RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005804
(676 letters)
>gnl|CDD|216343 pfam01171, ATP_bind_3, PP-loop family. This family of proteins
belongs to the PP-loop superfamily.
Length = 182
Score = 211 bits (539), Expect = 1e-64
Identities = 79/206 (38%), Positives = 107/206 (51%), Gaps = 26/206 (12%)
Query: 84 RIALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFIDGLLAITVDHGLREESKEEANIV 143
+I + VSGGPDSMAL L K +F L A VDHGLREES EA V
Sbjct: 1 KILVAVSGGPDSMALLYLLKKLKP----------KFGIDLTAAHVDHGLREESDREAQFV 50
Query: 144 SHRVSDMGIRCEIVRCDWLDGRPKQGHLQEAARDMRYRLFQKVCIQHQIGVLLIAHHADD 203
+ I E++R D + +L+EAAR+ RY F+++ ++ VLL AHHADD
Sbjct: 51 KELCRQLNIPLEVLRVDV--AKKSGLNLEEAAREARYDFFEEIAKKNGAEVLLTAHHADD 108
Query: 204 QAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCHDDLKNHSILLVRPLLDFSKDDMYK 263
QAE F++RL R SG+ GLAG+A + +VRPLL +K ++ +
Sbjct: 109 QAETFLMRLLRGSGLAGLAGIAPVRPLA--------------GGRIVRPLLKVTKSEIEE 154
Query: 264 ICQGGNRDWVEDPTNRSPLFVRNRIR 289
+ WVED +N + RNRIR
Sbjct: 155 YLKEHGIPWVEDESNADLRYTRNRIR 180
>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 = 206 bits (527), Expect = 8e-63
Identities = 77/206 (37%), Positives = 103/206 (50%), Gaps = 26/206 (12%)
Query: 84 RIALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFIDGLLAITVDHGLREESKEEANIV 143
+I + VSGGPDSMAL L + K L+A+ VDHGLR ES EEA V
Sbjct: 1 KILVAVSGGPDSMALLHLLSELKP----------RLGLRLVAVHVDHGLRPESDEEAAFV 50
Query: 144 SHRVSDMGIRCEIVRCDWLDGRPKQGHLQEAARDMRYRLFQKVCIQHQIGVLLIAHHADD 203
+ + +GI I+ G+L+ AAR+ RY F ++ +H VLL AHHADD
Sbjct: 51 ADLCAKLGIPLYILV--VALAPKPGGNLEAAAREARYDFFAEIAKEHGADVLLTAHHADD 108
Query: 204 QAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCHDDLKNHSILLVRPLLDFSKDDMYK 263
QAE ++RL R SG+ GLAGM L+RPLL ++ ++
Sbjct: 109 QAETVLMRLLRGSGLRGLAGMPARI--------------PFGGGRLIRPLLGITRAEIEA 154
Query: 264 ICQGGNRDWVEDPTNRSPLFVRNRIR 289
+ W EDP+N P + RNRIR
Sbjct: 155 YLRENGLPWWEDPSNEDPRYTRNRIR 180
>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 = 177 bits (452), Expect = 5e-52
Identities = 78/208 (37%), Positives = 104/208 (50%), Gaps = 26/208 (12%)
Query: 84 RIALGVSGGPDSMALC-VLTAGWKTGGFNQNGEAGEFIDGLLAITVDHGLREESKEEANI 142
RI + VSGG DSMAL +L L+A VDHGLR ES EEA
Sbjct: 1 RILVAVSGGVDSMALLHLLLKLQPKLKIR-----------LIAAHVDHGLRPESDEEAEF 49
Query: 143 VSHRVSDMGIRCEIVRCDWLDGRP-KQGHLQEAARDMRYRLFQKVCIQHQIGVLLIAHHA 201
V + I EI + D K+ +L+EAAR+ RY F+++ +H +L AHHA
Sbjct: 50 VQQFCKKLNIPLEIKKVDVKALAKGKKKNLEEAAREARYDFFEEIAKKHGADYILTAHHA 109
Query: 202 DDQAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCHDDLKNHSILLVRPLLDFSKDDM 261
DDQAE +LRL R SG+ GL+GM L N ++RPLL SK ++
Sbjct: 110 DDQAETILLRLLRGSGLRGLSGMKPIRI------------LGN-GGQIIRPLLGISKSEI 156
Query: 262 YKICQGGNRDWVEDPTNRSPLFVRNRIR 289
+ + W ED TN+ ++RNRIR
Sbjct: 157 EEYLKENGLPWFEDETNQDDKYLRNRIR 184
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 127 bits (320), Expect = 2e-32
Identities = 68/230 (29%), Positives = 101/230 (43%), Gaps = 30/230 (13%)
Query: 65 KYREAFSRRMAMAGLK---PHHRIALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFID 121
RE R++ A + ++I + VSGG DS+AL L E G I+
Sbjct: 1 CLREKLERKVKRAIREFNLIEYKILVAVSGGKDSLALLHLLK-----------ELGRRIE 49
Query: 122 GLLAITVDHGLREESKEEANIVSHRVSDMGIRCEIVR-CDWLDGRPKQG-HLQEAARDMR 179
+ A+ VDHGLR S +EA +V +GI + R D L G + A R +R
Sbjct: 50 -VEAVHVDHGLRGYSDQEAELVEKLCEKLGIPLIVERVTDDLGRETLDGKSICAACRRLR 108
Query: 180 YRLFQKVCIQHQIGVLLIAHHADDQAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCH 239
L K+ + + HH DDQAE F++ L R SG+ GL GM
Sbjct: 109 RGLLYKIAKELGADKIATGHHLDDQAETFLMNLLRGSGLRGLRGMPPKRPF--------- 159
Query: 240 DDLKNHSILLVRPLLDFSKDDMYKICQGGNRDWVEDPTNRSPLFVRNRIR 289
+L++RPLL + ++ + ++ED +N + RNRIR
Sbjct: 160 ----EGGLLIIRPLLYVREKEIELYAKEKGLPYIEDESNYDLRYTRNRIR 205
