RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 041164
(357 letters)
>gnl|CDD|238951 cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 185
Score = 257 bits (659), Expect = 4e-86
Identities = 91/188 (48%), Positives = 120/188 (63%), Gaps = 3/188 (1%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYG 122
RI + SGGKDS VL VL +L RR+ YG +L L++DEGI GYRD+SL+ V+R + G
Sbjct: 1 RILVALSGGKDSLVLLHVLKKLQRRYPYGFELEALTVDEGIPGYRDESLEVVERLAEELG 60
Query: 123 LPLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGHNADD 182
+ L+IVS+K+ Y T D VK G K+ C+ CGV RR L++ A L DK+ATGHN DD
Sbjct: 61 IELEIVSFKEEY--TDDIEVKKRGGKSPCSLCGVLRRGLLNKIAKELGADKLATGHNLDD 118
Query: 183 IAETVLLNILRGDIARLSRCTLITTGEDGPIPRCKPFKYTYEKEIMFTYAYFKRLDYFST 242
AET+L+N+LRG I RL R I ++G + R +P Y EKEI+ YA L +
Sbjct: 119 EAETLLMNLLRGGILRLMRPGPILYLDEGDVTRIRPLVYVREKEIV-LYAELNGLPFVEE 177
Query: 243 ECIYSPNA 250
EC Y+ NA
Sbjct: 178 ECPYAGNA 185
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 193 bits (493), Expect = 1e-59
Identities = 90/305 (29%), Positives = 127/305 (41%), Gaps = 20/305 (6%)
Query: 39 CFYEVFEEEIHQVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLS 98
C E E ++ + I L +I + SGGKDS L +L EL RR +++ +
Sbjct: 1 CLREKLERKVKRAIREFNLI--EYKILVAVSGGKDSLALLHLLKELGRR----IEVEAVH 54
Query: 99 IDEGISGYRDDSLQTVKRNEIQYGLPLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFR 158
+D G+ GY D + V++ + G+PL + D G + K+ C C R
Sbjct: 55 VDHGLRGYSDQEAELVEKLCEKLGIPLIVERVTDDLGRETLDG------KSICAACRRLR 108
Query: 159 RQALDRGASLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITTGEDGPIPRCKP 218
R L + A L DKIATGH+ DD AET L+N+LRG R R +G + +P
Sbjct: 109 RGLLYKIAKELGADKIATGHHLDDQAETFLMNLLRGSGLRGLRGMPPKRPFEGGLLIIRP 168
Query: 219 FKYTYEKEIMFTYAYFKRLDYFSTECIYSPNAYRGFAREFIKDLERLRPRAILDIIKSGE 278
Y EKEI YA K L Y E Y R RE + LE RP + ++ E
Sbjct: 169 LLYVREKEIE-LYAKEKGLPYIEDESNYDLRYTRNRIREELLPLEEERPGLKFSLARAFE 227
Query: 279 NFRISTSTKM----PEQGTCERCGY-ISSQKWCKACVLLEGLN--RGLPKMGIVRSRGQN 331
R + C CG S K C C L ++ ++R R +
Sbjct: 228 LLRELRLLLEKLSDEKLLRCLACGAKPSLGKICAFCRKELALEKLPFASRVRLIRKRFEK 287
Query: 332 NERTK 336
K
Sbjct: 288 GGLAK 292
>gnl|CDD|238950 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
PP-loop faimly implicated in cell cycle control [Cell
division and chromosome partitioning]. This is a
subfamily of Adenine nucleotide alpha hydrolases
superfamily.Adeninosine nucleotide alpha hydrolases
superfamily includes N type ATP PPases and ATP
sulphurylases. It forms a apha/beta/apha fold which
binds to Adenosine group. This domain has a strongly
conserved motif SGGXD at the N terminus.
Length = 185
Score = 83.4 bits (207), Expect = 4e-19
Identities = 52/198 (26%), Positives = 74/198 (37%), Gaps = 26/198 (13%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYG 122
+I + SGG DS L +LSEL R GL L + +D G+ D+ V + G
Sbjct: 1 KILVAVSGGPDSMALLHLLSELKPR--LGLRLVAVHVDHGLRPESDEEAAFVADLCAKLG 58
Query: 123 LPLKIVSYKDLYGWTMDEIVKVIGLKNNCTF---CGVFRRQALDRGASLLKVDKIATGHN 179
+PL I +V + K R A D + T H+
Sbjct: 59 IPLYI-------------LVVALAPKPGGNLEAAAREARYDFFAEIAKEHGADVLLTAHH 105
Query: 180 ADDIAETVLLNILRG-DIARLSRCTLITTGEDGPIPRCKPFKYTYEKEIMFTYAYFKRLD 238
ADD AETVL+ +LRG + L+ G + R P EI Y L
Sbjct: 106 ADDQAETVLMRLLRGSGLRGLAGMPARIPFGGGRLIR--PLLGITRAEIE-AYLRENGLP 162
Query: 239 YFS----TECIYSPNAYR 252
++ + Y+ N R
Sbjct: 163 WWEDPSNEDPRYTRNRIR 180
>gnl|CDD|236737 PRK10696, PRK10696, tRNA 2-thiocytidine biosynthesis protein TtcA;
Provisional.
