RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5134
(648 letters)
>gnl|CDD|219682 pfam07985, SRR1, SRR1. SRR1 proteins are signalling proteins
involved in regulating the circadian clock in
Arabidopsis.
Length = 56
Score = 68.7 bits (169), Expect = 9e-15
Identities = 23/55 (41%), Positives = 41/55 (74%), Gaps = 3/55 (5%)
Query: 182 QIICYGIGNFTDSIAAKYQFVLLLLLKIEYDC---EILIYDPIFNELELELIEIF 233
+I+C G+G+F++S AA+YQ LLLLLK +++ ++ +YDP+F+ L+ E++E
Sbjct: 1 RIVCLGLGSFSESEAARYQLALLLLLKEKFNIPPKDVSVYDPVFSPLDKEVLESL 55
>gnl|CDD|178641 PLN03093, PLN03093, Protein SENSITIVITY TO RED LIGHT REDUCED 1;
Provisional.
Length = 273
Score = 65.3 bits (159), Expect = 1e-11
Identities = 53/208 (25%), Positives = 103/208 (49%), Gaps = 13/208 (6%)
Query: 142 RRIESVKEELGSSDYYLQLINLISKSLNLSSANSTTQGIN---QIICYGIGNFTDSIAAK 198
+++E +++ SS +Y + + KS + + G Q++ YGIG+ +
Sbjct: 58 QKMEICIKKVESSQFYQAFLEQV-KSPEVLDSFHLVLGSELKMQMVIYGIGSIESYETPR 116
Query: 199 YQFVLLLLLKIEYDC--EILIYDPIFNELELELIEIFKLELIIQNEECKHTITHAKTLVY 256
+Q L +L+K E+D +I ++DP+ + E ++E ++ NE+ + T TL +
Sbjct: 117 FQLSLAILMKREFDWIGDIEVFDPVLSATESRVLESLGCSVLSVNEQGRREATKP-TLFF 175
Query: 257 MPRCPIQLINNILYSNWTRENLSNLILLSNSISTV---VDSNTDAFLKSNLQFLFHIKEF 313
MP C +L NN+L +NW E L+++ L NS V ++ + + + + ++F
Sbjct: 176 MPHCEAELYNNLLQANWRMERLNHIALFGNSFEMYEEQVSEFFNSEVVDSTKHILAARKF 235
Query: 314 LEE--VPVVNNFKFNDIFNDTSLHCFLP 339
E + V++ F F+D+S H F P
Sbjct: 236 TSEFAIKTVSDDYFA-AFHDSSWHFFSP 262
Score = 42.5 bits (100), Expect = 4e-04
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 21 TLVYMPRCPIQLINNILYSNWTRENLSNLILLSNSI------------STVVDS 62
TL +MP C +L NN+L +NW E L+++ L NS S VVDS
Sbjct: 172 TLFFMPHCEAELYNNLLQANWRMERLNHIALFGNSFEMYEEQVSEFFNSEVVDS 225
>gnl|CDD|238213 cd00353, Ribosomal_S15p_S13e, Ribosomal protein S15
(prokaryotic)_S13 (eukaryotic) binds the central domain
of 16S rRNA and is required for assembly of the small
ribosomal subunit and for intersubunit association, thus
representing a key element in the assembly of the whole
ribosome. S15 also plays an important autoregulatory
role by binding and preventing its own mRNA from being
translated. S15 has a predominantly alpha-helical fold
that is highly structured except for the N-terminal
alpha helix.
Length = 80
Score = 53.3 bits (129), Expect = 4e-09
Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 464 KKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHL 523
K++ + + D S EV + T I +L EH + DK +K L L+ KR + L
Sbjct: 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLL 61
Query: 524 RLLRTENYKVFEWLLDEL 541
+ L+ ++ +EWL+++L
Sbjct: 62 KYLKRKDRLRYEWLIEKL 79
>gnl|CDD|223262 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 38.7 bits (91), Expect = 6e-04
Identities = 22/80 (27%), Positives = 40/80 (50%)
Query: 464 KKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHL 523
K++ D ++D S EV + T I +L EH K D ++ L L+ KR + L
Sbjct: 8 KQELRDEYGIPEVDTGSGEVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKRRRLL 67
Query: 524 RLLRTENYKVFEWLLDELKI 543
+ L+ ++ + WL+ +L +
Sbjct: 68 KYLKRKDVLRYRWLIKKLGL 87
>gnl|CDD|130027 TIGR00952, S15_bact, ribosomal protein S15, bacterial/organelle.
