RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10683
(429 letters)
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 438 bits (1129), Expect = e-145
Identities = 182/347 (52%), Positives = 234/347 (67%), Gaps = 32/347 (9%)
Query: 81 RFDYLLKQTEIFSHFMTNQGVKGGGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVDPS 140
R YLL+QTEIF+HF A +A+ K +GR
Sbjct: 98 RLKYLLQQTEIFAHF-------------AKGDQSASAKKAKGRGR--------------- 129
Query: 141 DHRHRMTEQEEDEELLANAN--TEGKTIVSFENSPFYIKGGEMRDYQVRGLNWMISLYEN 198
H ++TE+EEDEE L G P IKG +MRDYQ+ GLNW+I LYEN
Sbjct: 130 -HASKLTEEEEDEEYLKEEEDGLGGSGGTRLLVQPSCIKG-KMRDYQLAGLNWLIRLYEN 187
Query: 199 GINGILADEMGLGKTLQTISLLGYMKHYRNIAGPHIVIVPKSTLLNWMNEFKKWCPTLRA 258
GINGILADEMGLGKTLQTISLLGY+ YR I GPH+V+ PKSTL NWMNE +++CP LRA
Sbjct: 188 GINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRA 247
Query: 259 ICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCIRERGVFKKFNWRYLVIDEAHRIKNEK 318
+ G+ + R ++++ G++DVC+TS+EM I+E+ K+F+WRY++IDEAHRIKNE
Sbjct: 248 VKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNEN 307
Query: 319 SKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDIFSSSDDFDSWFNTEEFMGD 378
S LS+ +R F T RLL+TGTPLQNNLHELWALLNFLLP+IFSS++ FD WF
Sbjct: 308 SLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQ 367
Query: 379 HSIIERLHSVLKPFLLRRLKSEVEKRLKPKKELKVYVGLSKMQREWY 425
++++LH VL+PFLLRRLKS+VEK L PKKE + VG+S+MQ+++Y
Sbjct: 368 QEVVQQLHKVLRPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYY 414
Score = 106 bits (267), Expect = 1e-24
Identities = 50/78 (64%), Positives = 55/78 (70%), Gaps = 3/78 (3%)
Query: 1 MTEQEEDEELLANAN--TEGKTIVSFENSPFYIKGGEMRDYQVRGLNWMISLYENGINGI 58
+TE+EEDEE L G P IKG +MRDYQ+ GLNW+I LYENGINGI
Sbjct: 134 LTEEEEDEEYLKEEEDGLGGSGGTRLLVQPSCIKG-KMRDYQLAGLNWLIRLYENGINGI 192
Query: 59 LADEMGLGKTLQTISLLG 76
LADEMGLGKTLQTISLLG
Sbjct: 193 LADEMGLGKTLQTISLLG 210
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 342 bits (878), Expect = e-116
Identities = 128/260 (49%), Positives = 167/260 (64%), Gaps = 15/260 (5%)
Query: 184 YQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLG-YMKHYRNIAGPHIVIVPKSTL 242
YQ+ G+NW+ISL NG+ GILADEMGLGKTLQTI+LL Y+K ++ GP +V+ P STL
Sbjct: 1 YQLEGVNWLISLESNGLGGILADEMGLGKTLQTIALLATYLKEGKDRRGPTLVVCPLSTL 60
Query: 243 LNWMNEFKKWCPTLRAICLIGDQDARNAMIRDVMMP-GEWDVCITSYEMCIRER---GVF 298
NW+NEF+KW P LR + GD R+ + + + +DV IT+YE+ +++ +
Sbjct: 61 HNWLNEFEKWAPALRVVVYHGDGRERSKLRQSMAKRLDTYDVVITTYEVLRKDKKLLSLL 120
Query: 299 KKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPD 358
K W +V+DEAHR+KN KSKL + +++ KT NRLLLTGTP+QNNL ELWALLNFL P
Sbjct: 121 NKVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEELWALLNFLRPG 180
Query: 359 IFSSSDDFDSWFNTEEFMGDHS----------IIERLHSVLKPFLLRRLKSEVEKRLKPK 408
F S F+ WFN + I RLH +LKPFLLRR K +VEK L PK
Sbjct: 181 PFGSFKVFEEWFNIPIANTADNKNKNLEKGKEGINRLHKLLKPFLLRRTKDDVEKSLPPK 240
Query: 409 KELKVYVGLSKMQREWYTKV 428
E +Y LS QR+ Y K+
Sbjct: 241 TEHVLYCNLSDEQRKLYKKL 260
Score = 79.3 bits (196), Expect = 1e-16
Identities = 28/38 (73%), Positives = 33/38 (86%)
Query: 39 YQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLG 76
YQ+ G+NW+ISL NG+ GILADEMGLGKTLQTI+LL
Sbjct: 1 YQLEGVNWLISLESNGLGGILADEMGLGKTLQTIALLA 38
