RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2406
(464 letters)
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 671 bits (1735), Expect = 0.0
Identities = 244/386 (63%), Positives = 314/386 (81%), Gaps = 6/386 (1%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTREFEINKVR 141
VGKTEIARRLAKL+NAPFIK+EATKFTEVGYVGRDV++IIRDL++I++K RE + KVR
Sbjct: 61 VGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVR 120
Query: 142 TRAEDAAEDRVIDILVPSKEKSNLDTDFNNENNNISTRQIFRKRLREGALDNKEIEIELN 201
+AE+AAE+R++D L+P + + + + E + TRQ FRK+LREG LD+KEIEIE+
Sbjct: 121 EKAEEAAEERILDALLPPAKNNWGEEEEKEEISA--TRQKFRKKLREGELDDKEIEIEVA 178
Query: 202 DTGPHMEIMSPPGMEEMTAQIKTMFSVIGNHRKKTRKIKIREAIKLLIDEEANKLLNEDE 261
+ P MEIM PPGMEEMT Q++ MF +G +KK RK+K++EA K+LI+EEA KL++ +E
Sbjct: 179 EAAPMMEIMGPPGMEEMTIQLQDMFGNLGPKKKKKRKLKVKEARKILIEEEAAKLIDMEE 238
Query: 262 IQQKAINNVEQNGIIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGII 321
I+Q+AI VEQNGI+F+DEIDKI R + D+SR GVQRDLLPLVEG+TV+TKYG++
Sbjct: 239 IKQEAIERVEQNGIVFIDEIDKIAARGGSSGP-DVSREGVQRDLLPLVEGSTVSTKYGMV 297
Query: 322 KTDHILFIASGAFHLAKPSDLIPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYEA 381
KTDHILFIASGAFH++KPSDLIPELQGRFPIRVELD+L+ DF RI+T L KQY+A
Sbjct: 298 KTDHILFIASGAFHVSKPSDLIPELQGRFPIRVELDALTEEDFVRILTEPKASLIKQYQA 357
Query: 382 LLATEGIKIEFVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSFNSNNIS--- 438
LLATEG+ +EF DD I+R+AEIAY +NE+TENIGARRL+T MEKLLE++SF + ++S
Sbjct: 358 LLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDMSGET 417
Query: 439 LLVDADYVNSRLGDLSINEDLSRYVL 464
+ +DA YV+ +LGDL +EDLSRY+L
Sbjct: 418 VTIDAAYVDEKLGDLVKDEDLSRYIL 443
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 578 bits (1492), Expect = 0.0
Identities = 239/387 (61%), Positives = 309/387 (79%), Gaps = 7/387 (1%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTREFEINKVR 141
VGKTEIARRLAKL+ APFIK+EATKFTEVGYVGRDV++IIRDL++I++K RE +I KV+
Sbjct: 61 VGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKLVREEKIEKVK 120
Query: 142 TRAEDAAEDRVIDILVPSKEKSNLDTDFNNENNNISTRQIFRKRLREGALDNKEIEIELN 201
+AE+ AE+R++D LVP + ++ E++ TR+ FRK+LREG LD+KEIEIE+
Sbjct: 121 DKAEELAEERILDALVPPAKNFWGQSENKQESSA--TREKFRKKLREGELDDKEIEIEVA 178
Query: 202 DTG-PHMEIMSPPGMEEMTAQIKTMFSVIGNHRKKTRKIKIREAIKLLIDEEANKLLNED 260
D G P EIM PPGMEEMT ++ MF +G +KK RK+K++EA KLLI+EEA+KL++++
Sbjct: 179 DKGPPGFEIMGPPGMEEMTNNLQDMFGNLGGKKKKKRKLKVKEAKKLLIEEEADKLIDQE 238
Query: 261 EIQQKAINNVEQNGIIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGI 320
EI+Q+AI+ EQNGI+F+DEIDKI R D+SR GVQRDLLPLVEG+TV+TKYG
Sbjct: 239 EIKQEAIDAAEQNGIVFIDEIDKIAKRGGSGGP-DVSREGVQRDLLPLVEGSTVSTKYGP 297
Query: 321 IKTDHILFIASGAFHLAKPSDLIPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYE 380
+KTDHILFIASGAFH+AKPSDLIPELQGRFPIRVELD+L+ DF RI+T L KQY+
Sbjct: 298 VKTDHILFIASGAFHVAKPSDLIPELQGRFPIRVELDALTKEDFERILTEPKASLIKQYK 357
Query: 381 ALLATEGIKIEFVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSFN---SNNI 437
ALL TEG+++EF DD I+R+AEIAY +NE+TENIGARRL+T +E+LLE++SF +
