RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1686
(448 letters)
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 326 bits (838), Expect = e-108
Identities = 138/258 (53%), Positives = 188/258 (72%), Gaps = 10/258 (3%)
Query: 77 KNPQKVKKISTATGREEEPDYDGWLADVTKDLRCPDGELQKRKTVVHTVTLHEIDVINSR 136
+VKK+ + R E D+D + T+ + P+GE+QKRK +V TVTLH++DV N+R
Sbjct: 197 AETGRVKKLGRSKARARE-DFDL---EDTRFVPLPEGEVQKRKEIVQTVTLHDLDVANAR 252
Query: 137 THGFLALFAGDTGEITPEVREQISAKVTEWREEGKAEIVPGVLFIDEVHMLDIECFSFLN 196
G L+LF+G TGEIT EVRE+++ KV +W EEGKAE+VPGVLFIDEVHMLDIECFSFLN
Sbjct: 253 AQGILSLFSGGTGEITDEVREEVNEKVKKWIEEGKAELVPGVLFIDEVHMLDIECFSFLN 312
Query: 197 RALESEMSPVVITATNRGVTKIRGTAYSSPHGIPIDLLDRMVIIPTQPYQDEEIQAILKI 256
RALESE++P++I ATNRG+TKIRGT SPHGIP+DLLDR++II T+PY EEI+ I++I
Sbjct: 313 RALESELAPIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIISTRPYSREEIREIIRI 372
Query: 257 R------LMQTDGLRVLTKIALDTSLRYAIQLITTASVVCRRRKATEICMEDIRKVYALF 310
R + D L LT I +TSLRYA+QL+T AS++ +RR + + +ED+ + LF
Sbjct: 373 RAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432
Query: 311 LDEGRSTQYLREHQNEYM 328
LD RS +Y+ +++ +
Sbjct: 433 LDVKRSVEYVEKYEGLLL 450
Score = 103 bits (259), Expect = 5e-24
Identities = 41/71 (57%), Positives = 55/71 (77%)
Query: 343 EVDKFVQCPDGELQKRKTVVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAK 402
E +FV P+GE+QKRK +V TVTLH++DV N+R G L+LF+G TGEIT EVRE+++ K
Sbjct: 219 EDTRFVPLPEGEVQKRKEIVQTVTLHDLDVANARAQGILSLFSGGTGEITDEVREEVNEK 278
Query: 403 VTEWREEGHSE 413
V +W EEG +E
Sbjct: 279 VKKWIEEGKAE 289
Score = 79.7 bits (197), Expect = 4e-16
Identities = 25/49 (51%), Positives = 37/49 (75%)
Query: 14 TRVERVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKE 62
ER+ AHSHI+GLGLD++ + + + G+VGQ +AR AAGV++ MIK+
Sbjct: 12 GERERIAAHSHIKGLGLDENGKAKFIGDGLVGQEEAREAAGVIVKMIKQ 60
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 315 bits (809), Expect = e-104
Identities = 130/219 (59%), Positives = 162/219 (73%), Gaps = 11/219 (5%)
Query: 77 KNPQKVKKISTATGREEEPDYDGWLADVTKDLRCPDGELQKRKTVVHTVTLHEIDVINSR 136
KN KVKK+ + R D+D + T+ + CP GE+ KRK VV TVTLH+IDV N+R
Sbjct: 182 KNTGKVKKLGRSFARAT--DFD---LEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANAR 236
Query: 137 THGFLALFAGDTGEITPEVREQISAKVTEWREEGKAEIVPGVLFIDEVHMLDIECFSFLN 196
G L+LF+ GEIT E+RE+I+ KV +W EEGKAEIVPGVLFIDEVHMLDIECFSFLN
Sbjct: 237 PQGILSLFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLN 296
Query: 197 RALESEMSPVVITATNRGVTKIRGTAYSSPHGIPIDLLDRMVIIPTQPYQDEEIQAILKI 256
RALESE++P+VI ATNRG+ IRGT SPHGIP+DLLDR++II T+PY EEI+ IL+I
Sbjct: 297 RALESELAPIVILATNRGICTIRGTDIISPHGIPLDLLDRLLIITTEPYTREEIKQILEI 356
Query: 257 R------LMQTDGLRVLTKIALDTSLRYAIQLITTASVV 289
R + + L +L KI +TSLRYAIQL+T AS++
Sbjct: 357 RAQEEGVEISEEALDLLAKIGEETSLRYAIQLLTPASIL 395
Score = 118 bits (298), Expect = 2e-29
Identities = 41/71 (57%), Positives = 52/71 (73%)
Query: 343 EVDKFVQCPDGELQKRKTVVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAK 402
E +FV CP GE+ KRK VV TVTLH+IDV N+R G L+LF+ GEIT E+RE+I+ K
Sbjct: 203 EATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQGILSLFSPKKGEITSELREEINKK 262
Query: 403 VTEWREEGHSE 413
V +W EEG +E
Sbjct: 263 VNKWIEEGKAE 273
Score = 82.0 bits (203), Expect = 6e-17
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 7/59 (11%)