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 214 bits (545), Expect = 9e-62
Identities = 119/329 (36%), Positives = 169/329 (51%), Gaps = 28/329 (8%)
Query: 125 RPKKSLTKEKKNVDPSDHRHRMTEQEEDEELLANANTEGKTIVSFENSPFYIKGGEMRDY 184
S EK + R + E E L +E + P + E+R Y
Sbjct: 287 LADLSQILEKFVRETLKLSARDLKDELKELLAELRLSED---LLNAPEPVDL-SAELRPY 342
Query: 185 QVRGLNWMIS-LYENGINGILADEMGLGKTLQTISLLGYMKH-YRNIAGPHIVIVPKSTL 242
Q+ G+NW+ L N + GILAD+MGLGKT+QTI+LL + + GP +++VP S L
Sbjct: 343 QLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLL 402
Query: 243 LNWMNEFKKWCPTLRAI-CLIGDQ---DARNAMIRDVM---MPGEWDVCITSYEMCIR-- 293
NW EF+K+ P LR + G++ D + +RD++ + +DV IT+YE+ R
Sbjct: 403 SNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFL 462
Query: 294 -ERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALL 352
+ G KK W +V+DEAHRIKN++S + ++ K NRL LTGTPL+N L ELW+LL
Sbjct: 463 VDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRLGELWSLL 522
Query: 353 N-FLLPDIFSSSDD-FDSWF--------NTEEFMGDHSIIERLHSVLKPFLLRRLKSEVE 402
FL P + +S F F + IE L +L PF+LRR K +VE
Sbjct: 523 QEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSPFILRRTKEDVE 582
Query: 403 --KRLKPKKELKVYVGLSKMQREWYTKVC 429
K L PK E + LS+ QRE Y +
Sbjct: 583 VLKELPPKIEKVLECELSEEQRELYEALL 611
Score = 64.8 bits (157), Expect = 4e-11
Identities = 25/44 (56%), Positives = 33/44 (75%), Gaps = 1/44 (2%)
Query: 33 GGEMRDYQVRGLNWMIS-LYENGINGILADEMGLGKTLQTISLL 75
E+R YQ+ G+NW+ L N + GILAD+MGLGKT+QTI+LL
Sbjct: 336 SAELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALL 379
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 118 bits (297), Expect = 3e-31
Identities = 48/200 (24%), Positives = 80/200 (40%), Gaps = 19/200 (9%)
Query: 177 KGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQ-TISLLGYMKHYRNIAGPHIV 235
+R YQ + ++S + I LA G GKTL + L +K R G +V
Sbjct: 5 GFEPLRPYQKEAIEALLSGLRDVI---LAAPTGSGKTLAALLPALEALK--RGKGGRVLV 59
Query: 236 IVP-KSTLLNWMNEFKKWCP--TLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCI 292
+VP + W E KK P L+ + L G R + G+ D+ +T+ +
Sbjct: 60 LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKR--EQLRKLESGKTDILVTTPGRLL 117
Query: 293 R--ERGVFKKFNWRYLVIDEAHRIKNE--KSKLSEIVREF-KTTNRLLLTGTP---LQNN 344
E N +++DEAHR+ + +L ++++ K LLL+ TP ++N
Sbjct: 118 DLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENL 177
Query: 345 LHELWALLNFLLPDIFSSSD 364
L F+
Sbjct: 178 LELFLNDPVFIDVGFTPLEP 197
Score = 44.4 bits (105), Expect = 3e-05
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 32 KGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQ 70
+R YQ + ++S + I LA G GKTL
Sbjct: 5 GFEPLRPYQKEAIEALLSGLRDVI---LAAPTGSGKTLA 40
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 105 bits (264), Expect = 3e-27
Identities = 35/147 (23%), Positives = 62/147 (42%), Gaps = 11/147 (7%)
Query: 201 NGILADEMGLGKTLQTISLLGYMKHYRNIAGPHIVIVPKSTLLNWMNEFKKWCP--TLRA 258
+ +LA G GKTL + + G +V+ P L N + E K ++
Sbjct: 2 DVLLAAPTGSGKTLAALLPILE-LLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 259 ICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCIRE--RGVFKKFNWRYLVIDEAHRIKN 316
LIG + ++ ++ G+ D+ + + + E R L++DEAHR+ N
Sbjct: 61 GYLIGGTSIKQ---QEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN 117
Query: 317 EKSK---LSEIVREFKTTNRLLLTGTP 340
+ L +++ K LLL+ TP