Length = 258
Score = 79.1 bits (196), Expect = 6e-17
Identities = 70/238 (29%), Positives = 104/238 (43%), Gaps = 17/238 (7%)
Query: 50 QVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDD 109
Q I + + G+R+ + SGGKDS L +L L +R +L +++D+ G+ +
Sbjct: 18 QAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFPEH 77
Query: 110 SLQTVKRNEIQYGLPLKIVSYKDLYGWTMDEIVK-VI--GLKNNCTFCGVFRRQALDRGA 166
L G+P I +D Y IVK I G K C+ C RR L R A
Sbjct: 78 VLPEYLE---SLGVPYHIE-EQDTYS-----IVKEKIPEG-KTTCSLCSRLRRGILYRTA 127
Query: 167 SLLKVDKIATGHNADDIAETVLLNILRGDIARLSRCTLITTGEDGPIPRCKPFKYTYEKE 226
L KIA GH+ DDI ET+ LN+ G +L +DG +P Y EK+
Sbjct: 128 RELGATKIALGHHRDDILETLFLNMFYG--GKLKAMPPKLLSDDGKHIVIRPLAYVAEKD 185
Query: 227 IMFTYAYFKRLDYFSTECIYS-PNAYRGFAREFIKDLERLRPRAILDIIKSGENFRIS 283
I+ +A K S N R +E ++D E+ P I + ++ +N S
Sbjct: 186 II-KFAEAKEFPIIPCNLCGSQENLQRQVVKEMLRDWEKEYPGRIETMFRALQNVVPS 242
>gnl|CDD|129370 TIGR00269, TIGR00269, TIGR00269 family protein. [Hypothetical
proteins, Conserved].
Length = 104
Score = 71.0 bits (174), Expect = 2e-15
Identities = 36/105 (34%), Positives = 51/105 (48%), Gaps = 3/105 (2%)
Query: 213 IPRCKPFKYTYEKEIMFTYAYFKRLDYFSTECIYSPNAYRGFAREFIKDLERLRPRAILD 272
+PR KP +Y EKE++ YA+ L EC YS + R R+F+ DLE +P
Sbjct: 1 VPRIKPLRYIPEKEVVL-YAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFS 59
Query: 273 IIKSGENFRISTSTKMP--EQGTCERCGYISSQKWCKACVLLEGL 315
+++ E + CERCG +S + CKAC LE L
Sbjct: 60 VLRGFEKLIPLLKELSEQEDLRRCERCGEPTSGRICKACKFLEEL 104
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
vs. UGG (Trp). In all bacteria, the wobble position of
the tRNA(Ile) recognizing AUA is lysidine, a lysine
derivative of cytidine. This family describes a protein
domain found, apparently, in all bacteria in a single
copy. Eukaryotic sequences appear to be organellar. The
domain archictecture of this protein family is variable;
some, including characterized proteins of E. coli and B.
subtilis known to be tRNA(Ile)-lysidine synthetase,
include a conserved 50-residue domain that many other
members lack. This protein belongs to the ATP-binding
PP-loop family ( pfam01171). It appears in the
literature and protein databases as TilS, YacA, and
putative cell cycle protein MesJ (a misnomer) [Protein
synthesis, tRNA and rRNA base modification].
Length = 189
Score = 72.3 bits (178), Expect = 5e-15
Identities = 38/135 (28%), Positives = 57/135 (42%), Gaps = 15/135 (11%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQT---VKRNEI 119
RI + SGG DS L +L +L + + L +D G+ R +S + V++
Sbjct: 1 RILVAVSGGVDSMALLHLLLKLQPK--LKIRLIAAHVDHGL---RPESDEEAEFVQQFCK 55
Query: 120 QYGLPLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGHN 179
+ +PL+I K L+ R + A D I T H+
Sbjct: 56 KLNIPLEIKKVD----VKALAKGKKKNLEEAARE---ARYDFFEEIAKKHGADYILTAHH 108
Query: 180 ADDIAETVLLNILRG 194
ADD AET+LL +LRG
Sbjct: 109 ADDQAETILLRLLRG 123
>gnl|CDD|216343 pfam01171, ATP_bind_3, PP-loop family. This family of proteins
belongs to the PP-loop superfamily.