This model is built to recognize specifically bacterial,
chloroplast, and mitochondrial ribosomal protein S15.
The homologous proteins of Archaea and Eukarya are
designated S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 86
Score = 38.1 bits (89), Expect = 0.001
Identities = 22/80 (27%), Positives = 40/80 (50%)
Query: 464 KKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHL 523
K++ + + H+ D S EV I T I L EH KA D ++ L +L+ +R + L
Sbjct: 5 KQEIIKEFQLHEKDTGSPEVQIALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLL 64
Query: 524 RLLRTENYKVFEWLLDELKI 543
+ L+ + + + L+ L +
Sbjct: 65 KYLKRTDVERYRSLIKRLGL 84
>gnl|CDD|238361 cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain.
This short domain consists of a helix-turn-helix
structure, which can bind to several types of RNA. It is
found in the ribosomal protein S15, the influenza A
viral nonstructural protein (NSA) and in several
eukaryotic aminoacyl tRNA synthetases (aaRSs), where it
occurs as a single or a repeated unit. It is involved in
both protein-RNA interactions by binding tRNA and
protein-protein interactions in the formation of
tRNA-synthetases into multienzyme complexes. While this
domain lacks significant sequence similarity between the
subgroups in which it is found, they share similar
electrostatic surface potentials and thus are likely to
bind to RNA via the same mechanism.
Length = 46
Score = 35.9 bits (84), Expect = 0.003
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 482 EVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHLRLLR 527
EV I T IR+L+EH DK +K L L+ KR + L+ L+
Sbjct: 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46
>gnl|CDD|109373 pfam00312, Ribosomal_S15, Ribosomal protein S15.
Length = 83
Score = 34.2 bits (79), Expect = 0.026
Identities = 19/82 (23%), Positives = 39/82 (47%)
Query: 462 LVKKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNK 521
+ + + + D S EV I T I L++H + D +K L +++ KR +
Sbjct: 1 MATGLIISEFLKAEKDTGSVEVQIALLTERIVRLRKHLEEHKKDYHSKRGLIKMVSKRRR 60
Query: 522 HLRLLRTENYKVFEWLLDELKI 543
L L+ ++ +E L+++L +
Sbjct: 61 LLAYLKKKDTARYENLIEQLGL 82
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 34.1 bits (79), Expect = 0.088
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 9/77 (11%)
Query: 573 KTERLTQLRNKFNQEKINFYKKKAEFLEWTMEQEKKYGKEPTVTKEEIESIWKKYEELAE 632
K+ + + ++ +AE + +Y KE K S K+ E A+
Sbjct: 47 KSIKQHLAELAADLLELEAAAPRAELQA----KIARYKKE----KARYRSEAKELEAKAK 98
Query: 633 KELEQYEPP-KHYHQFA 648
+ + + +H+FA
Sbjct: 99 EAEAESDHALHQHHRFA 115
>gnl|CDD|180170 PRK05626, rpsO, 30S ribosomal protein S15; Reviewed.
Length = 89
Score = 31.2 bits (72), Expect = 0.28
Identities = 21/80 (26%), Positives = 39/80 (48%)
Query: 464 KKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHL 523
K + + RH+ D S EV + T I L EH K D ++ L +++ +R K L
Sbjct: 8 KAEIIKEYGRHEGDTGSPEVQVALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLL 67
Query: 524 RLLRTENYKVFEWLLDELKI 543
L+ ++ + + L++ L +
Sbjct: 68 DYLKKKDVERYRALIERLGL 87
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 32.8 bits (74), Expect = 0.67
Identities = 45/214 (21%), Positives = 83/214 (38%), Gaps = 37/214 (17%)
Query: 424 ELDKPTLEYAKCESLKSADEHVKKIFSCAHRGRKQAVELVKKKHVDSVKRHDLDDTSREV 483
E K K E LK A+E KK VE +KKK + K+ + E+
Sbjct: 1611 EAKKAEEAKIKAEELKKAEEEKKK------------VEQLKKKEAEEKKK------AEEL 1652
Query: 484 LITKYTVSIRSLQEHHKAKPLDKRAKVWLKELIDKRNKHLRLLRTENYKVFEWLLDELKI 543
+ I++ +E KA+ K+A+ K D++ L + +E K
Sbjct: 1653 KKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEA---------EEAKK 1703
Query: 544 VFRPGPTILNKVHRKESLRFLVDKHIGDVKTERLTQLRNKFNQEKINFYKKKAEFLEWTM 603
+ + E L+ + + + + + ++ KKKAE +
Sbjct: 1704 AEELKKKEAEEKKKAEELK-----KAEEENKIKAEEAKKEAEED-----KKKAEEAKKDE 1753
Query: 604 EQEKKYGKEPTVTKEEIESIWKKYEELAEKELEQ 637
E++KK +++ E I K+ E + E+EL++
Sbjct: 1754 EEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDE 1787
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains are
found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of helix
C. Although the domain occurs in ultiple repeats along
sequences, the domains are actually stable on their own
- ie they act, biophysically, like domains rather than
repeats that along function when aggregated.