Sbjct: 358 ALLKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLLEDISFEAPDMSGQ 417
Query: 438 SLLVDADYVNSRLGDLSINEDLSRYVL 464
+ +DA+YV +LGDL NEDLSR++L
Sbjct: 418 KVTIDAEYVEEKLGDLVANEDLSRFIL 444
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 484 bits (1247), Expect = e-169
Identities = 233/387 (60%), Positives = 303/387 (78%), Gaps = 7/387 (1%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTREFEINKVR 141
VGKTEIARRLAKL+NAPFIK+EATKFTEVGYVGRDV++++RDL+DI++K +E I KVR
Sbjct: 58 VGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLVDIAVKLVKEEMIEKVR 117
Query: 142 TRAEDAAEDRVIDILVPSKEKSNLDTDFNNENNNISTRQIFRKRLREGALDNKEIEIELN 201
RAE+ AE+R++D L+P + + + S R+ FRK+LREG LD+KEIEIE++
Sbjct: 118 DRAEERAEERIVDSLLPPAKNQWGNME--EIQEEESVREAFRKKLREGELDDKEIEIEVS 175
Query: 202 DTGPHM-EIMSPPGMEEMTAQIKTMFSVIGNHRKKTRKIKIREAIKLLIDEEANKLLNED 260
P EIM+PPGMEEMT ++++F +G +KK RK+KI+EA K LI EEA KL++ +
Sbjct: 176 AKMPSGIEIMAPPGMEEMTMNLQSLFQNLGPDKKKKRKLKIKEAKKALIAEEAAKLVDPE 235
Query: 261 EIQQKAINNVEQNGIIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGI 320
EI+Q+AI+ VEQ+GIIF+DEIDKI + + D+SR GVQRDLLP+VEG+TVNTKYG
Sbjct: 236 EIKQEAIDRVEQSGIIFIDEIDKIAKKGESSGA-DVSREGVQRDLLPIVEGSTVNTKYGS 294
Query: 321 IKTDHILFIASGAFHLAKPSDLIPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYE 380
+KTDHILFIA+GAFHLAKPSDLIPELQGRFPIRVEL +L+I DF RI+T L KQY+
Sbjct: 295 VKTDHILFIAAGAFHLAKPSDLIPELQGRFPIRVELKALTIDDFERILTEPKNSLIKQYQ 354
Query: 381 ALLATEGIKIEFVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSFNSNNISL- 439
ALL TEG+ I F D+ I+R+AE+AY +N++TENIGARRL+T ME+LLE++SF + + S
Sbjct: 355 ALLKTEGVNIAFSDEAIKRIAELAYNVNQKTENIGARRLHTVMERLLEDISFEAPDSSGQ 414
Query: 440 --LVDADYVNSRLGDLSINEDLSRYVL 464
+ ADYVN +LG L +EDLSR++L
Sbjct: 415 KVTITADYVNKKLGILVADEDLSRFIL 441
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 118 bits (298), Expect = 3e-29
Identities = 74/262 (28%), Positives = 117/262 (44%), Gaps = 69/262 (26%)
Query: 255 KLLNEDEIQQKAINNVE--QNGIIFLDEIDKITTRSSQNNNT-DISRAGVQRDLLPLVEG 311
KLL Q A +VE Q GI+++DEIDKI +S + T D+S GVQ+ LL ++EG
Sbjct: 160 KLL------QAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEG 213
Query: 312 TTVN-----------TKYGIIKTDHILFIASGAF-------------------------- 334
T + ++ + T +ILFI GAF
Sbjct: 214 TVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKK 273
Query: 335 ---------HLAKPSDL-----IPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYE 380
+P DL IPE GR P+ L+ L RI+T L KQY+
Sbjct: 274 EKRTEGELLKQVEPEDLIKFGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQ 333
Query: 381 ALLATEGIKIEFVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSF---NSNNI 437
L +G+++EF D+ ++ +A+ A ER GAR L + +E++L +V F + ++
Sbjct: 334 KLFEMDGVELEFTDEALEAIAKKAI---ER--KTGARGLRSILEEILLDVMFELPSREDV 388
Query: 438 S-LLVDADYVNSRLGDLSINED 458
+++ + V + L I +
Sbjct: 389 EKVVITKEVVEGKAKPLLIYRE 410
Score = 52.1 bits (126), Expect = 3e-07
Identities = 20/43 (46%), Positives = 29/43 (67%)
Query: 83 GKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLI 125
