.
Length = 83
Score = 34.1 bits (79), Expect = 0.009
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 212 NATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
N +V + L I GKMR + I GD V V+ + + II++
Sbjct: 17 NGRLEVMCADGKERLARIPGKMR-KKVWIRRGDIVLVDPWDFQDVKADIIYK 67
>gnl|CDD|185558 PTZ00329, PTZ00329, eukaryotic translation initiation factor 1A;
Provisional.
Length = 155
Score = 32.9 bits (75), Expect = 0.083
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 226 LGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
L HI GKMR + I GD + V L + S+ +I +
Sbjct: 58 LCHIRGKMRKR-VWINIGDIILVSLRDFQDSKADVILK 94
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 30.4 bits (69), Expect = 0.12
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRM----NYIRILPGDKVTVELTPYDLSRGRI 260
+ ++ V+LE+ L HIS GD+V V++ D +GRI
Sbjct: 4 KVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRI 62
>gnl|CDD|239524 cd03440, hot_dog, The hotdog fold was initially identified in the
E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein
(ACP)-dehydratase) structure and subsequently in 4HBT
(4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A
number of other seemingly unrelated proteins also share
the hotdog fold. These proteins have related, but
distinct, catalytic activities that include metabolic
roles such as thioester hydrolysis in fatty acid
metabolism, and degradation of phenylacetic acid and the
environmental pollutant 4-chlorobenzoate. This
superfamily also includes the PaaI-like protein FapR, a
non-catalytic bacterial homolog involved in
transcriptional regulation of fatty acid biosynthesis.
Length = 100
Score = 29.8 bits (67), Expect = 0.46
Identities = 8/38 (21%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 229 ISGKMRMNYIR-ILPGDKVTVELTPYDLSRGRIIFRTK 265
++ + + ++R + PGD +TVE + R + +
Sbjct: 46 VTLSLDVRFLRPVRPGDTLTVEAEVVRVGRSSVTVEVE 83
>gnl|CDD|129614 TIGR00523, eIF-1A, eukaryotic/archaeal initiation factor 1A.
Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A
for Archaea. Also called eIF-4C [Protein synthesis,
Translation factors].
Length = 99
Score = 29.5 bits (66), Expect = 0.52
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 206 IIENLPNATFKVKLENDHVILGHISGKMRMNYIRILPGDKVTVEL 250
I + L KV+ + LG I GK++ I I GD V V+
Sbjct: 25 IEQMLGAGRVKVRCLDGKTRLGRIPGKLK-KRIWIREGDVVIVKP 68
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 29.9 bits (68), Expect = 1.4
Identities = 23/90 (25%), Positives = 34/90 (37%), Gaps = 24/90 (26%)
Query: 183 GIISS---------FPNILINLLKLVKIDLVNIIENLPNATFKVKLENDHVILGHISGKM 233
G+IS N I LV I L + + E ++G +GK+
Sbjct: 633 GVISGVTSFGLFVELENNTIE--GLVHI------STLKDDYYVFD-EKGLALVGERTGKV 683
Query: 234 RMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
R+ GD+V V + DL G+I F
Sbjct: 684 ----FRL--GDRVKVRVVKADLDTGKIDFE 707
>gnl|CDD|184386 PRK13906, murB, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 307
Score = 29.8 bits (67), Expect = 1.5
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 15/77 (19%)
Query: 172 LGNGTSIIICSGIISSFPNILINLLKLVKIDLVN--IIENLPNATFKV-KLENDHV---- 224
LGNG++III G I I+I+LL L I++ + II A V ++ D+
Sbjct: 66 LGNGSNIIIREGGIRG---IVISLLSLDHIEVSDDAIIAGSGAAIIDVSRVARDYALTGL 122
Query: 225 -----ILGHISGKMRMN 236
I G I G + MN
Sbjct: 123 EFACGIPGSIGGAVYMN 139
>gnl|CDD|177798 PLN00208, PLN00208, translation initiation factor (eIF);
Provisional.
Length = 145
Score = 29.0 bits (65), Expect = 1.6
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 226 LGHISGKMRMNYIRILPGDKVTVELTPYDLSRGRIIFR 263
L HI GKMR + I GD + V L Y + +I +
Sbjct: 58 LCHIRGKMRKK-VWIAAGDIILVGLRDYQDDKADVILK 94
>gnl|CDD|239912 cd04466, S1_YloQ_GTPase, S1_YloQ_GTPase: YloQ GTase family (also
known as YjeQ and CpgA), S1-like RNA-binding domain.