Length = 105
Score = 30.4 bits (69), Expect = 0.97
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 591 FYKKKAEFLEWTMEQEKKYGKEPTVTK-EEIESIWKKYEELAEKELEQYEP 640
F++ + W E+E E E ++++ KK++ L E EL ++
Sbjct: 6 FFRDADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKAL-EAELAAHQD 55
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 29.2 bits (66), Expect = 1.9
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 591 FYKKKAEFLEWTMEQEKKYGKEPTV-TKEEIESIWKKYEELAEKELEQYEP 640
F + E W E+E+ E E +E++ KK+E E ELE +E
Sbjct: 3 FLRDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAF-EAELEAHEE 52
>gnl|CDD|236673 PRK10340, ebgA, cryptic beta-D-galactosidase subunit alpha;
Reviewed.
Length = 1021
Score = 31.2 bits (71), Expect = 2.1
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 9/49 (18%)
Query: 588 KINFYKKKAEFLEWTMEQEKKYGKEPTVT---------KEEIESIWKKY 627
I F K + W + E +EP + K+E E +W+
Sbjct: 734 AITFSKVSGKLTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQPN 782
>gnl|CDD|145032 pfam01672, Plasmid_parti, Putative plasmid partition protein. This
family consists of conserved hypothetical proteins from
Borrelia burgdorferi the lyme disease spirochaete, some
of which are putative plasmid partition proteins.
Length = 85
Score = 28.7 bits (65), Expect = 2.2
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 558 KESLRFLVDKHIGDVKTERLTQ---LRNKF-NQEKINFYKKKAEFLEWTME 604
+ +F+ K ++K + LR + +QE +FYKK A+F + ++
Sbjct: 27 NNTYKFIKKKESSNIKKSKQNPIKPLRFQLKDQESYDFYKKNAKFTSFLLD 77
>gnl|CDD|237520 PRK13813, PRK13813, orotidine 5'-phosphate decarboxylase;
Provisional.
Length = 215
Score = 30.3 bits (69), Expect = 2.2
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 299 FLKSNLQFLFHIKEFLEEVPVVNNFKFNDIFNDTSLHC 336
L S L I+E PV+ + K DI N L C
Sbjct: 39 VLASGLGI---IEELKRYAPVIADLKVADIPNTNRLIC 73
>gnl|CDD|217691 pfam03720, UDPG_MGDP_dh_C, UDP-glucose/GDP-mannose dehydrogenase
family, UDP binding domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 103
Score = 29.1 bits (66), Expect = 2.3
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 209 IEYDCEILIYDPIFNELELELIEIFKLELIIQNEECKH 246
+E E+++YDP E +E + + L+ EE
Sbjct: 27 LEEGAEVVVYDPYVPEEAIEALGEDGVTLVDDLEEALK 64
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 31.1 bits (70), Expect = 2.3
Identities = 41/189 (21%), Positives = 83/189 (43%), Gaps = 35/189 (18%)
Query: 456 RKQAVELVKKKHVDSVKRHDLDDTSREVLITKYTVSIRSLQEHHKAKPLDKRAKVWLKEL 515
R + + + + VD++ R++L+ + +TK T S+++ QE + +++
Sbjct: 333 RAEQEKAILQTEVDAL-RYELE--RKHNTLTKKTASLQAAQEEKATYAGEIED---MRDR 386
Query: 516 IDKRNKHLRLLRTENYKVFEWL------LDELKIVFRPGPTILNKVHRKESLRFLVDKHI 569
+K + LR+L+ + + E L E K R T N E L +K +
Sbjct: 387 YEKTERKLRVLQKKIENLQETFRRKERRLKEEKERLRSLQTDTNTDTALEKL----EKAL 442
Query: 570 GDVKT--ERLTQLRNKFNQEKINFYKKKAEFLEWTMEQEKKYGKEPTVTKEEIESIWKKY 627
+ + ERL + R++ + + E+ + Y KE KEE++++ K
Sbjct: 443 AEKERIIERLKEQRDRDERYE--------------QEEFETYKKEFEDLKEEVQNLQLK- 487
Query: 628 EELAEKELE 636
L+E+EL+
Sbjct: 488 --LSERELQ 494
>gnl|CDD|240278 PTZ00119, PTZ00119, 40S ribosomal protein S15; Provisional.