Query: 18 RVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKEEVVMVWPCVMCGRG 76
R+ AHSHIRGLGLD+ E R VS+G+VGQ +AR AAGV++ MIKE + GR
Sbjct: 1 RIAAHSHIRGLGLDEDGEARYVSEGLVGQEKAREAAGVIVEMIKEG-------KIAGRA 52
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 36.7 bits (85), Expect = 0.021
Identities = 35/131 (26%), Positives = 56/131 (42%), Gaps = 20/131 (15%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPV-VITATNRGVTKIRGTAYSSPH-----GIPI 231
V IDEVHML F+ L + LE V I AT V KI T S IP
Sbjct: 119 VYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTE-VKKIPVTIISRCQRFDLQKIPT 177
Query: 232 D-LLDRMVIIPTQPYQDEEIQAILKIRLMQTDGLRVLTKIALDTSLRYAIQLITTASVVC 290
D L++ +V I + E I + L+++ + + S+R A+ L+ A++
Sbjct: 178 DKLVEHLVDIA----KKENI-------EHDEESLKLIAENS-SGSMRNALFLLEQAAIYS 225
Query: 291 RRRKATEICME 301
+ + + +
Sbjct: 226 NNKISEKSVRD 236
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 34.4 bits (79), Expect = 0.12
Identities = 32/114 (28%), Positives = 45/114 (39%), Gaps = 16/114 (14%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYSSPHGIPIDLLDRM 237
V IDEVHML F+ L + LE P I A + IP +L R
Sbjct: 122 VYLIDEVHMLSRHSFNALLKTLEE--PPQHIKFI---------LATTDVEKIPKTILSRC 170
Query: 238 VIIPTQPYQDEEIQAILKIRLMQ---TDGLRVLTKIA--LDTSLRYAIQLITTA 286
+ + +E+I LK L++ L IA S+R A+ L+ A
Sbjct: 171 LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHA 224
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 34.0 bits (78), Expect = 0.16
Identities = 32/137 (23%), Positives = 59/137 (43%), Gaps = 26/137 (18%)
Query: 181 IDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDRM-- 237
IDEVHML F+ L + LE V+ I AT + H IP+ +L R+
Sbjct: 124 IDEVHMLSKSAFNALLKTLEEPPKHVIFILAT------------TEVHKIPLTILSRVQR 171
Query: 238 -----VIIPTQPYQDEEIQAILKIRLMQTDGLRVLTKIALDTSLRYAIQLITTASVVCRR 292
+ + E I I + + L+++ K++ SLR A+ + S+
Sbjct: 172 FNFRRISEDEIVSRLEFILEKENISY-EKNALKLIAKLS-SGSLRDALSIAEQVSIFGNN 229
Query: 293 RKATEICMEDIRKVYAL 309
+ I ++++ +++ L
Sbjct: 230 K----ITLKNVEELFGL 242
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 33.5 bits (76), Expect = 0.21
Identities = 38/119 (31%), Positives = 52/119 (43%), Gaps = 18/119 (15%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPV-VITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDEVHML + F+ L + LE V I AT T Y H IP+ +L R
Sbjct: 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILAT---------TDY---HKIPVTILSR 169
Query: 237 MVIIPTQPYQDEEIQAILKIRLMQ---TDGLRVLTKIALDT--SLRYAIQLITTASVVC 290
+ + + +I+ LKI L + + L IA SLR A+ L+ A C
Sbjct: 170 CIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLDQAISFC 228
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 32.9 bits (76), Expect = 0.31
Identities = 40/138 (28%), Positives = 58/138 (42%), Gaps = 34/138 (24%)
Query: 181 IDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDRMVI 239
IDEVHML F+ L + LE VV I AT + PH IP +L R
Sbjct: 123 IDEVHMLSKSAFNALLKTLEEPPEHVVFILAT------------TEPHKIPATILSR--- 167
Query: 240 IPTQPYQ-----DEEIQAILKIRLMQTDGLRV----LTKIAL--DTSLRYAIQLITTASV 288
Q + E+I LK +++ +G+++ L IA D SLR A+ L+
Sbjct: 168 --CQRFDFKRIPLEDIVERLK-KILDKEGIKIEDEALELIARAADGSLRDALSLLDQLIS 224
Query: 289 VCRRRKATEICMEDIRKV 306
I ED+ ++
Sbjct: 225 FGNGN----ITYEDVNEL 238