GKT +A+ LA++ + PF +AT TE GYVG DV+ I+ L+
Sbjct: 120 GKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLL 162
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 103 bits (259), Expect = 4e-24
Identities = 71/245 (28%), Positives = 114/245 (46%), Gaps = 65/245 (26%)
Query: 264 QKAINNVE--QNGIIFLDEIDKITTRSSQNNNT--DISRAGVQRDLLPLVEGTTVNT--- 316
Q A +VE + GII++DEIDKI R S+N + D+S GVQ+ LL ++EGT +
Sbjct: 152 QAADYDVERAERGIIYIDEIDKIA-RKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQ 210
Query: 317 ---KYGI-----IKTDHILFIASGAF---------------------------------H 335
K+ + T +ILFI GAF
Sbjct: 211 GGRKHPQQEFIQVDTSNILFICGGAFAGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGEL 270
Query: 336 LAK--PSDL-----IPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYEALLATEGI 388
L + P DL IPE GR P+ L+ L +I+T L KQY+ L +G+
Sbjct: 271 LKQVEPEDLVKFGLIPEFIGRLPVIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGV 330
Query: 389 KIEFVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSF---NSNNIS-LLVDAD 444
++EF ++ ++ +A+ A I +T GAR L + +E+LL +V F + ++ +++ +
Sbjct: 331 ELEFTEEALKAIAKKA--IERKT---GARGLRSIIEELLLDVMFELPSLEDVEKVVITEE 385
Query: 445 YVNSR 449
V+
Sbjct: 386 VVDGN 390
Score = 49.5 bits (119), Expect = 2e-06
Identities = 22/43 (51%), Positives = 29/43 (67%)
Query: 83 GKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLI 125
GKT +A+ LAK+ N PF +AT TE GYVG DV+ I+ L+
Sbjct: 109 GKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLL 151
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 96.9 bits (242), Expect = 1e-23
Identities = 34/155 (21%), Positives = 51/155 (32%), Gaps = 54/155 (34%)
Query: 236 TRKIKIREAIKLLIDEEANKLLNEDEIQQKAINNVEQNG------------IIFLDEIDK 283
R + + + + + ++ E+ G I+ +DEI+K
Sbjct: 31 ERALIRIDMSEYMEE----HSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEK 86
Query: 284 ITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGI-IKTDHILFIASGAFHLAKPSD- 341
GVQ DLL ++EG T+ K G + + LFI +G F K SD
Sbjct: 87 AH-------------PGVQNDLLQILEGGTLTDKQGRKVDFRNTLFIMTGNFGSEKISDA 133
Query: 342 -----------------------LIPELQGRFPIR 353
IPE GR PI
Sbjct: 134 SRLGDSPDYELLKELVMDLLKKGFIPEFLGRLPII 168
Score = 32.9 bits (76), Expect = 0.18
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 82 VGKTEIARRLAKLSNA---PFIKIEATKFTE 109
VGKTE+A+ LA+L I+I+ +++ E
Sbjct: 14 VGKTELAKALAELLFGDERALIRIDMSEYME 44
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 94.4 bits (235), Expect = 6e-21
Identities = 69/221 (31%), Positives = 101/221 (45%), Gaps = 57/221 (25%)
Query: 264 QKAINNVE--QNGIIFLDEIDKITTRSSQNNNT-DISRAGVQRDLLPLVEGTTVNT---- 316
Q A +VE Q GII++DEIDKI+ +S + T D+S GVQ+ LL ++EGT N
Sbjct: 171 QAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQG 230
Query: 317 -------KYGIIKTDHILFIASGAF---------------------------------HL 336
++ I T +ILFI GAF
Sbjct: 231 GRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQ 290
Query: 337 AKPSDL-----IPELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYEALLATEGIKIE 391