Length = 302
Score = 30.7 bits (69), Expect = 2.5
Identities = 22/109 (20%), Positives = 50/109 (45%), Gaps = 6/109 (5%)
Query: 438 LKSADEHVKKIFS--CAH-RGRKQAVELVKKKHVDSVKRHDLDDTSREVLITKYTVSIRS 494
+K +++ + CA+ + + +L ++ + +R D S V I T I +
Sbjct: 84 IKHLRKNIINMLHLNCANSKQIHKYKKLCIRRCL---QRRPFDTGSAPVQIGCLTEKILN 140
Query: 495 LQEHHKAKPLDKRAKVWLKELIDKRNKHLRLLRTENYKVFEWLLDELKI 543
L+ H + D K + L+ +R K ++ L ++++++ + LKI
Sbjct: 141 LRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTDFELYKHTCNLLKI 189
>gnl|CDD|214560 smart00210, TSPN, Thrombospondin N-terminal -like domains.
Heparin-binding and cell adhesion domain of
thrombospondin.
Length = 184
Score = 29.6 bits (67), Expect = 3.1
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 502 KPLDKRAKVWLKELIDKRNKHLRLLRTENYKVFEWLLDELKIVFRP 547
+PLD+ + ID +R + + K F+ L +LKIV P
Sbjct: 143 RPLDRPGQ----PPIDTDGIEVRGAQAADRKPFQGDLQQLKIVCDP 184
>gnl|CDD|225795 COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion
transport and metabolism].
Length = 717
Score = 30.5 bits (69), Expect = 3.7
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 354 FLEPEYTECNFEKTKSGAFVSSLIKVGAGLGETNVCGYKQLIKIKWKRPEPVAF 407
+L PE F++ S + +L V G GY QL+ P P F
Sbjct: 320 YLLPELGGPKFQELGSPKLLIALFFVVVGSLAGAWLGYLQLL------PAPFWF 367
>gnl|CDD|183621 PRK12607, PRK12607, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 313
Score = 29.5 bits (67), Expect = 5.0
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 597 EFL-EWTMEQEKKYGKE-PTVTKEEIESIWKKYEELAEKEL-EQYEPPKHYH 645
EF+ +W +E+ YG+E P + E I S+ ++Y EL EK E + P
Sbjct: 247 EFVRQWLIERCGPYGQEIPEIPDEVIVSVSERYIELYEKITGETFVPDSGSP 298
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 29.7 bits (67), Expect = 5.3
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 597 EFLEWTMEQEKKY-GKEPTVTKEEIES-IWK 625
E L W + ++K G+EP TKE++E +W
Sbjct: 276 EVLGWIQQFQEKLGGEEP--TKEQVEQALWD 304
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding preferences.
Two phylogenically distinct groups of Class I proteins
bind DNA in a sequence specific fashion and contain a
single HMG box. One group (SOX-TCF) includes
transcription factors, TCF-1, -3, -4; and also SRY and
LEF-1, which bind four-way DNA junctions and duplex DNA
targets. The second group (MATA) includes fungal mating
type gene products MC, MATA1 and Ste11. Class II and III
proteins (HMGB-UBF) bind DNA in a non-sequence specific
fashion and contain two or more tandem HMG boxes. Class
II members include non-histone chromosomal proteins,
HMG1 and HMG2, which bind to bent or distorted DNA such
as four-way DNA junctions, synthetic DNA cruciforms,
kinked cisplatin-modified DNA, DNA bulges, cross-overs
in supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 26.8 bits (60), Expect = 6.3
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 598 FLEWTMEQEKKYGKE-PTVTKEEIESI----WK--------KYEELAEKELEQYE 639
+ ++ E + E P ++ EI I WK KYEE AEK+ E+YE
Sbjct: 8 YFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYE 62
>gnl|CDD|200397 TIGR04146, GGGPS_Afulg, phosphoglycerol
geranylgeranyltransferase. This enzyme, known also as
GGGP synthase and GGGPS, catalyzes the stereospecific
first step in the biosynthesis of the characteristic
membrane diether lipids of archaea. Interestingly, the
closest homologs outside this family are not the
functionally equivalent enzymes of other archaea, but
rather functionally distinct bacterial enzymes.