>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 = 31.7 bits (72), Expect = 0.37
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 176 PGVLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRG-TAYSSPHGIPIDLL 234
PGVLFIDE+ L AL + + +R ++ G T + L
Sbjct: 85 PGVLFIDEIDSLSRG----AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALY 140
Query: 235 DRMVII 240
DR+ I
Sbjct: 141 DRLDIR 146
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.8 bits (75), Expect = 0.39
Identities = 23/61 (37%), Positives = 29/61 (47%), Gaps = 15/61 (24%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV--ITATNRGVTKIRGTAYSSPHGIPIDLLD 235
+ IDEVHML F+ L + LE E P V I AT + PH +PI +L
Sbjct: 122 IFIIDEVHMLSTNAFNALLKTLE-EPPPHVKFIFAT------------TEPHKVPITILS 168
Query: 236 R 236
R
Sbjct: 169 R 169
>gnl|CDD|218551 pfam05314, Baculo_ODV-E27, Baculovirus occlusion-derived virus
envelope protein EC27. This family consists of several
baculovirus occlusion-derived virus envelope proteins
(EC27 or E27). The ODV-E27 protein has distinct
functional characteristics compared to cellular and
viral cyclins. Depending on the cdk protein, and perhaps
other viral or cellular proteins yet to be described,
the kinase-EC27 complex may have either cyclin B- or
D-like activity.
Length = 280
Score = 32.2 bits (74), Expect = 0.44
Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 17/104 (16%)
Query: 231 IDLLDRMVIIPTQPY--------QDEEIQ------AILKIRLMQTDGLRVLTKIALDTSL 276
+ DR IP +P +D+ I +IL+I D V K+ D
Sbjct: 107 VITEDRKTSIPGEPIVFKSIRDNEDQTIVCYIDRPSILRILEKPFD---VNVKVEEDDKK 163
Query: 277 RYAIQLITTASVVCRRRKATEICMEDIRKVYALFLDEGRSTQYL 320
+ ++L T ++++ + + + L E TQY+
Sbjct: 164 KNKLKLAKTFKSSEKKKRRSSYDNDYEFIESDIKLTETYVTQYV 207
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 32.5 bits (75), Expect = 0.45
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 12/98 (12%)
Query: 239 IIPTQPYQDEEIQAILKIRLMQ--------TDGLRVLTKIALDTS--LRYAIQLITTASV 288
I PY +EI ILK R+ + + L ++ + R AI L+ A +
Sbjct: 201 EIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGL 260
Query: 289 VCRRRKATEICMEDIRKVYA--LFLDEGRSTQYLREHQ 324
+ R + ++ ED+RK Y + + L H+
Sbjct: 261 IAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHE 298
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 32.0 bits (73), Expect = 0.62
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 13/79 (16%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDEVHML E F+ L + LE S VV + AT ++ +P ++ R
Sbjct: 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLAT------------TNLEKVPPTIISR 167
Query: 237 MVIIPTQPYQDEEIQAILK 255
+I + DE I L+
Sbjct: 168 CQVIEFRNISDELIIKRLQ 186
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 32.1 bits (73), Expect = 0.71
Identities = 35/120 (29%), Positives = 48/120 (40%), Gaps = 24/120 (20%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSP--VVITATNRGVTKIRGTAYSSPHGIPIDLLD 235
V IDE HML E F+ L + LE E P + I T T Y IP +L
Sbjct: 122 VYIIDEAHMLTKEAFNALLKTLE-EPPPRTIFILCT---------TEY---DKIPPTILS 168
Query: 236 RMVIIPTQPYQDEEIQAILKIRLMQTDG-------LRVLTKIALDTSLRYAIQLITTASV 288
R E+I+ LK R+ + L +L + A + +R A L+ AS
Sbjct: 169 RCQRFIFSKPTKEQIKEYLK-RICNEEKIEYEEKALDLLAQ-ASEGGMRDAASLLDQAST 226
>gnl|CDD|180620 PRK06555, PRK06555, pyrophosphate--fructose-6-phosphate
1-phosphotransferase; Validated.