Length = 182
Score = 69.5 bits (171), Expect = 4e-14
Identities = 42/180 (23%), Positives = 69/180 (38%), Gaps = 18/180 (10%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYG 122
+I + SGG DS L ++L +L + +G+DL +D G+ D Q VK Q
Sbjct: 1 KILVAVSGGPDSMALLYLLKKLKPK--FGIDLTAAHVDHGLREESDREAQFVKELCRQLN 58
Query: 123 LPLKI--VSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGHNA 180
+PL++ V G ++E + R + A + + T H+A
Sbjct: 59 IPLEVLRVDVAKKSGLNLEEAAREA------------RYDFFEEIAKKNGAEVLLTAHHA 106
Query: 181 DDIAETVLLNILRGDIARLSRCTLITTGEDGPIPRCKPFKYTYEKEIMFTYAYFKRLDYF 240
DD AET L+ +LRG + +P + EI Y + +
Sbjct: 107 DDQAETFLMRLLRGS-GLAGLAGIAPVRPLAGGRIVRPLLKVTKSEIE-EYLKEHGIPWV 164
>gnl|CDD|238944 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
superfamily including N type ATP PPases and ATP
sulphurylases. The domain forms a apha/beta/apha fold
which binds to Adenosine group..
Length = 103
Score = 47.5 bits (113), Expect = 4e-07
Identities = 29/128 (22%), Positives = 44/128 (34%), Gaps = 46/128 (35%)
Query: 64 IAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYGL 123
+ + SGGKDS+V A +L +L G + +++D GIS +D+ + K
Sbjct: 1 VLVAFSGGKDSSVAAALLKKL------GYQVIAVTVDHGISPRLEDAKEIAKEA------ 48
Query: 124 PLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGHNADDI 183
R +A R A + IATG DD+
Sbjct: 49 ----------------------------------REEAAKRIAKEKGAETIATGTRRDDV 74
Query: 184 AETVLLNI 191
A L
Sbjct: 75 ANRALGLT 82
>gnl|CDD|224522 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
[General function prediction only].
Length = 269
Score = 44.7 bits (106), Expect = 3e-05
Identities = 26/145 (17%), Positives = 55/145 (37%), Gaps = 20/145 (13%)
Query: 43 VFEEEIHQVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEG 102
+ ++ ++ + K +++ + SGG DS++LA + E G ++ +++D
Sbjct: 2 MLLSKLERLK---KAIKEKKKVVVAFSGGVDSSLLAKLAKE-----ALGDNVVAVTVDSP 53
Query: 103 ISGYRDDSLQTVKRNEIQYGLPLKIVSYKDLYGWTMDEIVKVIGLK--NNCTFCGVFRRQ 160
R ++ K + G+ + + M+ + N C C
Sbjct: 54 YIPRR--EIEEAKNIAKEIGIRHEFIK--------MNRMDPEFKENPENRCYLCKRAVYS 103
Query: 161 ALDRGASLLKVDKIATGHNADDIAE 185
L A D +A G NA D+ +
Sbjct: 104 TLVEEAEKRGYDVVADGTNASDLFD 128
>gnl|CDD|238956 cd01998, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs. This family of enzyme only
presents in bacteria and eukaryote. The archaeal
counterpart of this enzyme performs same function, but
is completely unrelated in sequence.
Length = 349
Score = 42.5 bits (101), Expect = 2e-04
Identities = 40/149 (26%), Positives = 60/149 (40%), Gaps = 35/149 (23%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNY-GLDLFLLSIDEGISG-YRDDSLQTVKRNEIQ 120
++ + SGG DS+V A +L E + + G+ + D+G G ++ L+ +R Q
Sbjct: 1 KVVVAMSGGVDSSVAAALLKE--QGYEVIGVFMKNWDEDDGKGGCCSEEDLKDARRVADQ 58
Query: 121 YGLPLKIVSYKDLYGWTMDEIVKVI---------GLKNN-CTFC------GVFRRQALDR 164
G+P +V+++ Y W KV G N C G A
Sbjct: 59 LGIPHYVVNFEKEY-WE-----KVFEPFLEEYKKGRTPNPDILCNKEIKFGALLDYAKKL 112
Query: 165 GASLLKVDKIATGHNA----DDIAETVLL 189
GA D IATGH A D+ LL
Sbjct: 113 GA-----DYIATGHYARIEEDNNGRYRLL 136
>gnl|CDD|217339 pfam03054, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs.