Proteins in the YloQ GTase family bind the ribosome and
have GTPase activity. The precise role of this family is
unknown. The protein structure is composed of three
domains: an N-terminal S1 domain, a central GTPase
domain, and a C-terminal zinc finger domain. This
N-terminal S1 domain binds ssRNA. The central GTPase
domain contains nucleotide-binding signature motifs: G1
(walker A), G3 (walker B) and G4 motifs. Experiments
show that the bacterial YloQ and YjeQ proteins have low
intrinsic GTPase activity. The C-terminal zinc-finger
domain has structural similarity to a portion of the
DNA-repair protein Rad51. This suggests a possible role
for this GTPase as a regulator of translation, perhaps
as a translation initiation factor. This family is
classified based on the N-terminal S1 domain.
Length = 68
Score = 27.1 bits (61), Expect = 2.1
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 215 FKVKLENDHVILGHISGKMRMNYIRILPGDKVTVELTP 252
+ V+ E+ + + GK R + GD+V E
Sbjct: 13 YYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPED 50
>gnl|CDD|238329 cd00586, 4HBT, 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes
the final step in the 4-chlorobenzoate degradation
pathway in which 4-chlorobenzoate is converted to
4-hydroxybenzoate in certain soil-dwelling bacteria.
4HBT forms a homotetramer with four active sites. There
is no evidence to suggest that 4HBT is related to the
type I thioesterases functioning in primary or secondary
metabolic pathways. Each subunit of the 4HBT tetramer
adopts a so-called hot-dog fold similar to those of
beta-hydroxydecanoyl-ACP dehydratase, (R)-specific
enoyl-CoA hydratase, and type II, thioesterase (TEII).
Length = 110
Score = 28.0 bits (63), Expect = 2.3
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 232 KMRMNYIR-ILPGDKVTVELTPYDLSRGRIIFR 263
++ ++Y+R + GD++TVE L R F
Sbjct: 56 ELEIDYLRPLRLGDRLTVETRVLRLGRKSFTFE 88
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 28.6 bits (65), Expect = 3.1
Identities = 10/38 (26%), Positives = 13/38 (34%)
Query: 217 VKLENDHVILGHISGKMRMNYIRILPGDKVTVELTPYD 254
V+ E+ V GK R GD+V D
Sbjct: 15 VESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAENND 52
>gnl|CDD|218828 pfam05962, HutD, HutD. HutD from Pseudomonas fluorescens SBW25 is
a component of the histidine uptake and utilisation
operon. HutD is operonic with the well characterized
repressor protein HutC. Genetic analysis using
transcriptional fusions (lacZ) and deletion mutants
shows that hutD is necessary to maintain fitness in
environments replete with histidine. Evidence outlined
by Zhang & Rainey (2007) suggests that HutD functions as
a governor that sets an upper bound on the level of hut
operon transcription. The mechanistic basis is unknown,
but in silico molecular docking studies based on the
crystal structure of PA5104 (HutD from Pseudomonas
aeruginosa) show that urocanate (the first breakdown
product of histidine) docks with the active site of
HutD.
Length = 182
Score = 28.0 bits (63), Expect = 3.6
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 13/62 (20%)
Query: 114 FSTL-----ILAILQGSGISLILKSQKNLVLDTSFY-FHFT----TVLTLVSGTI--F-L 160
FS IL +L+G G++L + L F F T TL+ G I F L
Sbjct: 48 FSLFPGIDRILTLLEGDGMTLDHAGGEEHTLLAPLDPFAFAGDTATDATLLDGPIRDFNL 107
Query: 161 MW 162
M
Sbjct: 108 MT 109
>gnl|CDD|223894 COG0824, FcbC, Predicted thioesterase [General function prediction
only].
Length = 137
Score = 27.6 bits (62), Expect = 3.7
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 232 KMRMNYIRIL-PGDKVTVELTPYDLSRGRIIFR 263
+ ++Y+R GD +TV +L +
Sbjct: 61 EAEIDYLRPARLGDVLTVRTRVEELGGKSLTLG 93
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents a
clade of proteins of unknown function including the E.
coli yfcH protein [Hypothetical proteins, Conserved].
Length = 291
Score = 28.4 bits (64), Expect = 4.2
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 117 LILAILQGSGISLILKSQKNL---VLDTSFYFHFTTV 150
+L L G +L+LK Q+ L +L+ F F + +
Sbjct: 251 FVLRALLGEMAALLLKGQRVLPEKLLEAGFQFQYPDL 287
>gnl|CDD|237303 PRK13203, ureB, urease subunit beta; Reviewed.