Length = 403
Score = 31.9 bits (73), Expect = 0.78
Identities = 29/81 (35%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 353 GELQKRKTVVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWREEGHS 412
G L +R T + E+++I R G+ L GD+ EITP VR A + R G
Sbjct: 23 GGLIERYTEIAP----EVEIIAYR-SGYQGLLLGDSIEITPAVRAN--AGLLH-RYGGSP 74
Query: 413 EKN-RVKLTMFL----RGLIE 428
N RVKLT RGL++
Sbjct: 75 IGNSRVKLTNVADCVKRGLVK 95
Score = 30.0 bits (68), Expect = 2.8
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 113 GELQKRKTVVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQ 158
G L +R T + E+++I R G+ L GD+ EITP VR
Sbjct: 23 GGLIERYTEIAP----EVEIIAYR-SGYQGLLLGDSIEITPAVRAN 63
>gnl|CDD|200596 cd10974, CE4_CDA_like_1, Putative catalytic domain of chitin
deacetylase-like proteins with additional chitin-binding
peritrophin-A domain (ChBD) and/or a low-density
lipoprotein receptor class A domain (LDLa). Chitin
deacetylases (CDAs, EC 3.5.1.41) are secreted
metalloproteins belonging to a family of extracellular
chitin-modifying enzymes that catalyze the
N-deacetylation of chitin, a beta-1,4-linked
N-acetylglucosamine polymer, to form chitosan, a polymer
of beta-(1,4)-linked d-glucosamine residues. CDAs have
been isolated and characterized from various bacterial
and fungal species and belong to the larger carbohydrate
esterase 4 (CE4) superfamily. This family includes many
CDA-like proteins mainly from insects, which contain a
putative CDA-like catalytic domain similar to the
catalytic NodB homology domain of CE4 esterases. In
addition to the CDA-like domain, family members contain
two additional domains, a chitin-binding peritrophin-A
domain (ChBD) and a low-density lipoprotein receptor
class A domain (LDLa), or have the ChBD domain but do
not have the LDLa domain.
Length = 269
Score = 31.2 bits (71), Expect = 1.0
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 298 ICMEDIRKVYALFLDEGRSTQYLREHQNEYMFDSTVT 334
I +I + A FL G + Q+ + +++DS++T
Sbjct: 98 ITDNEIVGMRAPFLRVGGNRQFEMMEEFGFLYDSSIT 134
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 31.2 bits (71), Expect = 1.2
Identities = 26/79 (32%), Positives = 32/79 (40%), Gaps = 13/79 (16%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDEVHML + F+ L + LE S V I AT + P IP +L R
Sbjct: 122 VYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILAT------------TEPQKIPNTILSR 169
Query: 237 MVIIPTQPYQDEEIQAILK 255
+ EEI L
Sbjct: 170 CQRFDFKRLDLEEIAKHLA 188
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 31.2 bits (71), Expect = 1.2
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 92 EEEPDYDGWLADVTKDLRCPDGELQKRKTVVHTVTLHEIDVINSRTHGFLALFAG 146
+E P G L+D+T D DG++ K ++ LHE++ + +L +F G
Sbjct: 416 DERPTVRGILSDLTCD---SDGKIDKFIGGEGSLPLHELEKNGGGPY-YLGMFLG 466
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 29.5 bits (67), Expect = 2.5
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 17/68 (25%)
Query: 154 EVREQISAKVTEWREEGKAEIVPGVLFIDEVHMLDI--------------ECFSFLNRAL 199
EV+E+I ++ + E+ I+ VL +D ++I E F FL
Sbjct: 71 EVQEKIKDEIVRYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIPIDVEMFDFLR--- 127
Query: 200 ESEMSPVV 207
E + P+V
Sbjct: 128 ELGIPPIV 135
>gnl|CDD|234198 TIGR03400, 18S_RNA_Rcl1p, 18S rRNA biogenesis protein RCL1.
