RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026839
(232 letters)
>gnl|CDD|216422 pfam01300, Sua5_yciO_yrdC, Telomere recombination. This domain has
been shown to bind preferentially to dsRNA. The domain
is found in SUA5 as well as HypF and YrdC. It has also
been shown to be required for telomere recombniation in
yeast.
Length = 178
Score = 164 bits (418), Expect = 2e-51
Identities = 75/181 (41%), Positives = 107/181 (59%), Gaps = 5/181 (2%)
Query: 32 QALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVT 91
+AL+ G ++A PTDT+YG CDA + EAV R+ EIKGR PLA+ V D+ + ++A
Sbjct: 1 EALRQGGIVAYPTDTVYGLGCDATNEEAVERLREIKGRPRDKPLAVMVSDLEQLKKYADE 60
Query: 92 -DHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESA 150
+ L + PGP+T++L S+L K + PGL ++GVR+PD R++ L
Sbjct: 61 LEEAALKLAERFWPGPITLIL-PASKSSLPKLVTPGLGTVGVRLPDHPLARLLLEALGEP 119
Query: 151 LALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRP 209
L TSANL+G+PS+ ++ E L + DGG +P STVVDLT GK +ILR
Sbjct: 120 LVATSANLSGEPSATDAEEVLEELGGIVDLILDGGRIP-VGVDSTVVDLTD-GKPRILRR 177
Query: 210 G 210
G
Sbjct: 178 G 178
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 152 bits (387), Expect = 2e-46
Identities = 71/192 (36%), Positives = 102/192 (53%), Gaps = 4/192 (2%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 87
E+A++AL+ G V+A PTDT+YG DA + EAV R+YEIK R PL + V + +
Sbjct: 17 EKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLILHVASLEQLKE 76
Query: 88 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 147
+A + LL + PGP+T +L + + GL +I VRVPD + L
Sbjct: 77 YADVPDVARKLLKAFWPGPLTFILPATKEVPRRL-VTAGLSTIAVRVPDHPIALALIEAL 135
Query: 148 ESALALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKI 206
LA TSANL+GQPS + ++ + + + DGG G ST++DLT +I
Sbjct: 136 GEPLASTSANLSGQPSPTTAEEVRADFGGQVDLIIDGGPCRGGLP-STIIDLTD-DPPRI 193
Query: 207 LRPGSAKEETIA 218
LRPG+ E I
Sbjct: 194 LRPGAISLEEIE 205
>gnl|CDD|232802 TIGR00057, TIGR00057, tRNA threonylcarbamoyl adenosine modification
protein, Sua5/YciO/YrdC/YwlC family. Has paralogs, but
YrdC called a tRNA modification protein. Ref 2 authors
say probably heteromultimeric complex. Paralogs may mean
its does the final binding to the tRNA [Protein
synthesis, tRNA and rRNA base modification].
Length = 201
Score = 142 bits (359), Expect = 2e-42
Identities = 65/194 (33%), Positives = 104/194 (53%), Gaps = 5/194 (2%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 87
E+A++ L+ G ++ PTDT+YG DA +AV R+Y IKGR PL + V D+S+I +
Sbjct: 12 EQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIEK 71
Query: 88 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 147
+A L+ PGP+T+VL + + ++ ++IG+RVPD+ + L
Sbjct: 72 YAYVPDDAKRLMKKFWPGPLTLVLKKTPEIP--RRVSGKRKTIGIRVPDNPIALELLEEL 129
Query: 148 ESALALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKI 206
+ TSANL+G+PS+ V++ + L + + D G G ST++DLT K+
Sbjct: 130 GKPIVATSANLSGKPSATDVEEAVDELGKLVDLIIDAGPCLGGEP-STIIDLT-DDTPKV 187
Query: 207 LRPGSAKEETIAIL 220
LR G E +L
Sbjct: 188 LREGVGSEPIEKVL 201
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 67.5 bits (165), Expect = 4e-13
Identities = 44/143 (30%), Positives = 68/143 (47%), Gaps = 7/143 (4%)
Query: 24 EAHAEEAIQA----LKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICV 79
A ++A+ LK GK+IA+ + ACDA + E V R+ K R P A+
Sbjct: 158 HAEQDDALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKNRP-LKPFAVMS 216
Query: 80 GDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNF 139
D+ + A ++L LL S P V+L + L ++ P L +IGV +P +
Sbjct: 217 PDLESAEQHAELNNLECELLTS--PAAPIVLLRKKPDIKLAPNIAPNLPTIGVMLPYTPL 274
Query: 140 VRVIARGLESALALTSANLTGQP 162
++ + L L +TSANL G P
Sbjct: 275 HHLLLQLLAFPLVMTSANLPGLP 297
>gnl|CDD|182603 PRK10634, PRK10634, tRNA(ANN) t(6)A37 threonylcarbamoyladenosine
modification protein; Provisional.