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 90.1 bits (224), Expect = 4e-19
Identities = 67/225 (29%), Positives = 93/225 (41%), Gaps = 48/225 (21%)
Query: 76 MAGLKPHHRIALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFIDGLLAITVDHGLREE 135
L +I + SGG DS L L W+T L AI V HGL
Sbjct: 9 NRQLLTSRQILVAFSGGLDSTVLLHLLVQWRTENPGVT---------LRAIHVHHGL--- 56
Query: 136 SKEEANIVSHRVSDMGIRCEIVRCDW----------LDGRPKQGHLQEAARDMRYRLFQK 185
S + V H CE V W LD R ++ AAR RY+ F +
Sbjct: 57 SPNADSWVKH--------CEQVCQQWQVPLVVERVQLDQR--GLGIEAAARQARYQAFAR 106
Query: 186 VCIQHQIGVLLIAHHADDQAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCHDDLKNH 245
+ + VL+ A H DDQ E F+L L R SG GL+ MA S +
Sbjct: 107 TLLPGE--VLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSPFAGT------------ 152
Query: 246 SILLVRPLLDFSKDDMYKICQGGNRDWVEDPTNRSPLFVRNRIRM 290
L+RPLL S++++ + Q W+ED +N+ + RN +R+
Sbjct: 153 --RLIRPLLARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRL 195
>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 = 47.2 bits (113), Expect = 5e-06
Identities = 39/190 (20%), Positives = 62/190 (32%), Gaps = 55/190 (28%)
Query: 84 RIALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFIDGLLAITVD---HGLREESKEEA 140
RI + +SGG DS+ L + + L A+TVD G R+ES E
Sbjct: 1 RILVALSGGKDSLVLLHVLK-------KLQRRYPYGFE-LEALTVDEGIPGYRDESLEV- 51
Query: 141 NIVSHRVSDMGIRCEIV------RCDWLDGRPKQGHLQEAARDM---------RYRLFQK 185
V + I + ++ D +++ R L K
Sbjct: 52 ------VERLAEELGIELEIVSFKEEYTDDI----EVKKRGGKSPCSLCGVLRRGLLN-K 100
Query: 186 VCIQHQIGVLLIAHHADDQAELFILRLSRNSGVLGLAGMAFSSQIFSSYAYSCHDDLKNH 245
+ + L H+ DD+AE ++ L R G+L L L
Sbjct: 101 IAKELGADKLATGHNLDDEAETLLMNLLRG-GILRLMR--------------PGPILYLD 145
Query: 246 S--ILLVRPL 253
+ +RPL
Sbjct: 146 EGDVTRIRPL 155
>gnl|CDD|146463 pfam03842, Silic_transp, Silicon transporter.
Length = 513
Score = 30.6 bits (69), Expect = 3.3
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 315 RSYVEHVCSNLINEAVTVMDQGYAVIDLEILNPSKIEDIFLSKFLALVLQFICQRQRPVR 374
R ++ +IN + ++ V+ L P IE+IFL +A++L + Q +
Sbjct: 103 RQFMVLFIVFVINLCGSPLEPAMEVLGL----PQIIEEIFLGSGIAMILTTVTIGQLTAQ 158
Query: 375 GSTSKLLLHYIRTF 388
+ S ++ +I +
Sbjct: 159 VNASHCMIDFINNY 172
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 30.6 bits (70), Expect = 3.3
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 540 MNRFFVTWKLIKENGSRAFPREVHNDGGLG 569
+ FF T ++ K+ GS A PR V+ G LG
Sbjct: 287 RSIFFATTEMKKDTGSDAKPRPVNKVGVLG 316
>gnl|CDD|179167 PRK00919, PRK00919, GMP synthase subunit B; Validated.
Length = 307
Score = 30.3 bits (69), Expect = 3.6
Identities = 21/67 (31%), Positives = 27/67 (40%), Gaps = 19/67 (28%)
Query: 85 IALGVSGGPDSMALCVLTAGWKTGGFNQNGEAGEFI-DGLLAITVDHGL-RE-ESKEEAN 141
IAL SGG DS VL A I D L + VD GL R+ E++
Sbjct: 26 IAL--SGGVDSSVAAVL--------------AHRAIGDRLTPVFVDTGLMRKGETERIKE 69
Query: 142 IVSHRVS 148
S ++
Sbjct: 70 TFSDMLN 76
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 29.8 bits (67), Expect = 6.0
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 543 FFVTWKLIKENGSRAFPREVHNDGGLG 569
FF T ++ KE GS A P ++ G LG
Sbjct: 285 FFATTEMKKETGSDATPAKIKKVGILG 311
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 0.135 0.403
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,875,900
Number of extensions: 3290887
Number of successful extensions: 2602
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2586
Number of HSP's successfully gapped: 16
Length of query: 676
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 573
Effective length of database: 6,369,140
Effective search space: 3649517220
Effective search space used: 3649517220
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 (21.9 bits)
S2: 62 (27.6 bits)