Length = 102
Score = 26.7 bits (60), Expect = 4.6
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 233 MRMNY-----IRILPGDKVTVELTPYDLSRGRIIF 262
MR+N +R PG VEL P + R ++
Sbjct: 59 MRLNIPAGTAVRFEPGQTREVELVPL--AGARRVY 91
>gnl|CDD|235940 PRK07115, PRK07115, AMP nucleosidase; Provisional.
Length = 258
Score = 27.6 bits (62), Expect = 6.8
Identities = 33/98 (33%), Positives = 50/98 (51%), Gaps = 14/98 (14%)
Query: 37 NYSQLTKLF-EKNQNNILG-MFNMFSGGALSRLTIFSLGIMPYISSSIIMQLLSSIMPK- 93
N+S ++F E + G MF+M A +TI + G M +++ IM LLS++ PK
Sbjct: 31 NFSYYVEVFAELFGVPVSGSMFSMAHATAEG-ITIINFG-MGSPNAATIMDLLSALNPKA 88
Query: 94 --FENLKKEGEL-GKYKIAQYIRFSTLILAILQGSGIS 128
F L K G L KY++ Y L +A ++G G S
Sbjct: 89 VLF--LGKCGGLKSKYQVGDYF----LPIAAIRGEGTS 120
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably acts
to resolve the disulfide which forms after oxidation of
the active site cysteine in AphC. This proteins contains
two paired conserved cysteine motifs, CxxCP and CxHCDGP
[Cellular processes, Detoxification, Cellular processes,
Adaptations to atypical conditions].
Length = 515
Score = 27.7 bits (62), Expect = 7.3
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 114 FSTLILAILQGSGISLILKSQ-KNLVLDTSFYFHFTTVLTL 153
F++L+LAILQ G L + + + HF T ++L
Sbjct: 87 FTSLVLAILQVGGHGPKLDEGIIDRIRRLNGPLHFETYVSL 127
>gnl|CDD|234485 TIGR04154, archaeo_STT3, oligosaccharyl transferase, archaeosortase
A system-associated. Members of this protein family
occur, one to three members per genome, in the same
species of Euryarchaeota as contain the predicted
protein-sorting enzyme archaeosortase (TIGR04125) and
its cognate protein-sorting signal PGF-CTERM
(TIGR04126).
Length = 815
Score = 27.7 bits (62), Expect = 7.8
Identities = 20/94 (21%), Positives = 31/94 (32%), Gaps = 14/94 (14%)
Query: 117 LILAILQGSGISLILKSQKNLVLDTSFYFHFTTVLTLVSGTIFLMWLSEQITEYGLGNGT 176
L+L G S S F +L + G + L LS L
Sbjct: 252 LVLPFGFKLGFSATYYS----------LFQPLALLGVALGAVLLAGLSRFWERKDLPRYY 301
Query: 177 SIIICSGIISSFPNILINLLKLVKIDLVNIIENL 210
+G+ + + I +L L DL ++I N
Sbjct: 302 YPAAVAGLAA----LGILVLALALPDLFSLINNG 331
>gnl|CDD|171438 PRK12363, PRK12363, phosphoglycerol transferase I; Provisional.
Length = 703
Score = 27.6 bits (61), Expect = 9.2
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 10/47 (21%)
Query: 54 GMFNMFSGGALSRLTIFSLG----------IMPYISSSIIMQLLSSI 90
G+ + SG ++ T++ L YI+ I M LLS
Sbjct: 41 GLVDRLSGDGVNAATLYHLRADMDGAGVSDFSGYIAVFIGMILLSLS 87
>gnl|CDD|218750 pfam05789, Baculo_VP1054, Baculovirus VP1054 protein. This family
consists of several VP1054 proteins from the
Baculoviruses. VP1054 is a virus structural protein
required for nucleocapsid assembly.
Length = 314
Score = 27.2 bits (61), Expect = 9.5
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 132 KSQKNLVLDTSFYFHFTTV-LTLVS--GTIFLMWL---SEQITEYG-LGNGTSIIIC 181
+ K LD +FY H+T + + G + WL E G N T +I
Sbjct: 33 RLIKTKNLDKTFYLHYTVIDSRYLDYNGEPYYEWLLPSDEDRETRGRYLNATEMICY 89
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
0.323 0.141 0.400
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,569,610
Number of extensions: 1327421
Number of successful extensions: 1565
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1527
Number of HSP's successfully gapped: 98
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)