Length = 355
Score = 42.6 bits (101), Expect = 2e-04
Identities = 35/139 (25%), Positives = 57/139 (41%), Gaps = 33/139 (23%)
Query: 62 ERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYR----DDSLQTVKRN 117
++ + SGG DS+V A++L E + + + +F+ + DE ++ L +R
Sbjct: 1 MKVVVAMSGGVDSSVAAYLLKE--QGYEV-IGVFMKNWDEEDEEGHGCCSEEDLADAQRV 57
Query: 118 EIQYGLPLKIVSYKDLYGWTMDEIVKVI---------GLK-NNCTFC------GVFRRQA 161
Q G+PL +V+++ Y W KV G N C G A
Sbjct: 58 CEQLGIPLYVVNFEKEY-WE-----KVFEPFLDEYKNGRTPNPDILCNREIKFGALLDYA 111
Query: 162 LDRGASLLKVDKIATGHNA 180
+ L D +ATGH A
Sbjct: 112 KE----NLGADYLATGHYA 126
>gnl|CDD|238846 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. A highly modified
version of the P loop, the fingerprint peptide of
mononucleotide-binding proteins, is present in the
active site of the protein, which appears to be a
positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) .
Length = 173
Score = 39.7 bits (93), Expect = 6e-04
Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 8/79 (10%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGIS-----GYRDDSLQTVKRN 117
+ + SGGKDSTVL + + + ++ +D G + D +
Sbjct: 1 NVVVSFSGGKDSTVLLHLALKALPEL---KPVPVIFLDTGYEFPETYEFVDRVAERYGLP 57
Query: 118 EIQYGLPLKIVSYKDLYGW 136
+ P L
Sbjct: 58 LVVVRPPDSPAEGLALGLK 76
>gnl|CDD|238948 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily. Adenine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins probably binds ATP. This
domain is about 200 amino acids long with a strongly
conserved motif SGGKD at the N terminus.
Length = 202
Score = 39.1 bits (92), Expect = 0.001
Identities = 27/122 (22%), Positives = 49/122 (40%), Gaps = 12/122 (9%)
Query: 64 IAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYGL 123
+A+ SGG DST+L + G + ++ + + L+ KR + G+
Sbjct: 1 VAVAFSGGVDSTLLLKAAVD-----ALGDRVLAVTATSPL--FPRRELEEAKRLAKEIGI 53
Query: 124 PLKIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGHNADDI 183
+++ +L D + C C +AL A L +D + G NADD+
Sbjct: 54 RHEVIETDEL----DDPEFA-KNPPDRCYLCKKALYEALKEIAEELGLDVVLDGTNADDL 108
Query: 184 AE 185
+
Sbjct: 109 GD 110
>gnl|CDD|238942 cd01984, AANH_like, Adenine nucleotide alpha hydrolases superfamily
including N type ATP PPases, ATP sulphurylases
Universal Stress Response protein and electron transfer
flavoprotein (ETF). The domain forms a apha/beta/apha
fold which binds to Adenosine nucleotide.
Length = 86
Score = 36.6 bits (85), Expect = 0.002
Identities = 14/39 (35%), Positives = 17/39 (43%)
Query: 156 VFRRQALDRGASLLKVDKIATGHNADDIAETVLLNILRG 194
V + L R A+ D I GHNADD+A L
Sbjct: 34 VAFVRILKRLAAEEGADVIILGHNADDVAGRRLGASANV 72
>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 = 38.2 bits (89), Expect = 0.004
Identities = 28/133 (21%), Positives = 53/133 (39%), Gaps = 18/133 (13%)
Query: 55 NQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTV 114
K +++ I SGG DS++LA V S+ G ++ +++ R L+
Sbjct: 6 RNFLKEFKKVLIAYSGGVDSSLLAAVCSDA------GTEVLAITVVSPSISPR--ELEDA 57
Query: 115 KRNEIQYGLPLKIVSYKDLYGWTMDEIVKVI--GLKNNCTFCGVFRRQALDRGASLLKVD 172
+ G+ + V +D+++ ++ C FC L + A D
Sbjct: 58 IIIAKEIGVNHEFVK--------IDKMINPFRANVEERCYFCKKMVLSILVKEAEKRGYD 109
Query: 173 KIATGHNADDIAE 185
+ G NADD+ +
Sbjct: 110 VVVDGTNADDLFD 122
>gnl|CDD|235877 PRK06850, PRK06850, hypothetical protein; Provisional.
Length = 507
Score = 37.6 bits (88), Expect = 0.009
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 14/72 (19%)
Query: 66 IGASGGKDST-VLAFV---LSEL--NRRHNYGLDLFLLSID---EG--ISGYRDDSLQTV 114
IG SGGKDST VL V L+ L +R ++++S D E + + + SL+ +
Sbjct: 39 IGYSGGKDSTAVLQLVWNALAGLPPEKRTK---PVYVISSDTLVENPVVVDWVNKSLERI 95
Query: 115 KRNEIQYGLPLK 126
+ GLP+
Sbjct: 96 NEAAKKQGLPIT 107
>gnl|CDD|238954 cd01996, Alpha_ANH_like_III, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domain has a strongly conserved motif SGGKD at the
N terminus.
