RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1861
(661 letters)
>gnl|CDD|110234 pfam01217, Clat_adaptor_s, Clathrin adaptor complex small chain.
Length = 142
Score = 153 bits (389), Expect = 6e-44
Identities = 61/176 (34%), Positives = 86/176 (48%), Gaps = 58/176 (32%)
Query: 1 MNFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCY 60
+ D E+QKLIE+++A+++ R K +NF+EF + K++Y+RYA LYF + VD DN L
Sbjct: 21 TPYSDPEQQKLIEQIYALISARKPKMSNFIEFNDLKVIYKRYATLYFVVIVDDQDNELII 80
Query: 61 LEAIHNFVEVLNEYFHNVCELDLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLE 120
LE IH FVE L+ YF NVCELDL+FNF K +Y
Sbjct: 81 LELIHRFVESLDRYFGNVCELDLIFNFEK-------------VYL--------------- 112
Query: 121 AIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKELRVL 176
+L+E M + GEI ETS+ +VL + +L
Sbjct: 113 -------ILDE-----------------------MVMGGEILETSKNEVLHRVALL 138
>gnl|CDD|227363 COG5030, APS2, Clathrin adaptor complex, small subunit
[Intracellular trafficking and secretion].
Length = 152
Score = 125 bits (316), Expect = 1e-33
Identities = 48/87 (55%), Positives = 63/87 (72%)
Query: 3 FDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLE 62
D E+ KLI +++ +++ R K +NF+E +N KIVYRRYA LYF VD +DN L LE
Sbjct: 23 VSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELIILE 82
Query: 63 AIHNFVEVLNEYFHNVCELDLVFNFYK 89
IHNFVE+L+ +F NVCELDL+FNF K
Sbjct: 83 LIHNFVEILDRFFGNVCELDLIFNFQK 109
Score = 125 bits (316), Expect = 1e-33
Identities = 54/91 (59%), Positives = 68/91 (74%)
Query: 86 NFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNF 145
NF + +N KIVYRRYA LYF VD +DN L LE IHNFVE+L+ +F NVCELDL+FNF
Sbjct: 48 NFIEGKNEKIVYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNF 107
Query: 146 YKVYTVVDEMFLAGEIRETSQTKVLKELRVL 176
KVY ++DEM L GEI E+S+ +VL+ + L
Sbjct: 108 QKVYAILDEMILGGEIIESSKNEVLEHVYAL 138
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 122 bits (307), Expect = 7e-31
Identities = 45/150 (30%), Positives = 79/150 (52%), Gaps = 3/150 (2%)
Query: 236 RESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYM 295
++E L + + + L L + ET+ +Y+ A+ + L +GR V AAC+Y
Sbjct: 90 SSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYA 149
Query: 296 TCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGA 355
CR+ G L + ++ L + E+GRTY L + L + IP +DP Y+ R++++L
Sbjct: 150 ACRINGVPRTLDEIAKALGVSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSD 209
Query: 356 KTHEVTMTALRILQRMKKDMLHSGRRPNGL 385
EV A+ I+++ K+ L +G+ P GL
Sbjct: 210 ---EVRRKAIEIVKKAKRAGLTAGKSPAGL 236
Score = 35.8 bits (83), Expect = 0.057
Identities = 13/52 (25%), Positives = 22/52 (42%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEG 301
I ++L L+ + + K A LT G+ + AA +Y+ L G
Sbjct: 198 IPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLG 249
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region covers
both the Brf homology II and III regions. This region is
involved in binding TATA binding protein.