+P DL IPE GR P+ L+ L I+T L KQY+AL + ++++
Sbjct: 291 VEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELD 350
Query: 392 FVDDGIQRLAEIAYCINERTENIGARRLYTAMEKLLEEVSF 432
F ++ ++ +A+ A ER GAR L + +E LL +V F
Sbjct: 351 FEEEALKAIAKKAL---ER--KTGARGLRSIVEGLLLDVMF 386
Score = 47.8 bits (114), Expect = 7e-06
Identities = 21/43 (48%), Positives = 29/43 (67%)
Query: 83 GKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLI 125
GKT +A+ LA++ N PF +AT TE GYVG DV+ I+ L+
Sbjct: 128 GKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLL 170
>gnl|CDD|198154 smart01086, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA) it lacks the long coiled-coil
insertion, and instead of helix C4 contains a
beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N at the N-terminus as well as
AAA and AAA_2.
Length = 90
Score = 42.8 bits (102), Expect = 2e-05
Identities = 23/78 (29%), Positives = 32/78 (41%), Gaps = 15/78 (19%)
Query: 359 LSISDFTRIMTSTNVCLTKQYEAL---LATEGIKIEFVDDGIQRLAEIAYCINERTENIG 415
L D RI + AL LA +GI +EF D+ + LAE Y G
Sbjct: 1 LDKEDLVRI-------VDLPLNALQKRLAEKGITLEFTDEALDWLAEKGY-----DPKYG 48
Query: 416 ARRLYTAMEKLLEEVSFN 433
AR L +++ LE+
Sbjct: 49 ARPLRRIIQRELEDPLAE 66
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 40.3 bits (95), Expect = 3e-04
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 275 IIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGIIKTDHILFIASGAF 334
+IF+DEID + +++ R V LL ++G T + ++ IA+
Sbjct: 60 VIFIDEIDALAGSRGSGGDSESRR--VVNQLLTELDGFTSS-------LSKVIVIAAT-- 108
Query: 335 HLAKPSDLIPEL-QGRFPIRVELD 357
+P L P L +GRF +E
Sbjct: 109 --NRPDKLDPALLRGRFDRIIEFP 130
Score = 33.0 bits (76), Expect = 0.097
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTR------EF 135
GKT +A+ +AK APFI+I ++ YVG + + +R+L + + K E
Sbjct: 9 TGKTTLAKAVAKELGAPFIEISGSELVSK-YVG-ESEKRLRELFEAAKKLAPCVIFIDEI 66
Query: 136 E-INKVRTRAEDAAEDRVIDILVP 158
+ + R D+ RV++ L+
Sbjct: 67 DALAGSRGSGGDSESRRVVNQLLT 90
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 39.8 bits (93), Expect = 7e-04
Identities = 21/110 (19%), Positives = 36/110 (32%), Gaps = 19/110 (17%)
Query: 249 IDEEANKLLNEDEIQQKAINNVEQNGIIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPL 308
A + + + G++F+DEID + G Q LL +
Sbjct: 61 GLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL-------------SRGAQNALLRV 107
Query: 309 VEGTTVNTKYGIIKTDHILFIASGAFHLAKPSDLIPELQGRFPIRVELDS 358
+E I +++ I + L DL L R IR+ +
Sbjct: 108 LET----LNDLRIDRENVRVIGATNRPL--LGDLDRALYDRLDIRIVIPL 151
Score = 33.3 bits (76), Expect = 0.12
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 9/86 (10%)
Query: 82 VGKTEIARRLAKLS---NAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTREF--- 135
GKT +AR +A APF+ + A+ E V + L+ ++ +
Sbjct: 30 TGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLF 89
Query: 136 --EINKVRTRAEDAAEDRVIDILVPS 159
EI+ + A++A RV++ L
Sbjct: 90 IDEIDSLSRGAQNALL-RVLETLNDL 114
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 32.4 bits (74), Expect = 0.40