Length = 154
Score = 36.1 bits (84), Expect = 0.010
Identities = 30/122 (24%), Positives = 51/122 (41%), Gaps = 22/122 (18%)
Query: 66 IGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYGLPL 125
IG SGGKDS+ ++L E YGL+ +++D G +++++ +K N I+ GL L
Sbjct: 6 IGVSGGKDSSYALYLLKEK-----YGLNPLAVTVDNGF--NSEEAVKNIK-NLIKKGLDL 57
Query: 126 -------KIVSYKDLYGWTMDEIVKVIGLKNNCTFCGVFRRQALDRGASLLKVDKIATGH 178
+ + L + + C C +L + A + I TG
Sbjct: 58 DHLVINPEEMKDLQLAR-------FKAKVGDPCWPCDTAIFTSLYKVALKFGIPLIITGE 110
Query: 179 NA 180
N
Sbjct: 111 NP 112
>gnl|CDD|232968 TIGR00420, trmU, tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase.
tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase
(trmU, asuE, or mnmA) is involved in the biosynthesis of
the modified nucleoside
5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
the wobble position of some tRNAs. This enzyme appears
not to occur in the Archaea [Protein synthesis, tRNA and
rRNA base modification].
Length = 352
Score = 34.7 bits (80), Expect = 0.067
Identities = 33/131 (25%), Positives = 57/131 (43%), Gaps = 18/131 (13%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHN---YGLDLFLLSIDEGISG-YRDDSLQTVKRNE 118
++ +G SGG DS+V A++L + + + + G + L+ +
Sbjct: 2 KVIVGLSGGVDSSVSAYLLK--QQGYEVVGVFMKNWEEDDKNDGHGCTSAEDLRDAQAIC 59
Query: 119 IQYGLPLKIVSYKDLYGWT--MDEIVKVIGLK-----NNCTFCGVFRR--QALDRGASLL 169
+ G+PL+ V+++ Y W + ++ K N C F + L+ A LL
Sbjct: 60 EKLGIPLEKVNFQKEY-WNKVFEPFIQ--EYKEGRTPNPDILCNKFIKFGAFLEYAAELL 116
Query: 170 KVDKIATGHNA 180
DKIATGH A
Sbjct: 117 GNDKIATGHYA 127
>gnl|CDD|234664 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
Length = 346
Score = 33.1 bits (77), Expect = 0.19
Identities = 36/137 (26%), Positives = 58/137 (42%), Gaps = 35/137 (25%)
Query: 63 RIAIGASGGKDSTVLAFVLSELNRRHNYGLD---LFL-LSIDEGISGYRD----DSLQTV 114
R+ +G SGG DS+V A +L E G + +F+ L D+ +G + +
Sbjct: 2 RVVVGMSGGVDSSVAAALLKEQ------GYEVIGVFMKLWDDDDETGKGGCCAEEDIADA 55
Query: 115 KRNEIQYGLPLKIVSYKDLYGWTMDEIVK--VIGLK-----NNCTFC------GVFRRQA 161
+R + G+P +V ++ + W D ++ + K N C C F A
Sbjct: 56 RRVADKLGIPHYVVDFEKEF-W--DRVIDYFLDEYKAGRTPNPCVLCNKEIKFKAFLEYA 112
Query: 162 LDRGASLLKVDKIATGH 178
+ GA D IATGH
Sbjct: 113 RELGA-----DYIATGH 124
>gnl|CDD|223593 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
transport and metabolism].
Length = 315
Score = 32.2 bits (74), Expect = 0.37
Identities = 37/163 (22%), Positives = 58/163 (35%), Gaps = 49/163 (30%)
Query: 45 EEEIHQV--IVGNQLFKAGERIAIGASGGKDSTVLAFVLSEL--NRRHNYGLDLFLLSID 100
EE I ++ VG+ ++ + SGG DS+V A + ++ +D LL
Sbjct: 9 EEAIEEIREQVGD------GKVILALSGGVDSSVAAVLAHRAIGDQLTCVFVDHGLLRKG 62
Query: 101 EGISGYRDDSLQTVKRNEIQYGLPLKIVSYKDLYGWTMDEIV---------KVIGLKNNC 151
E + + + R GL L +V KD + + + K+IG
Sbjct: 63 EA------EQVVEMFRE--HLGLNLIVVDAKDRF---LSALKGVTDPEEKRKIIGR---- 107
Query: 152 TFCGVFRRQALDRGASLL---------------KVDKIATGHN 179
F VF +A GA L K I + HN
Sbjct: 108 EFIEVFEEEAKKLGAEFLAQGTIYPDVIESGTGKAGTIKSHHN 150
>gnl|CDD|223253 COG0175, CysH, 3'-phosphoadenosine 5'-phosphosulfate
sulfotransferase (PAPS reductase)/FAD synthetase and
related enzymes [Amino acid transport and metabolism /
Coenzyme metabolism].