Length = 95
Score = 104 bits (261), Expect = 7e-27
Identities = 47/94 (50%), Positives = 62/94 (65%), Gaps = 5/94 (5%)
Query: 469 DEEINSYILTEGEATNKAKLWEVLNREYLTLQAER----KAREEVEGKKEKKKRKPKANK 524
D+EI+SYIL+E E K ++W+ LN++YL Q E+ KA E K+KKKRK K +
Sbjct: 1 DDEIDSYILSEEEVKLKERIWDELNKDYLEEQEEKELKQKADEGNNSGKKKKKRKAKKKR 60
Query: 525 A-TSVAKTAGEAIEKMLKEKKISTKINYDVLKSL 557
A TA EA++KML++KK S KINYD LKSL
Sbjct: 61 DEAGPASTAAEAVKKMLQKKKFSKKINYDALKSL 94
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed.
Length = 310
Score = 76.2 bits (188), Expect = 5e-15
Identities = 43/133 (32%), Positives = 69/133 (51%), Gaps = 3/133 (2%)
Query: 253 LCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSEL 312
+ +QL L + E + +Y+ A+ + L +GR V AA +Y CR L + +E+
Sbjct: 132 IASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEV 191
Query: 313 LQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMK 372
++ E+GR Y L + L + +P DP YV R+++ L EV A+ ILQ+ K
Sbjct: 192 SRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG---EVQKKAIEILQKAK 248
Query: 373 KDMLHSGRRPNGL 385
+ L SG+ P GL
Sbjct: 249 EKGLTSGKGPTGL 261
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat.
Length = 71
Score = 63.1 bits (154), Expect = 1e-12
Identities = 23/66 (34%), Positives = 34/66 (51%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
I + L L + + + L K+AL NL KGR + AAC+Y+ CRLE L +
Sbjct: 1 IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVKRTLKEI 60
Query: 310 SELLQI 315
S + Q+
Sbjct: 61 SSVAQV 66
Score = 26.5 bits (59), Expect = 9.6
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 346 RYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIG 387
R+++ L+ K V A + + D L GR P +
Sbjct: 3 RFADALELPKK---VADAANELAKLALDDNLLKGRSPESIAA 41
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
functioning in cell-cycle and transcription control.
Present in cyclins, TFIIB and Retinoblastoma (RB).The
cyclins consist of 8 classes of cell cycle regulators
that regulate cyclin dependent kinases (CDKs). TFIIB is
a transcription factor that binds the TATA box. Cyclins,
TFIIB and RB contain 2 copies of the domain.
Length = 88
Score = 58.4 bits (142), Expect = 9e-11
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 1/79 (1%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
+ + L L+ L + NL L GR LV AA +Y+ ++E L D
Sbjct: 9 LRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDL 68
Query: 310 SELLQIC-IFELGRTYLRL 327
+ E+ R L
Sbjct: 69 VHVTGYATEEEILRMEKLL 87
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins and
TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 48.4 bits (116), Expect = 2e-07
Identities = 17/79 (21%), Positives = 27/79 (34%), Gaps = 1/79 (1%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
+ +C L L+ L + NL LS L+ AA +Y+ + E T +
Sbjct: 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKEL 62
Query: 310 SELLQIC-IFELGRTYLRL 327
E+ R L
Sbjct: 63 VHYTGYFTEEEILRMERLL 81
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 40.2 bits (94), Expect = 0.004
Identities = 26/145 (17%), Positives = 46/145 (31%), Gaps = 15/145 (10%)
Query: 485 KAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKK 544
+ L +E +A + ++EVE + K K K +KA + K K+K