Sbjct: 118 QGFGLLGLKILLKLPKDRQVLLLSATP 144
Score = 33.9 bits (78), Expect = 0.058
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 56 NGILADEMGLGKTLQTISLL 75
+ +LA G GKTL + +
Sbjct: 2 DVLLAAPTGSGKTLAALLPI 21
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 45.3 bits (108), Expect = 1e-05
Identities = 36/143 (25%), Positives = 56/143 (39%), Gaps = 15/143 (10%)
Query: 209 GLGKTLQTISLLGYMKHYRNIAGPH--IVIVPKSTLLNWM-NEFKKWC--PTLRAICLIG 263
G GKTL LL ++ G +V+ P L + E KK LR L G
Sbjct: 24 GSGKTL--AFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTG 81
Query: 264 DQDARNAMIRDVMMPGEWDVCITSYEMC---IRERGVFKKFNWRYLVIDEAHRI--KNEK 318
+ + + G+ D+ + + +R + N + LV+DEAHR+
Sbjct: 82 GTSLKEQARK--LKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFG 139
Query: 319 SKLSEIVREFKTTNR-LLLTGTP 340
L EI+ + LLL+ T
Sbjct: 140 DDLEEILSRLPPDRQILLLSATL 162
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 41.0 bits (97), Expect = 8e-05
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 303 WRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTP 340
++IDEAH + K+K +I+ +FK L LT TP
Sbjct: 62 ALVIIIDEAHHS-SAKTKYRKILEKFKPAFLLGLTATP 98
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 44.0 bits (104), Expect = 9e-05
Identities = 35/169 (20%), Positives = 65/169 (38%), Gaps = 23/169 (13%)
Query: 177 KGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGPHIVI 236
E+R YQ L+ ++ G++ G GKT+ ++ + R+ +V+
Sbjct: 33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTV--VAAEAIAELKRST----LVL 86
Query: 237 VPKSTLLN-WMNEFKKWCPTLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCIRER 295
VP LL+ W KK+ I + G + V + + + R R
Sbjct: 87 VPTKELLDQWAEALKKFLLLNDEIGIYGGGEKE---------LEPAKVTVATVQTLAR-R 136
Query: 296 GVFKKF---NWRYLVIDEAHRIKNEKSK-LSEIVREFKTTNRLLLTGTP 340
+ +F + ++ DE H + + + E++ RL LT TP
Sbjct: 137 QLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAAYP--RLGLTATP 183
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 33.4 bits (77), Expect = 0.069
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 81 RFDYLLKQTEIFSHFMTN 98
+ ++L+ QTE++SHFM
Sbjct: 115 KLNFLITQTELYSHFMGK 132
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 35.2 bits (82), Expect = 0.076
Identities = 50/181 (27%), Positives = 76/181 (41%), Gaps = 31/181 (17%)
Query: 204 LADEMGLGKTLQTISLLGYMKHYRNIAGPH---IVIVPKSTLLNWMNEFKKWCPTLRAIC 260
LADE+GLGKT++ G + H + + G +++VP++ W+ E LR
Sbjct: 174 LADEVGLGKTIEA----GMIIHQQLLTGRAERVLILVPETLQHQWLVEM------LRRFN 223
Query: 261 L---IGDQDARNAMIRDVMMPGEWDVC-ITSYEMCIRERGVFKKF---NWRYLVIDEAHR 313
L + D++ D P E + I S + R + ++ W LV+DEAH
Sbjct: 224 LRFSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHH 283
Query: 314 IKNEKSKLSEIVREF--------KTTNRLLLTGTPLQNNLHELWALLNFLLPDIFSSSDD 365
+ + S RE+ LLLT TP Q +A L L PD F +
Sbjct: 284 LVWSEEAPS---REYQVVEQLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEA 340
Query: 366 F 366
F
Sbjct: 341 F 341
Score = 28.6 bits (65), Expect = 7.8
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 59 LADEMGLGKTL 69
LADE+GLGKT+
Sbjct: 174 LADEVGLGKTI 184
>gnl|CDD|219106 pfam06614, Neuromodulin, Neuromodulin. This family consists of
several neuromodulin (Axonal membrane protein GAP-43)
sequences and is found in conjunction with pfam00612.