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQTREFEI 137
VGKT +AR LA+ PF++I+ T D + + + EF
Sbjct: 54 VGKTLLARALARALGLPFVRIQCTPDLLPS------DLLGTYAYAALLLEPGEFRF 103
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 30.7 bits (69), Expect = 0.53
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 9/86 (10%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRD--------VDTIIRDLIDISIKQTR 133
GK+ +A++LA+ P I ++ E D ++ +++D KQ
Sbjct: 10 SGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEILDELAKQEW 69
Query: 134 EFEINKVRTRAEDAAE-DRVIDILVP 158
+ + T E D V+ + +P
Sbjct: 70 VIDGVRESTLELRLEEADLVVFLDLP 95
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 32.2 bits (74), Expect = 0.63
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFT 108
GKT +AR +A +NA F + A
Sbjct: 59 TGKTTLARLIAGTTNAAFEALSAVTSG 85
>gnl|CDD|178754 PLN03215, PLN03215, ascorbic acid mannose pathway regulator 1;
Provisional.
Length = 373
Score = 31.1 bits (70), Expect = 1.1
Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 275 IIFLDEIDKITTRSSQNNNTDISRAGVQRDLLPLVEGTTVNTKYGIIKTDHILFIASGAF 334
+I + I+ T + + A + R V ++ +K +IK+D + + SG F
Sbjct: 53 LILFNPINPSETLTDDRSYISRPGAFLSRAAFFRVTLSSSPSKGWLIKSD--MDVNSGRF 110
Query: 335 HLAKPSDLIPELQGRFPIRVELDSLSISDFT 365
HL P R P+R +S+ + +FT
Sbjct: 111 HLLNP-------LSRLPLRHSSESVDLLEFT 134
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 31.2 bits (72), Expect = 1.3
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEAT 105
GKT +AR +A ++APF + A
Sbjct: 47 TGKTTLARIIAGATDAPFEALSAV 70
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 30.8 bits (70), Expect = 1.7
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 11/46 (23%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTE-----------VGYVGRD 116
VGKTE+A++LA+ ++ + +++ E GYVG +
Sbjct: 494 VGKTELAKQLAEELGVHLLRFDMSEYMEKHTVSRLIGSPPGYVGFE 539
Score = 30.4 bits (69), Expect = 2.5
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 344 PELQGRFPIRVELDSLSISDFTRIMTSTNVCLTKQYEALLATEGIKIEFVDDGIQRLAEI 403
PE + R + + LS +I+ + + L + I++E DD + LAE
Sbjct: 633 PEFRNRLDAIIHFNDLSEEMAEKIVKK----FLDELQDQLNEKNIELELTDDAKKYLAEK 688
Query: 404 AYCINERTENIGARRL 419
Y E GAR L
Sbjct: 689 GY-----DEEFGARPL 699
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 29.8 bits (68), Expect = 1.8
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 82 VGKTEIARRLAKLSNAPFI 100
GKT + R LAK PF+
Sbjct: 10 AGKTTVGRLLAKALGLPFV 28
>gnl|CDD|239334 cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown
subfamily; uncharacterized proteins containing a CXXC
motif with similarity to thioredoxin (TRX)-fold arsenic
reductases, ArsC. Proteins containing a redox active
CXXC motif like TRX and glutaredoxin (GRX) function as
protein disulfide oxidoreductases, altering the redox
state of target proteins via the reversible oxidation of
the active site dithiol. ArsC catalyzes the reduction of
arsenate [As(V)] to arsenite [As(III)], using reducing
equivalents derived from glutathione via GRX, through a
single catalytic cysteine.