Sbjct: 559 ERNKKLELEKEAQ--EALKALKKEVESIIRELKEK-KIHKAKEIKSIEDLVKLKETKQKI 615
Query: 545 ISTKINYDVLKSLDFTVDVNTGEMS--TEQKSAPRIIENLEI------TSSIKKTRAKPT 596
N+ K D G+ + + + S ++K P
Sbjct: 616 PQKPTNFQADKIGDKVRIRYFGQKGKIVQILGGNKWNVTVGGMRMKVHGSELEKINKAPP 675
Query: 597 KEKREPTPKTPPKVAGDNYIKSNEL 621
+K + T P+ S L
Sbjct: 676 PKKFKVPKTTKPE----PKEASLTL 696
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 36.1 bits (83), Expect = 0.040
Identities = 24/114 (21%), Positives = 45/114 (39%), Gaps = 13/114 (11%)
Query: 512 KKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVDVNTGEMSTE 571
KK +++KP A KAT T+ E + K STK K + +
Sbjct: 10 KKTTEEKKPAAKKAT----TSKETAKTKKTAKTTSTKAAKKAAK---------VKKTKSV 56
Query: 572 QKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPKVAGDNYIKSNELPRVI 625
+ + ++ E T S+KK K+E + + + +++LP+ +
Sbjct: 57 KTTTKKVTVKFEKTESVKKESVAKKTVKKEAVSAEVFEASNKLFKNTSKLPKKL 110
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 35.6 bits (83), Expect = 0.093
Identities = 39/157 (24%), Positives = 73/157 (46%), Gaps = 31/157 (19%)
Query: 453 NDQIVDDAEDDLGDIDDEEINSYI--LTEGEATNKAKLWEVLNREYLTLQAERKAREEVE 510
+ I+++A+ +G+ D E++N I L E E + K E E L +AE+ +EE+E
Sbjct: 500 PENIIEEAKKLIGE-DKEKLNELIASLEELERELEQKAEEA---EALLKEAEKL-KEELE 554
Query: 511 GKKEK---------KKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTV 561
KKEK ++ + +A +A AK + ++++KE + K Y +K+
Sbjct: 555 EKKEKLQEEEDKLLEEAEKEAQQAIKEAK---KEADEIIKELRQLQKGGYASVKA----- 606
Query: 562 DVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKE 598
E+ +K R+ + E KK + + +E
Sbjct: 607 ----HELIEARK---RLNKANEKKEKKKKKQKEKQEE 636
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly related
to archaeal Holliday junction resolvase [Nucleotide
transport and metabolism].
Length = 175
Score = 34.0 bits (78), Expect = 0.11
Identities = 32/133 (24%), Positives = 55/133 (41%), Gaps = 24/133 (18%)
Query: 481 EATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKML 540
E KA+ ++N + E K +E +E KK ++ R+ K S A G E++
Sbjct: 40 ETLQKAERERLVNEAQARKEEEWKLKEWIE-KKIEEAREDAVRK--SRAVILGRVTEQLA 96
Query: 541 ----------KEKK-ISTKINYDVLKSLD-------FTVDVNTGE---MSTEQKSAPRII 579
K+ + I T +++ V L V+V TG+ +S +K+ I
Sbjct: 97 PFFPEFKYNPKDARFIGTPVDFIVFDGLSEGNIESIVFVEVKTGKTSSLSEREKAVRDAI 156
Query: 580 ENLEITSSIKKTR 592
EN ++ I R
Sbjct: 157 ENGRVSWEIYHIR 169
>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH/TFIIK, cyclin H subunit [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 297
Score = 34.3 bits (79), Expect = 0.15
Identities = 16/55 (29%), Positives = 24/55 (43%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSH 304
I LC +L L Q L T+ + +N + V CVY+ C++E T
Sbjct: 52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR 106
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 33.2 bits (76), Expect = 0.17
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 7/75 (9%)
Query: 535 AIEKMLKEKKISTKINYDVLKSLDFTVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAK 594
A+ K+ +E S + T + +T E E + + + K + +
Sbjct: 83 AMWKIFRELSSSDDEEEE-------TEEESTDETEQEDPPETKTESKEKKKREVPKPKTE 135
Query: 595 PTKEKREPTPKTPPK 609
K K EP P K
Sbjct: 136 KEKPKTEPKKPKPSK 150
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 34.5 bits (80), Expect = 0.19
Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 10/99 (10%)
Query: 450 AERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEV 509
+ N ++ L + +EEI ++ +AT K K + +AE+K EE
Sbjct: 378 FKHNPELAARLAAFLE-LTEEEIE-FLTGSKKATKKIK--------KIVEKAEKKREEEK 427
Query: 510 EGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTK 548
+ KK+K K + K E ++ +E+ K
Sbjct: 428 KEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEK 466
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 34.0 bits (78), Expect = 0.25
Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 455 QIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKKE 514
D +++ +D++ ++ ++ G + + + +E KK+
Sbjct: 311 LPESDIHEEIPKLDEKSLSEFLGYMGGIDEDDE------------DEDDEESKEEVEKKQ 358
Query: 515 KKKRKPKANKATSVA 529
K K+KP+ K V+
Sbjct: 359 KVKKKPRKRKVNPVS 373
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 33.9 bits (77), Expect = 0.26
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 492 LNREYLTLQAERKAREEVEGKKEKKKRKPKANKAT 526
++ +Y+ L+ ER+ R+ +E K +KK++ K +
Sbjct: 77 MSDQYVKLEEERRHRQRLEKDKREKKKREKEKRGR 111
Score = 29.3 bits (65), Expect = 8.8
Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 6/106 (5%)
Query: 501 AERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFT 560
E+K++ K +KK++K K + K E + +L S V ++ + +
Sbjct: 195 VEKKSK-----KPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEAS 249
Query: 561 VDVN-TGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPK 605
+ +G + P+ E E S K + K KEK E K
Sbjct: 250 LANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKK 295
>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 548
Score = 34.0 bits (78), Expect = 0.27
Identities = 26/143 (18%), Positives = 48/143 (33%), Gaps = 18/143 (12%)
Query: 420 EDADLEEET----EGEIRGIGPTPAMLGMATNQDAER-NDQIVDDAEDDLGDIDDEEINS 474
DLE+ EG +R + + + N+D + + DDL ++S
Sbjct: 132 SREDLEQLAEDTLEGALRAVLAQMTVEEL--NEDRLGFAQVVQEVVGDDL-SKMGLVLDS 188
Query: 475 YILTEGEATNKAKLWEV--LNREYLTLQAERKAR---EEVEGKKEKKKRKPKANKATSVA 529
+ + T+K L+ A+ E E +KE + +AN+ +
Sbjct: 189 LAINDINDTSKENQDPNNYLDALGRRRIAQVLQDAEIAENEAEKETEIAIAEANRDAKLV 248
Query: 530 KTAGEAIEKML-----KEKKIST 547
+ E +E KI
Sbjct: 249 ELEVEQQPAGKTAEQTREVKIIL 271
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 33.8 bits (77), Expect = 0.28
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 500 QAERKAREEVEGK-KEKKKRKPKANKATSVAKTAGEAIEKMLKEKK 544
A K + E E K +K + KA + K A EK EKK
Sbjct: 189 AAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKK 234
Score = 29.9 bits (67), Expect = 4.6
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 479 EGEATNKAKLWEVLNREYLTLQAERKAREEVEGK----KEKKKRKPKANKATSVAKTAGE 534
+ EA KA + +AE+KA E K K+K K KA+KA + AK A
Sbjct: 195 KAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAAAAAKAAER 254
Query: 535 A 535
Sbjct: 255 K 255
Score = 29.9 bits (67), Expect = 4.7
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 500 QAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKK 544
+A +A+ + E KKK + +A A AK EA K K+ +
Sbjct: 178 KAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAE 222
>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation,
ribosomal structure and biogenesis / Posttranslational
modification, protein turnover, chaperones].