Length = 261
Score = 32.0 bits (73), Expect = 0.41
Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 8/102 (7%)
Query: 42 EVFEEEIHQVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDE 101
+ E E I+ + + + SGGKDSTVL + ++ D ++ +D
Sbjct: 20 DKLEAESPIEILRWAAEEFSNPVVVSFSGGKDSTVLLHLAAKAFP------DFPVIFLDT 73
Query: 102 GISGYRDDSLQTVKRNEIQYGLPLKIVSYKDLYGWTMDEIVK 143
G + ++ + R +YGL LK+ D K
Sbjct: 74 GY--HFPETYEFRDRLAEEYGLDLKVYRPDDEVAEGEKYGGK 113
>gnl|CDD|226478 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate
sulfotransferase [General function prediction only].
Length = 407
Score = 30.8 bits (70), Expect = 1.1
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 36 CRECFYEVFEEEIHQVIVGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLF 95
E E E + + F R+ + SGGKDS ++ +++E+ R + +
Sbjct: 8 LDENVLEAAIERLEWI------FNTFPRVCVSFSGGKDSGLMLHLVAEVARENGRD-KIS 60
Query: 96 LLSID 100
+L ID
Sbjct: 61 VLFID 65
>gnl|CDD|100616 PRK00611, PRK00611, putative disulfide oxidoreductase; Provisional.
Length = 135
Score = 29.8 bits (67), Expect = 1.2
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 94 LFLLSIDEGISGYRDDSLQTVKRNEIQYGLPLKIV 128
LF L + GI+ YR+DS + Y LPL +V
Sbjct: 46 LFPLVVILGIAAYREDSSIKI------YALPLALV 74
>gnl|CDD|238612 cd01285, nucleoside_deaminase, Nucleoside deaminases include
adenosine, guanine and cytosine deaminases. These
enzymes are Zn dependent and catalyze the deamination of
nucleosides. The zinc ion in the active site plays a
central role in the proposed catalytic mechanism,
activating a water molecule to form a hydroxide ion that
performs a nucleophilic attack on the substrate. The
functional enzyme is a homodimer. Cytosine deaminase
catalyzes the deamination of cytosine to uracil and
ammonia and is a member of the pyrimidine salvage
pathway. Cytosine deaminase is found in bacteria and
fungi but is not present in mammals; for this reason,
the enzyme is currently of interest for antimicrobial
drug design and gene therapy applications against
tumors. Some members of this family are tRNA-specific
adenosine deaminases that generate inosine at the first
position of their anticodon (position 34) of specific
tRNAs; this modification is thought to enlarge the codon
recognition capacity during protein synthesis. Other
members of the family are guanine deaminases which
deaminate guanine to xanthine as part of the utilization
of guanine as a nitrogen source.
Length = 109
Score = 28.4 bits (64), Expect = 2.1
Identities = 27/75 (36%), Positives = 31/75 (41%), Gaps = 20/75 (26%)
Query: 159 RQALDR-----GASLLKVDK--IATGHNA-----DDI--AETVLLNI---LRGDIARLSR 201
R+AL GA ++ D IA GHN D AE V + G LS
Sbjct: 9 RKALAEGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGS-YLLSG 67
Query: 202 CTLITTGEDGPIPRC 216
CTL TT E P P C
Sbjct: 68 CTLYTTLE--PCPMC 80
>gnl|CDD|163177 TIGR03183, DNA_S_dndC, putative sulfurtransferase DndC. Members of
this protein family are the DndC protein from the dnd
(degradation during electrophoresis) operon. The dnd
phenotype reflects a sulfur-containing modification to
DNA. This operon is sparsely and sporadically
distributed among bactera; among the first eight
examples are members from the Actinobacteria,
Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is
suggested to be a sulfurtransferase [DNA metabolism,
Restriction/modification].