Length = 190
Score = 63.6 bits (155), Expect = 1e-12
Identities = 44/141 (31%), Positives = 64/141 (45%), Gaps = 11/141 (7%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSD--- 84
A+ L +VIA PT+ ++G CD S AV R+ E+K R L I + +
Sbjct: 11 AAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGL-ILIAANYEQLK 69
Query: 85 --INRFAVTDHLPHGLLDSLLPGPVTVVL-SRGESSNLEKSLNPGLESIGVRVPDSNFVR 141
I+ +TD + S PGPVT V + + + L +S+ VRV D V
Sbjct: 70 PYIDDSMLTDAQRETIF-SCWPGPVTFVFPAPATTP---RWLTGRFDSLAVRVTDHPLVV 125
Query: 142 VIARGLESALALTSANLTGQP 162
+ + L TSANL+G P
Sbjct: 126 ALCQAYGKPLVSTSANLSGLP 146
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 65.9 bits (161), Expect = 2e-12
Identities = 48/152 (31%), Positives = 78/152 (51%), Gaps = 5/152 (3%)
Query: 12 VENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH 71
V + + A EA +A + LK GK++A+ + ACDA + EAV ++ + K R
Sbjct: 186 VNHDGEAIAEANEA-IRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKNRPL 244
Query: 72 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIG 131
P A+ D+ I FA + LL S P+ V+L + + LE ++ PGL +IG
Sbjct: 245 -KPFAVMAKDLETIEEFAEVNDEEEELLTSPS-RPI-VLLKKKKVFLLESNIAPGLHTIG 301
Query: 132 VRVPDSNFVRVIARG-LESALALTSANLTGQP 162
V +P + ++ + L+ +TSANL G+P
Sbjct: 302 VMLPYTPLHHLLLQESLDIPYVMTSANLPGEP 333
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 56.8 bits (137), Expect = 6e-10
Identities = 44/177 (24%), Positives = 80/177 (45%), Gaps = 13/177 (7%)
Query: 29 EAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRF 88
+A++ ++ G VI PTD+ Y C A+ RI I+ + D+S+++ +
Sbjct: 19 QAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTY 78
Query: 89 AVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLE 148
+ D++ L+ + PG T +L +G + L ++IG+RVP + + L
Sbjct: 79 SFVDNVAFRLMKNNTPGNYTFIL-KGTKEVPRRLLQEKRKTIGLRVPSNPIALALLEALG 137
Query: 149 SALALTSANLTGQ------PSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLT 199
+ TS L G P + + L ++ + GG L G+ +TV+DLT
Sbjct: 138 EPMLSTSLMLPGSDFTESDPEEIK----DRLEKQVDLIIHGGYL--GQQPTTVIDLT 188
>gnl|CDD|217663 pfam03659, Glyco_hydro_71, Glycosyl hydrolase family 71. Family of
alpha-1,3-glucanases.
Length = 386
Score = 30.7 bits (70), Expect = 0.57
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 149 SALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKF 204
SAL + A +T + W A +Y G V G G V L+R GK
Sbjct: 328 SALLKSPATVTVTIGGSNTG---ASWTGGAGIYHGSVPFGGATGEVVFSLSRNGKT 380
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 29.2 bits (65), Expect = 2.2
Identities = 29/114 (25%), Positives = 39/114 (34%), Gaps = 7/114 (6%)
Query: 64 YEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSL 123
YE +G +H + GD+ I F + G L LPG S G E+
Sbjct: 346 YEFRGGEHLAGFYSAFGDIKRILLFTWSFK-KLGTLLPSLPG-----YSSGGMDYGEEYR 399
Query: 124 NPGLESIG-VRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWER 176
+ E V PDS VR R + S G+ F +ER
Sbjct: 400 SLLWELGSEVGDPDSGPVRKWMRKDLFDAKVRSGVSFGKQEEFVSDIFNITFER 453
>gnl|CDD|198433 cd10035, UDG_like_3, Uncharacterized subfamily of Uracil-DNA
glycosylases. This is a subfamily of Uracil-DNA
glycosylase superfamily. Uracil-DNA glycosylases (UDG)
catalyze the removal of uracil from DNA to initiate DNA
base excision repair pathway. Uracil in DNA can arise as
a result of mis-incorporation of dUMP residues by DNA
polymerase or deamination of cytosine. Uracil mispaired
with guanine in DNA is one of the major pro-mutagenic
events, causing G:C->A:T mutations. UDG is an essential
enzyme for maintaining the integrity of genetic
information. This ubiquitously found enzyme hydrolyzes
the N-glycosidic bond of deoxyuridine in DNA.