Members of this strictly eukaryotic protein family are
not RNA 3'-phosphate cyclase (6.5.1.4), but rather a
homolog with a distinct function, found in the nucleolus
and required for ribosomal RNA processing. Homo sapiens
has both a member of this RCL (RNA terminal phosphate
cyclase like) family and EC 6.5.1.4, while Saccharomyces
has a member of this family only.
Length = 360
Score = 29.9 bits (68), Expect = 2.7
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 204 SPVVITATNRG-VTKIRGTAYSSPHGIPIDLLDRMV 238
I T RG V +IRG AYS+ + L +RM+
Sbjct: 169 QLKTIHLTERGRVKRIRGVAYST--RVSPSLANRMI 202
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 29.6 bits (67), Expect = 3.0
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 265 RVLTKIALDTSLRYAIQLITTASVVCRRRKATEICMEDIRKVYALFLDEG 314
R LT +D L Y+I + + ++ + ++IR+VY L++G
Sbjct: 22 RSLTAAGVDPDLAYSIAIEIQEEL--KKEGIRLVTKDEIREVYQKLLEKG 69
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 29.8 bits (67), Expect = 3.2
Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 15/61 (24%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV--ITATNRGVTKIRGTAYSSPHGIPIDLLD 235
V IDEVHML F+ + + LE E P V I AT + P IP+ +L
Sbjct: 122 VYMIDEVHMLTNHAFNAMLKTLE-EPPPHVKFILAT------------TDPQKIPVTVLS 168
Query: 236 R 236
R
Sbjct: 169 R 169
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 30.0 bits (68), Expect = 3.3
Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 181 IDEVHMLDIECFSFLNRALESEMSPV-VITAT 211
IDEVHML E F+ L + LE S V I AT
Sbjct: 123 IDEVHMLTKEAFNALLKTLEEPPSYVKFILAT 154
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 29.8 bits (68), Expect = 3.6
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 13/57 (22%)
Query: 181 IDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
IDEVHML F+ L + LE + V+ I AT + PH IP +L R
Sbjct: 125 IDEVHMLSTGAFNALLKTLEEPPAHVIFILAT------------TEPHKIPATILSR 169
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 29.7 bits (66), Expect = 3.6
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 13/60 (21%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPV-VITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDEVHML F+ + + LE V I AT + PH +P+ +L R
Sbjct: 122 VYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILAT------------TDPHKVPVTVLSR 169
>gnl|CDD|223905 COG0835, CheW, Chemotaxis signal transduction protein [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 165
Score = 28.8 bits (65), Expect = 3.9
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 2 IAAAKVQEVREITRVERV-GAHSHIRGL 28
I KV+E+ + V A ++ G+
Sbjct: 32 IDILKVREIVGYPPITPVPNAPPYVLGV 59
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 29.6 bits (66), Expect = 4.0
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDE HML E F+ L + LE + V A + PH P+ ++ R
Sbjct: 122 VFIIDEAHMLTREAFNALLKTLEEPPARVTFV-----------LATTEPHKFPVTIVSR 169
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 29.6 bits (67), Expect = 4.7
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 229 IPIDLLDRMVIIPTQPYQDEEIQAILKIRLMQTDGLRVLTKIALDTS 275
IP LLDRM +I Y +EE I K L+ + L L
Sbjct: 476 IPRPLLDRMEVIELSGYTEEEKLEIAKKYLIP----KALEDHGLKPD 518
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 29.0 bits (65), Expect = 5.2
Identities = 20/45 (44%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 181 IDEVHMLDIECFSFLNRALESEMSPV-VITATNRGVTKIRGTAYS 224
IDEVHML E F+ L + LE V AT + KI GT S
Sbjct: 127 IDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTE-IHKIPGTILS 170
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 29.1 bits (65), Expect = 5.5
Identities = 16/47 (34%), Positives = 21/47 (44%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYS 224
+ IDEVHML F+ L + LE ++ V KI T S
Sbjct: 131 IFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIIS 177
>gnl|CDD|226622 COG4138, BtuD, ABC-type cobalamin transport system, ATPase
component [Coenzyme metabolism].