Length = 447
Score = 30.1 bits (68), Expect = 2.1
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 66 IGASGGKDST-VLAFV---LSEL--NRRHNYGLDLFLLSID---EG--ISGYRDDSLQTV 114
+G SGGKDST VL + L+ L +R + ++S D E ++ + + SL+ +
Sbjct: 18 VGYSGGKDSTAVLQLIWNALAALPAEQRTK---KIHVISTDTLVENPIVAAWVNASLERM 74
Query: 115 KRNEIQYGLPL 125
+ GLP+
Sbjct: 75 QEAAQDQGLPI 85
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 29.2 bits (66), Expect = 3.5
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 53 VGNQLFKAGERIAIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRD 108
+ QL +I + SGG DSTVL +L + R N G+ L + + G+S D
Sbjct: 8 LNRQLL-TSRQILVAFSGGLDSTVLLHLLVQW-RTENPGVTLRAIHVHHGLSPNAD 61
>gnl|CDD|111000 pfam02057, Glyco_hydro_59, Glycosyl hydrolase family 59.
Length = 669
Score = 29.2 bits (65), Expect = 3.6
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 203 TLITTGEDG---PIPRCKPFKYTYEKEIMFTYAYFKRLDYFSTE 243
T +TTG G P+ KPF Y+ + Y +F F+ +
Sbjct: 451 TTLTTGRKGSYPLPPKSKPFPTNYKDDFNVDYPFFSEAPNFADQ 494
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.9 bits (65), Expect = 5.0
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 59 KAGERIAI-GASGGKDSTVLAFVLSELNRRH-NYGLD 93
GER+AI G SG ST+LA + L+ LD
Sbjct: 359 PPGERVAILGPSGSGKSTLLATLAGLLDPLQGEVTLD 395
>gnl|CDD|184435 PRK13980, PRK13980, NAD synthetase; Provisional.
Length = 265
Score = 28.3 bits (64), Expect = 5.4
Identities = 14/42 (33%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 46 EEIHQVIVG---NQLFKAG-ERIAIGASGGKDSTVLAFVLSE 83
E++ ++IV ++ KAG + + +G SGG DS V+A++ +
Sbjct: 11 EKVREIIVDFIREEVEKAGAKGVVLGLSGGIDSAVVAYLAVK 52
>gnl|CDD|239450 cd03334, Fab1_TCP, TCP-1 like domain of the eukaryotic
phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase
Fab1. Fab1p is important for vacuole size regulation,
presumably by modulating PtdIns(3,5)P2 effector
activity. In the human homolog p235/PIKfyve deletion of
this domain leads to loss of catalytic activity. However
no exact function this domain has been defined. In
general, chaperonins are involved in productive folding
of proteins.
Length = 261
Score = 28.3 bits (64), Expect = 5.5
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 13/85 (15%)
Query: 163 DRGASLLKVDKIATGHNADDIAE---TVLLNILRGDIARLSRCT---LITTGED----GP 212
++ V+K + D + E T++LN+ + R+SRCT +I++ +D
Sbjct: 128 ALRPDVILVEKSVSRIAQDLLLEAGITLVLNVKPSVLERISRCTGADIISSMDDLLTSPK 187
Query: 213 IPRCKPF---KYTYEKEIMFTYAYF 234
+ C+ F Y E T +F
Sbjct: 188 LGTCESFRVRTYVEEHGRSKTLMFF 212
>gnl|CDD|234267 TIGR03573, WbuX, N-acetyl sugar amidotransferase. This enzyme has
been implicated in the formation of the acetamido moiety
(sugar-NC(=NH)CH3) which is found on some
exopolysaccharides and is positively charged at neutral
pH. The reaction involves ligation of ammonia with a
sugar N-acetyl group, displacing water. In E. coli (O145
strain) and Pseudomonas aeruginosa (O12 strain) this
gene is known as wbuX and ifnA respectively and likely
acts on sialic acid. In Campylobacter jejuni, the gene
is known as pseA and acts on pseudaminic acid in the
process of flagellin glycosylation. In other Pseudomonas
strains and various organisms it is unclear what the
identity of the sugar substrate is, and in fact, the
phylogenetic tree of this family sports a considerably
deep branching suggestive of possible major differences
in substrate structure. Nevertheless, the family is
characterized by a conserved tetracysteine motif
(CxxC.....[GN]xCxxC) possibly indicative of a metal
binding site, as well as an invariable contextual
association with homologs of the HisH and HisF proteins
known as WbuY and WbuZ, respectively. These two proteins
are believed to supply the enzyme with ammonium by
hydrolysis of glutamine and delivery through an ammonium
conduit.
Length = 343
Score = 28.4 bits (64), Expect = 5.7
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 65 AIGASGGKDSTVLAFVLSELNRRHNYGLDLFLLSIDEG 102
IG SGGKDST A VL + GL+ L+++D G
Sbjct: 63 IIGVSGGKDSTYQAHVL-----KKKLGLNPLLVTVDPG 95
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 28.1 bits (63), Expect = 6.4
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 59 KAGERIAI-GASGGKDSTVLAFVLSELNR 86
K GE +AI G SG ST+LA VL+ L+
Sbjct: 34 KRGETVAIVGPSGSGKSTLLA-VLAGLDD 61
>gnl|CDD|216460 pfam01369, Sec7, Sec7 domain. The Sec7 domain is a
guanine-nucleotide-exchange-factor (GEF) for the
pfam00025 family.