Length = 221
Score = 28.9 bits (65), Expect = 6.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 56 ISTVVDSNTDALCILALANVVKDKLKQ 82
I+ + DS TDAL + NV K+ + +
Sbjct: 21 IAEIADSGTDALMLSGTQNVTKENVAE 47
>gnl|CDD|237196 PRK12768, PRK12768, CysZ-like protein; Reviewed.
Length = 240
Score = 28.8 bits (65), Expect = 7.5
Identities = 9/15 (60%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 95 LTPVMLAMVMMVHLH 109
LTP + A MVHLH
Sbjct: 211 LTP-LFAAAFMVHLH 224
>gnl|CDD|220716 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
Fmp27_WPPW is a conserved domain of a family of proteins
involved in RNA polymerase II transcription initiation.
It contains characteristic HQR and WPPW sequence motifs.
and is towards the C-terminal in members which contain
Fmp27_SW pfam10305.
Length = 470
Score = 29.2 bits (66), Expect = 7.6
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 256 YMPRCPIQLINNILYSNWTRENLSNLILLSNSISTVVDSNTDAFLKSNLQFLFHIKEFLE 315
YM ++ I +++ + S S +IS D + KS+ + L +E L
Sbjct: 298 YMSYKAVKFIEDLIKERLKSDKTSESESGSENISQEKDPSEKEE-KSDEELLDRFEELLR 356
Query: 316 EVPVVNNFK 324
EV ++F
Sbjct: 357 EVKKSDDFD 365
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.3 bits (66), Expect = 8.0
Identities = 42/217 (19%), Positives = 82/217 (37%), Gaps = 42/217 (19%)
Query: 433 AKCESLKSADEHVKKIFSCAHRGRKQAVELVKKKHVDSVKRHDLDDTSREVLITKYTVSI 492
K L+ A+E + K+ + + + EL ++ + +R L + E L +
Sbjct: 312 EKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE-LKEELEDLR 370
Query: 493 RSLQEHHKAKPLDKRAKVW----------LKELIDKRNKHLRLLRTENYKVFEWLLDELK 542
L+E +DK L++L + N+ R L L +EL+
Sbjct: 371 AELEE------VDKEFAETRDELKDYREKLEKLKREINELKRELDR--------LQEELQ 416
Query: 543 IVFRPGPTILNKVHRKESLRFLVDKHIGDVKTERLTQLRNKFNQEKINFYKKKAEFLEWT 602
+ + + E+ I +++ E+ + +I KK+ LE
Sbjct: 417 RLSEELADLNAAIAGIEA-------KINELEEEKEDK------ALEI---KKQEWKLEQL 460
Query: 603 MEQEKKYGKEPTVTKEEIESIWKKYEELAEKELEQYE 639
KY +E KEE + + K+ +L ++EL + E
Sbjct: 461 AADLSKYEQELYDLKEEYDRVEKELSKL-QRELAEAE 496
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA in
a non-sequence specific fashion and contain two or more
tandem HMG boxes. Class II members include non-histone
chromosomal proteins, HMG1 and HMG2, which bind to bent
or distorted DNA such as four-way DNA junctions,
synthetic DNA cruciforms, kinked cisplatin-modified DNA,
DNA bulges, cross-overs in supercoiled DNA, and can
cause looping of linear DNA. Class III members include
nucleolar and mitochondrial transcription factors, UBF
and mtTF1, which bind four-way DNA junctions.
Length = 66
Score = 26.4 bits (59), Expect = 8.4
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 13/55 (23%)
Query: 598 FLEWTMEQEKKYGKE-PTVTKEEIESI----WK--------KYEELAEKELEQYE 639
+ ++ EQ K KE P + E+ I WK KYEE AEK+ E+YE
Sbjct: 8 YFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYE 62
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 9.9
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 575 ERLTQLRNKFNQE-KINFYKKKAEFLEWTMEQEKKYGKEPTVTKEEIESIWKKYEELAEK 633
+ L +L +E ++ K+ AE L+ E+ KKY E E+E ++YE+L EK
Sbjct: 480 KELRELEKVLKKESELIKLKELAEQLKELEEKLKKYNLE------ELEKKAEEYEKLKEK 533
Query: 634 ELE 636
++
Sbjct: 534 LIK 536
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
0.320 0.135 0.396
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,280,802
Number of extensions: 3174562
Number of successful extensions: 3275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3252
Number of HSP's successfully gapped: 93
Length of query: 648
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 545
Effective length of database: 6,369,140
Effective search space: 3471181300
Effective search space used: 3471181300
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: 62 (27.7 bits)