Length = 379
Score = 33.1 bits (75), Expect = 0.43
Identities = 31/128 (24%), Positives = 43/128 (33%), Gaps = 15/128 (11%)
Query: 447 NQDAERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAR 506
NQD R ++V A+ D I S+ E E K + WE R
Sbjct: 212 NQDNARLKRLVQIAKKR-----DPRIKSFKEQEKEMK-KIRKWE-------REAGARLKA 258
Query: 507 EEVEGKKEKKKRKPK--ANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVDVN 564
K + K K + A S +A E M K K+ K + K D+ D +
Sbjct: 259 LAALKGKAEAKNKAEIEAEALASATAVKKKAKEVMKKALKMEKKAIKNAAKDADYFGDAD 318
Query: 565 TGEMSTEQ 572
E E
Sbjct: 319 KAEHIDED 326
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 32.9 bits (75), Expect = 0.45
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 500 QAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKK 544
+AE KA+ E + K + ++ K KA A AK A EA K E
Sbjct: 176 EAEAKAKAEAKAKAKAEEAKAKAEAAK--AKAAAEAAAKAEAEAA 218
Score = 31.0 bits (70), Expect = 2.3
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 500 QAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKK 544
+ E++A E K+ ++ K K K A EA K E K
Sbjct: 93 ELEQRAAAEKAAKQAEQAAKQAEEKQ----KQAEEAKAKQAAEAK 133
Score = 29.8 bits (67), Expect = 4.6
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 500 QAERKAREEVEGKKEKKKRKP-----KANKATSVAKTAGEAIEKMLKEKK 544
+AE+KA+EE + + E++ + K A + K EA K + K
Sbjct: 139 EAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAK 188
Score = 29.4 bits (66), Expect = 6.9
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 481 EATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAI-EKM 539
E + +L + E QAE+ A++ E +K+ ++ K K AK EA EK
Sbjct: 87 EQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAE---AKAKAEAEAEKK 143
Query: 540 LKEK 543
KE+
Sbjct: 144 AKEE 147
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 32.2 bits (74), Expect = 0.53
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 501 AERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFT 560
++ + E G+KEK R+ + K + K +K E + + + L
Sbjct: 116 EQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQK--PEPQHTPVSDISELTVGQ-A 172
Query: 561 VDVNTG 566
V V G
Sbjct: 173 VKVKAG 178
>gnl|CDD|234547 TIGR04330, cas_Cpf1, CRISPR-associated protein Cpf1, subtype
PREFRAN. This family is the long protein of a novel
CRISPR subtype, PREFRAN, which is most common in
Prevotella and Francisella, although widely distributed.
The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the
helicase Cas3 and endonuclease Cas3-HD.
Length = 1287
Score = 32.9 bits (75), Expect = 0.71
Identities = 21/120 (17%), Positives = 46/120 (38%), Gaps = 3/120 (2%)
Query: 454 DQIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKK 513
D+ ++ +L I D+ +I E + +L L EY L + K ++ +
Sbjct: 37 DKARAESYKELKKIIDKYHKDFI---EETLSNVELSFDLLEEYFDLYNKLKKFKKDKKDL 93
Query: 514 EKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVDVNTGEMSTEQK 573
K++ + S+ E I K + KK+ + D +K+ + + ++
Sbjct: 94 AKEQDTLRKQIVKSLQDNLPEEIFKNIFSKKLLKGVLEDFIKNTHKDSEDEQNILIDIKE 153
Score = 30.6 bits (69), Expect = 3.9
Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 19/115 (16%)
Query: 494 REYLTLQAE-RKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKIS------ 546
EY+ Q E RK + + E +EK K+ K S+ + +EK +KE