GAP-43 is a neuronal calmodulin-binding phosphoprotein
that is concentrated in growth cones and pre-synaptic
terminals.
Length = 174
Score = 32.5 bits (73), Expect = 0.21
Identities = 26/78 (33%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 102 KGGGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSDHRHRMTEQ------EEDEEL 155
K G KTA A+ A + S +EKK SD + EQ EE
Sbjct: 15 KKGEAKTATEATEAETPKTDEPTKDGSSPAEEKKGEGSSD---KPQEQPAPQAPASSEEK 71
Query: 156 LANANTEGKTIVSFENSP 173
A+A TE T S +NSP
Sbjct: 72 QASAETESATKASTDNSP 89
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 31.5 bits (72), Expect = 0.21
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 95 FMTNQGVKGGGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVD 138
++N G GGG AA A+AAA +AK KK +E+ + D
Sbjct: 54 LLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDD 97
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 31.1 bits (71), Expect = 0.24
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 90 EIFSHFMTNQGVK-----GGGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSD 141
E+ F+ + +K G +AA A+AAA A + KE++ + D
Sbjct: 24 ELLVKFLEGKNIKELIANGSAKLSAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEED 80
>gnl|CDD|182447 PRK10422, PRK10422, lipopolysaccharide core biosynthesis protein;
Provisional.
Length = 352
Score = 32.4 bits (74), Expect = 0.37
Identities = 33/112 (29%), Positives = 48/112 (42%), Gaps = 13/112 (11%)
Query: 308 IDEAHRIKNEKSKLSEIVREFKTTNRLLLTGT-PLQNNLHELW--ALLNFLLPDIFSSSD 364
I+ + IKN+K+ SE ++ F + ++L L NL + W ALL LL S
Sbjct: 56 INALYGIKNKKAGASEKIKNFFSLIKVLRANKYDLIVNLTDQWMVALLVRLLNARVKISQ 115
Query: 365 DFD---------SWFNTEEFMGDHSIIERLHSVLKPFLLRRLKSEVEKRLKP 407
D+ S+ + G H I+E SVL P L L E +P
Sbjct: 116 DYHHRQSAFWRKSFTHLVPLQGGH-IVESNLSVLTPLGLSSLVKETTMSYRP 166
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 32.7 bits (75), Expect = 0.47
Identities = 32/131 (24%), Positives = 51/131 (38%), Gaps = 17/131 (12%)
Query: 194 SLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGPHIVIVPKSTLLNWM-NEFKKW 252
L + N +++ G GKTL I+LL + G + IVP L EF +
Sbjct: 43 GLLSDE-NVLISAPTGSGKTL--IALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRL 99
Query: 253 CP-TLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYE---MCIRERGVFKKFNW-RYLV 307
+R GD D + + +DV +T+ E R+R + +V
Sbjct: 100 EELGIRVGISTGDYDLDDERL------ARYDVIVTTPEKLDSLTRKRPSW--IEEVDLVV 151
Query: 308 IDEAHRIKNEK 318
IDE H + +
Sbjct: 152 IDEIHLLGDRT 162
>gnl|CDD|220596 pfam10138, Tellurium_res, Tellurium resistance protein. Members of
this family confer resistance to the metalloid element
tellurium and its salts.