Length = 248
Score = 28.7 bits (64), Expect = 6.2
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 10/54 (18%)
Query: 17 ERVGAHSHI-RGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKEEVVMVWP 69
R + + L LDD L R +Q G+ Q R A VVL + P
Sbjct: 101 TRTELLNDVAGALALDDKL-GRSTNQLSGGEWQRVRLAAVVL--------QITP 145
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 28.4 bits (64), Expect = 7.5
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 12/85 (14%)
Query: 233 LLDRMVIIPTQPYQDEEIQAILKIRL--------MQTDGLRVLTKIALDT--SLRYAIQL 282
L + +I P PY EE++ IL+ R + + + +A R AI L
Sbjct: 189 LCEEEIIFP--PYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDL 246
Query: 283 ITTASVVCRRRKATEICMEDIRKVY 307
+ A + R A + + + K
Sbjct: 247 LRVAGEIAEREGAERVTEDHVEKAQ 271
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 27.7 bits (61), Expect = 7.8
Identities = 22/139 (15%), Positives = 39/139 (28%), Gaps = 28/139 (20%)
Query: 124 TVTLHEI-DVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWREEGKAEI-------- 174
T + + G + + D E + I + G+ +
Sbjct: 16 TTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALAR 75
Query: 175 --VPGVLFIDEVHMLD---------IECFSFLNRALESEMSPVVITATNRGVTKIRGTAY 223
P VL +DE+ L + L L+SE + VI TN
Sbjct: 76 KLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGP---- 131
Query: 224 SSPHGIPIDLLDRMVIIPT 242
+ DR +++
Sbjct: 132 ----ALLRRRFDRRIVLLL 146
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 28.5 bits (63), Expect = 8.3
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 11/73 (15%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYSSPHGIPIDLLDRM 237
V IDEVHML F+ L + LE V A + P +PI ++ R
Sbjct: 121 VYLIDEVHMLSTHSFNALLKTLEEPPEHVKFL-----------FATTDPQKLPITVISRC 169
Query: 238 VIIPTQPYQDEEI 250
+ +P +EI
Sbjct: 170 LQFTLRPLAVDEI 182
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.8 bits (65), Expect = 8.5
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 168 EEGKAEIVPGVLFIDEVHML 187
+E KA P +LFIDE H L
Sbjct: 273 DEVKASPQPIILFIDEAHTL 292
Score = 28.8 bits (65), Expect = 8.5
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 233 LLDRMVIIPTQPYQDEEIQAILKIRL 258
L RM +IP P D+ + AI++++L
Sbjct: 755 FLGRMTVIPYLPLDDDVLAAIVRLKL 780
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 28.4 bits (63), Expect = 8.9
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 13/60 (21%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV-ITATNRGVTKIRGTAYSSPHGIPIDLLDR 236
V IDEVHML + F+ L + LE + +V I AT T + H IP +L R
Sbjct: 124 VYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILAT---------TEF---HKIPETILSR 171
>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 = 27.2 bits (61), Expect = 9.0
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 15/53 (28%)
Query: 176 PGVLFIDEVHML-----------DIECFSFLNRALE---SEMSPV-VITATNR 213
P V+FIDE+ L + L L+ S +S V VI ATNR
Sbjct: 58 PCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNR 110
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 27.7 bits (63), Expect = 9.8
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 12/49 (24%)
Query: 177 GVLFIDEVHMLDIECFSFLNRALE---------SEMSPV---VITATNR 213
G LF+DE+ L +E + L R L+ ++ V +I ATNR
Sbjct: 95 GTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNR 143
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 28.3 bits (63), Expect = 9.9
Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 15/61 (24%)
Query: 178 VLFIDEVHMLDIECFSFLNRALESEMSPVV--ITATNRGVTKIRGTAYSSPHGIPIDLLD 235
V IDEVHML F+ + + LE E V I AT + P IP+ +L
Sbjct: 127 VYMIDEVHMLTNHAFNAMLKTLE-EPPEHVKFILAT------------TDPQKIPVTVLS 173
Query: 236 R 236
R
Sbjct: 174 R 174
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
0.319 0.135 0.388
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,047,741
Number of extensions: 2279793
Number of successful extensions: 2021
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2012
Number of HSP's successfully gapped: 69
Length of query: 448
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 348
Effective length of database: 6,502,202
Effective search space: 2262766296
Effective search space used: 2262766296
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: 61 (27.7 bits)