Length = 111
Score = 29.1 bits (66), Expect = 1.9
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 17/78 (21%)
Query: 191 LDNKEIEIELNDTGPHMEIMSPPGMEEMTAQIKTMFSVIGNHRKK--------TRKIKIR 242
LD ++ D + PP EE +K G KK R++ ++
Sbjct: 19 LDEHGVDYTAIDI-----VEEPPSKEE----LKKWLEKSGLPLKKFFNTSGKSYRELGLK 69
Query: 243 EAIKLLIDEEANKLLNED 260
+ + L +EEA +LL+ D
Sbjct: 70 DKLPSLSEEEALELLSSD 87
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 30.5 bits (69), Expect = 2.3
Identities = 15/52 (28%), Positives = 22/52 (42%)
Query: 136 EINKVRTRAEDAAEDRVIDILVPSKEKSNLDTDFNNENNNISTRQIFRKRLR 187
+K R R++ R + I V S+ K N +N R I K+LR
Sbjct: 19 SRSKSRARSQSRGRGRSVKITVNSRNKGRRQNGRNKYQSNQRVRNIVNKQLR 70
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 29.8 bits (67), Expect = 2.6
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 123 DLIDISIKQTREFEINKVRTRAEDAAEDRVIDILVPSKEKSNLDTDFNNENN-NISTRQI 181
DL D++I T++ + N++ E+ E + + +K TD N N + TRQI
Sbjct: 142 DLPDLTIDTTKKIDYNEI---LEEILEISENKLKIEKPKKPKRRTDENILNKIDKRTRQI 198
Query: 182 FRKRLREGALDNKEI 196
+ ++ G LD + I
Sbjct: 199 VGELIKTGKLDKELI 213
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.2 bits (64), Expect = 7.0
Identities = 14/48 (29%), Positives = 16/48 (33%), Gaps = 15/48 (31%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISI 129
GK+ I R LAK FI D D +I SI
Sbjct: 15 AGKSTIGRLLAKRLGYDFI---------------DTDHLIEARAGKSI 47
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 28.8 bits (65), Expect = 7.5
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 275 IIFLDEIDKI-TTRSSQNNNTDISRAGVQRDLLPL 308
IIF+DEID I R + D VQR +L L
Sbjct: 247 IIFIDEIDAIGAKRFDSGTSGD---REVQRTMLEL 278
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 28.4 bits (63), Expect = 8.1
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 238 KIKIREAIKLLIDEEANKLLNEDE 261
KI +RE + L++ + N++LNEDE
Sbjct: 409 KISLREGLPLMVSDFRNRILNEDE 432
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 28.3 bits (64), Expect = 9.4
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 82 VGKTEIARRLAK 93
VGKT IAR LAK
Sbjct: 49 VGKTTIARLLAK 60
>gnl|CDD|226333 COG3812, COG3812, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 193
Score = 27.9 bits (62), Expect = 9.6
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 116 DVDTIIRDLIDISIKQTREFEINKVRTRAEDAAEDRVIDILVPSKEKSNLDTDF 169
DV+T +L I +T F + + D +EDRVI + + +E + D+
Sbjct: 106 DVETSFAELE-ARIAKTLAF-VEGIDPADFDGSEDRVITLKLRGRETTFAGLDY 157
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.6 bits (62), Expect = 9.8
Identities = 15/50 (30%), Positives = 18/50 (36%), Gaps = 15/50 (30%)
Query: 82 VGKTEIARRLAKLSNAPFIKIEATKFTEVGYVGRDVDTIIRDLIDISIKQ 131
GK+ I R LAK PFI D D I +SI +
Sbjct: 3 AGKSTIGRLLAKALGLPFI---------------DTDQEIEKRTGMSIAE 37
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
0.317 0.135 0.363
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,786,086
Number of extensions: 2421045
Number of successful extensions: 2682
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2651
Number of HSP's successfully gapped: 104
Length of query: 464
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 364
Effective length of database: 6,502,202
Effective search space: 2366801528
Effective search space used: 2366801528
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: 41 (21.6 bits)
S2: 61 (27.0 bits)