Length = 98
Score = 29.7 bits (67), Expect = 0.81
Identities = 13/36 (36%), Positives = 14/36 (38%), Gaps = 8/36 (22%)
Query: 106 PKTAAPASAAAPGTPKA--------KGRPKKSLTKE 133
P A PA A P P K P SLTK+
Sbjct: 8 PAPAPPAPAPPPAAPPVSLSKITLTKEGPSVSLTKQ 43
>gnl|CDD|180167 PRK05620, PRK05620, long-chain-fatty-acid--CoA ligase; Validated.
Length = 576
Score = 30.5 bits (69), Expect = 1.9
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 235 VIVPKSTLLNWMNEFKKWCPTLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCIRE 294
VIV L + E K CP +RA+ IG DA +A MP + + SYE +
Sbjct: 114 VIVADPRLAEQLGEILKECPCVRAVVFIGPSDADSAAAH---MPEG--IKVYSYEALLDG 168
Query: 295 RGVFKKFNW 303
R ++W
Sbjct: 169 RSTV--YDW 175
>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
protein; Provisional.
Length = 311
Score = 30.0 bits (67), Expect = 2.2
Identities = 15/80 (18%), Positives = 23/80 (28%), Gaps = 3/80 (3%)
Query: 99 QGVKGGGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSDHRHRMTEQE---EDEEL 155
+K K P A K +P K K + + D EQ+ E+
Sbjct: 120 AAIKAKKSKKPLPVEPKAKVETKKVAKPSKVEVKPVEKDENVDPELLKREQQVLKVVEKT 179
Query: 156 LANANTEGKTIVSFENSPFY 175
+ E + SP
Sbjct: 180 ASQKEEETTETIMISTSPKN 199
>gnl|CDD|236573 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 30.0 bits (68), Expect = 2.6
Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 11/65 (16%)
Query: 99 QGVKGGGPKTAAPASAAAPGTPKAK--------GRPKKSLTKE---KKNVDPSDHRHRMT 147
+ +G A AA P P A K L + K+ +P D R+
Sbjct: 26 RATRGAAGGQTPAAPAAEPTGPDAIHIKAQDRFLAAGKKLCDQEKWKREENPFDAWDRLK 85
Query: 148 EQEED 152
Q
Sbjct: 86 AQAAA 90
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 28.4 bits (64), Expect = 2.9
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 12/49 (24%)
Query: 109 AAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSDHRHRMTEQEEDEELLA 157
AA A+AAA A K+ +E++ ++E +EE A
Sbjct: 63 AAAAAAAAAAAAAAAEEKKEEEEEEEE------------KEESEEEAAA 99
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 30.1 bits (68), Expect = 3.0
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 11/51 (21%)
Query: 268 RNAMIRDVMMPGEWDVCITSYEM----CIR--ERGVFKKFNWRYLVIDEAH 312
R A+IR+ P D+ +T+ +M +R + ++ N +YLV+DE H
Sbjct: 160 RRAIIRN---PP--DILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELH 205
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 29.6 bits (67), Expect = 3.1
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 180 EMRDYQVRGL-NWMISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAG-PHIVIV 237
E+RDYQ + W ++N GIL G GKTL ++ K Y I +V+
Sbjct: 8 ELRDYQKEAIRAW----FKNNGRGILKMATGTGKTLTALAAA--SKLYEKIGLLVLLVVC 61
Query: 238 PKSTLLN-WMNEFKK 251
P L++ W E +K
Sbjct: 62 PYQHLVDQWAREAEK 76
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 29.8 bits (67), Expect = 3.2
Identities = 22/121 (18%), Positives = 41/121 (33%), Gaps = 25/121 (20%)
Query: 209 GLGKT----LQTISLLGYMKHYRNIAGPHIVIVPKSTLLNW--MNEFKKWC---PTLRAI 259
G GKT L + + K +++ P + L E +K LR
Sbjct: 76 GTGKTAAFLLPLLQKIL--KSVERKYVSALILAP-TRELAVQIAEELRKLGKNLGGLRVA 132
Query: 260 CLIG--DQDARNAMIRDVMMPGEWDVCITS----YEMCIRERGVFKKFNWRYLVIDEAHR 313
+ G + ++ D+ + + ++ +RG LV+DEA R
Sbjct: 133 VVYGGVSIRKQIEALKRG-----VDIVVATPGRLLDLI--KRGKLDLSGVETLVLDEADR 185
Query: 314 I 314
+
Sbjct: 186 M 186
>gnl|CDD|215299 PLN02543, PLN02543, pfkB-type carbohydrate kinase family protein.