Length = 188
Score = 28.0 bits (63), Expect = 6.5
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 217 KPFKYTYEKEI-MFTYAYFKRLDYFSTECIYSPNAYRGFAREFIKDLERLRPRAILDIIK 275
K K E+ I F K ++Y + + + A+ F+++ L +AI + +
Sbjct: 2 KQRKKLLEEGISKFNKKPKKGIEYLIENGLIDEDDPKEIAK-FLRETPGLDKKAIGEYLG 60
Query: 276 SGENFRI 282
+ F
Sbjct: 61 KNDPFNR 67
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 28.4 bits (64), Expect = 7.0
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 58 FKAGERIAI-GASGGKDSTVLAFVL 81
GER+A+ G SG ST+L +L
Sbjct: 345 VPPGERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|237509 PRK13794, PRK13794, hypothetical protein; Provisional.
Length = 479
Score = 28.5 bits (64), Expect = 7.0
Identities = 28/131 (21%), Positives = 48/131 (36%), Gaps = 31/131 (23%)
Query: 22 RKAALKRPKTLEQICRECFYEVFEEEIHQVIVGNQ-LFKAGERIAIG------------- 67
RK+ + + EE ++ N+ + ER +IG
Sbjct: 196 RKSEEPKNSNILSEYGP-----GEETWKDMVEANKNVLDKYERNSIGFIRNTAEKINKPV 250
Query: 68 ---ASGGKDS-TVLAFVLSELNRRHNYGLDLFLLSIDEGISGYRDDSLQTVKRNEIQYGL 123
SGGKDS L L L G++ +L D G+ ++L+ V+ E YGL
Sbjct: 251 TVAYSGGKDSLATLLLALKAL------GINFPVLFNDTGLE--FPETLENVEDVEKHYGL 302
Query: 124 PLKIVSYKDLY 134
+ ++ +
Sbjct: 303 EIIRTKSEEFW 313
>gnl|CDD|163544 TIGR03832, Tyr_2_3_mutase, tyrosine 2,3-aminomutase. Members of
this protein family are tyrosine 2,3-aminomutase. It is
variable from member to member as to whether the
(R)-beta-Tyr or (S)-beta-Tyr is the preferred product
from L-Tyr. This enzyme tends to occur in secondary
metabolite biosynthesis systems, as in the production of
chondramides in Chondromyces crocatus.
Length = 507
Score = 28.3 bits (63), Expect = 7.3
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 6/31 (19%)
Query: 80 VLSE------LNRRHNYGLDLFLLSIDEGIS 104
VLSE LNR +YGL FL++ D G+
Sbjct: 363 VLSERRLNRLLNRHLSYGLPEFLVAGDPGLH 393
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 28.0 bits (63), Expect = 7.7
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 59 KAGERIAI-GASGGKDSTVL 77
+ GER+AI G SG ST+L
Sbjct: 23 ERGERVAILGPSGAGKSTLL 42
>gnl|CDD|133043 cd06421, CESA_CelA_like, CESA_CelA_like are involved in the
elongation of the glucan chain of cellulose. Family of
proteins related to Agrobacterium tumefaciens CelA and
Gluconacetobacter xylinus BscA. These proteins are
involved in the elongation of the glucan chain of
cellulose, an aggregate of unbranched polymers of
beta-1,4-linked glucose residues. They are putative
catalytic subunit of cellulose synthase, which is a
glycosyltransferase using UDP-glucose as the substrate.
The catalytic subunit is an integral membrane protein
with 6 transmembrane segments and it is postulated that
the protein is anchored in the membrane at the
N-terminal end.
Length = 234
Score = 27.9 bits (63), Expect = 7.8
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 152 TFCG---VFRRQALDRGASLLKVDKIATGHNADDIAETVLLN 190
CG V RR+ALD ++ T +D+A ++ L+
Sbjct: 159 FCCGSGAVVRREALD------EIGGFPTDSVTEDLATSLRLH 194
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease. This family includes a variety of
exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 161
Score = 27.3 bits (61), Expect = 9.3
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 157 FRRQALDRGASLLKVDKIATGHNA-DDIAETVLL 189
F+R++LD A L ++KI H A DD T L
Sbjct: 127 FKRRSLDALAEKLGLEKIQRAHRALDDARATAEL 160
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 0.138 0.411
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,039,495
Number of extensions: 1761799
Number of successful extensions: 1558
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1537
Number of HSP's successfully gapped: 59
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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: 60 (26.8 bits)