Length = 133
Score = 27.3 bits (61), Expect = 3.5
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 101 SLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVP 135
+LLP V+ ++++ L PGL I VR P
Sbjct: 98 ALLPRLAVVIAVGRKAADALARLRPGLPVIKVRHP 132
>gnl|CDD|232994 TIGR00482, TIGR00482, nicotinate (nicotinamide) nucleotide
adenylyltransferase. This model represents the
predominant bacterial/eukaryotic adenylyltransferase
for nicotinamide-nucleotide, its deamido form
nicotinate nucleotide, or both. The first activity,
nicotinamide-nucleotide adenylyltransferase (EC
2.7.7.1), synthesizes NAD by the salvage pathway, while
the second, nicotinate-nucleotide adenylyltransferase
(EC 2.7.7.18) synthesizes the immediate precursor of
NAD by the de novo pathway. In E. coli, NadD activity
is biased toward the de novo pathway while salvage
activity is channeled through the multifunctional NadR
protein, but this division of labor may be exceptional.
The given name of this model, nicotinate (nicotinamide)
nucleotide adenylyltransferase, reflects the lack of
absolute specificity with respect to substrate
amidation state in most species [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridine
nucleotides].
Length = 193
Score = 27.7 bits (62), Expect = 4.5
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 21 PATEAH---AEEAIQALKTGKVIAVPT 44
P H AEEA+ L KVI VPT
Sbjct: 8 PIHYGHLLLAEEALDHLDLDKVIFVPT 34
>gnl|CDD|215199 PLN02349, PLN02349, glycerol-3-phosphate acyltransferase.
Length = 426
Score = 27.8 bits (62), Expect = 4.9
Identities = 15/108 (13%), Positives = 39/108 (36%), Gaps = 3/108 (2%)
Query: 95 PHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALT 154
++LP +++ LS +++ + + G ++ +A + +A T
Sbjct: 7 VAPARTAILPALLSLRLSTSKATLPPLRATGRVSARGRSPLVTDKESSVAASIAAAETAT 66
Query: 155 SANL--TGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTR 200
S+ L + + + L + G LP+ + + +L
Sbjct: 67 SSPLEDLKSHTFKDARSEQELLAGIKKEVEAGRLPA-NVAAGMEELYA 113
>gnl|CDD|204665 pfam11494, Ta0938, Ta0938. Ta0938 is a protein of unknown
function however the structure has been determined. The
protein has a novel fold and a putative Zn-binding
motif. The structure has two different parts, one
region contains a beta sheet flanked by two alpha
helices and the other contains a bundle of loops which
contain all cysteines in the protein.
Length = 106
Score = 26.4 bits (58), Expect = 6.1
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 50 FACDACSSEAVNRIYEIKGRKHT 72
F CD C+ E VN + E+K K T
Sbjct: 38 FCCDICALEFVNMLNEVK--KRT 58
>gnl|CDD|223186 COG0108, RibB, 3,4-dihydroxy-2-butanone 4-phosphate synthase
[Coenzyme metabolism].
Length = 203
Score = 26.8 bits (60), Expect = 7.5
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 12/58 (20%)
Query: 28 EEAIQALKTGK-VIAVPTDTLYG-----FACDACSSEAVNRIYEIKGRKHTSPLAICV 79
EEAI+AL+ GK VI V + FA +A + E + + R+H S L ICV
Sbjct: 7 EEAIEALRAGKPVIVVDDEDRENEGDLIFAAEAVTPEQIAFM-----RRHASGL-ICV 58
>gnl|CDD|216197 pfam00926, DHBP_synthase, 3,4-dihydroxy-2-butanone 4-phosphate
synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is
biosynthesised from ribulose 5-phosphate and serves as
the biosynthetic precursor for the xylene ring of
riboflavin. Sometimes found as a bifunctional enzyme
with pfam00925.
Length = 193
Score = 26.7 bits (60), Expect = 9.4
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 16/60 (26%)
Query: 28 EEAIQALKTGKVIAV--------PTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICV 79
EEAI+ALK GK + V D + A + + E+VN + +H L ICV
Sbjct: 2 EEAIEALKAGKPVIVVDDEDRENEGDLV--IAAEKVTPESVNFM-----IRHARGL-ICV 53
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
0.315 0.132 0.377
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,589,826
Number of extensions: 1075678
Number of successful extensions: 812
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 24
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 57 (26.0 bits)