Length = 496
Score = 29.5 bits (66), Expect = 4.2
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 3/80 (3%)
Query: 94 HFMTNQGVKGGGPKTAAPASAAAPGTPKA--KGRPKKSLTKEKKNVDPSDHRHRMTEQEE 151
+ +K P + AA P +PK +GR KK T + R + T+QE
Sbjct: 38 KASLHPSIKRSRPGRCSTNGAAVPESPKPSRRGR-KKKPTSSPPKAKTTRRRTKKTDQEL 96
Query: 152 DEELLANANTEGKTIVSFEN 171
D E + +++
Sbjct: 97 DPEGAEEDQEAAEDGEDYDD 116
>gnl|CDD|233775 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
This family consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 314
Score = 28.8 bits (65), Expect = 5.0
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 17 EGKTIVSFENSPFYIKGGEMRDY-QVRGL-NWMISLYENGINGILADEMGLGK 67
G + F++S + G ++RD+ V+ + + + L ENG++GI +G G+
Sbjct: 194 AGGNVKLFKSSEGFKDGEQLRDFVYVKDVVDVNLWLLENGVSGIF--NLGTGR 244
Score = 28.8 bits (65), Expect = 5.0
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 162 EGKTIVSFENSPFYIKGGEMRDY-QVRGL-NWMISLYENGINGILADEMGLGK 212
G + F++S + G ++RD+ V+ + + + L ENG++GI +G G+
Sbjct: 194 AGGNVKLFKSSEGFKDGEQLRDFVYVKDVVDVNLWLLENGVSGIF--NLGTGR 244
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 27.5 bits (61), Expect = 5.4
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 12/49 (24%)
Query: 109 AAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSDHRHRMTEQEEDEELLA 157
AAPA+AAA + ++ KE++ ++EE+EE LA
Sbjct: 64 AAPAAAAAAAAEEKAEEKEEEKKKEEE------------KEEEEEEALA 100
>gnl|CDD|237701 PRK14398, PRK14398, membrane protein; Provisional.
Length = 191
Score = 28.3 bits (63), Expect = 6.3
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 213 TLQTISLLGYMKHYRNIA 230
TL T+++L ++KHYRNI
Sbjct: 163 TLLTVAILIFLKHYRNIV 180
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 27.2 bits (60), Expect = 7.4
Identities = 20/51 (39%), Positives = 23/51 (45%), Gaps = 15/51 (29%)
Query: 104 GGPKTAAPASAAAPGTPKAKGRPKKSLTKEKKNVDPSDHRHRMTEQEEDEE 154
GG AA A AA T AK KK +EKK E+EE+EE
Sbjct: 68 GGGVAAAAAPAAGAATAGAKAEAKK---EEKK------------EEEEEEE 103
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 27.2 bits (61), Expect = 9.0
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 306 LVIDEAHRIKNEKSKLSEIVR--EFKTTN-RLLLTGTP-LQNNL 345
L+IDEA + E L E+ + +++L GTP L+ L
Sbjct: 83 LIIDEAQHLSLE--ALEELRDLYDLSEKGIQVILVGTPELRKLL 124
>gnl|CDD|185313 PRK15415, PRK15415, propanediol utilization protein PduB;
Provisional.
Length = 266
Score = 28.1 bits (63), Expect = 9.5
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 200 INGILADEMGLGKTLQTISLLGYMKHYRNIAGPHI 234
++ L + M L K ++I +LG R AGP I
Sbjct: 60 VDSALLEAMKLEKKYRSIGILG----ARTGAGPQI 90
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
0.318 0.136 0.407
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,401,782
Number of extensions: 2218406
Number of successful extensions: 2546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2503
Number of HSP's successfully gapped: 54
Length of query: 429
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 329
Effective length of database: 6,502,202
Effective search space: 2139224458
Effective search space used: 2139224458
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 (21.7 bits)
S2: 60 (27.1 bits)