Sbjct: 378 EEYIKKQIEPRKGKSKKEKYEEKVKKVVKKQDYLSIQ-FINDLLEKYIKEFDSKDRLFEN 436
Query: 547 --------TKINYDVLKSLDFTVDVNTGEMSTE---QKSAPRIIENLEITSSIKK 590
+ + + ++ D ++ T + E QK + ++ E+ IK
Sbjct: 437 IRDYFAEISLMRNEDFQTNDNIANIKTAYQTFERILQKERKDLKQDEEVVKLIKS 491
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 32.1 bits (73), Expect = 1.1
Identities = 21/129 (16%), Positives = 46/129 (35%), Gaps = 12/129 (9%)
Query: 514 EKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVDVNTGE-----M 568
+K K+ K + KT + +K +KK+ +YD G M
Sbjct: 58 KKNKKFNKTDDLKDSKKT--KLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLM 115
Query: 569 STEQKSAPRIIENLEITSSIKKTRAKPTKEKREPT---PKTPPKVAGDNYIKSNELPRVI 625
+ ++ + + + S K + K K E P ++ + + EL ++
Sbjct: 116 RKPKPKTEKLKKKITVNKSTNKKKKKVLSSKDELIKYDNNKPKSISIHSPLTIQELSTLL 175
Query: 626 KECLEDADL 634
C+ + ++
Sbjct: 176 --CIPETEI 182
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 31.6 bits (72), Expect = 1.7
Identities = 40/200 (20%), Positives = 69/200 (34%), Gaps = 24/200 (12%)
Query: 419 LEDADLEEETEGEIRGIGPTPAMLGMATNQDAERNDQIVDDAEDDLGDIDDEEINSYILT 478
D++ E+E + E G P ML + E D + + ++ +
Sbjct: 331 DSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDD----------EENSGLLSMKFMQ 380
Query: 479 EGEATNKA---KLWEVLNREYLTLQAERKAREEVEGKKEKKKRK--PKANKATSVAKTAG 533
EA K E L RE + + E KK +RK P+ + + +K
Sbjct: 381 RAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLK 440
Query: 534 EAIEKMLKEKKIS-------TKINYDVLKSLDFTVDVNTGEMSTEQKSAPRIIEN-LEIT 585
+ + KEKK S + V K + + + E++ EN T
Sbjct: 441 KENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEK-AQKEEEEEELDEENPWLKT 499
Query: 586 SSIKKTRAKPTKEKREPTPK 605
+S AK K++ + K
Sbjct: 500 TSSVGKSAKKQDSKKKSSSK 519
>gnl|CDD|219047 pfam06473, FGF-BP1, FGF binding protein 1 (FGF-BP1). This family
consists of several mammalian FGF binding protein 1.
Fibroblast growth factors (FGFs) play important roles
during fetal and embryonic development. Fibroblast
growth factor-binding protein (FGF-BP) 1 is a secreted
protein that can bind fibroblast growth factors (FGFs) 1
and 2.
Length = 229
Score = 31.0 bits (70), Expect = 1.8
Identities = 19/84 (22%), Positives = 28/84 (33%), Gaps = 19/84 (22%)
Query: 572 QKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPKVAG------DNYIKSNELPRVI 625
+K+ P +L+ +S + P +E R P+P K SN
Sbjct: 124 RKAFP--ESHLKQVTSTLEGSEGPRQEPRSPSPSEHDKGKEKSSEEKKLKKDSNSGVTKT 181
Query: 626 K-----------ECLEDADLEEDM 638
K +ED DLEE
Sbjct: 182 KATKLPECKPTQAGVEDEDLEEQR 205
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 30.8 bits (70), Expect = 1.9
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 507 EEVEGKKEKKKRKPKAN-KATSVAKTAGEAIEKMLKEKK 544
E+ E ++EK K KA K AK + K KE+K
Sbjct: 41 EDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEK 79
>gnl|CDD|200380 TIGR04129, CxxH_BA5709, CxxH/CxxC protein, BA_5709 family. Members
of this protein family occur exclusively in the
Firmicutes, in at least 50 different species. Members
average about 55 residues in length, and four of the
five invariant or nearly invariant residues occur in
motifs CxxH and CxxC. The function is unknown.
Length = 49
Score = 28.0 bits (63), Expect = 2.0
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 388 KYSCDSHVDISRVAGDDYIKSNELPRVIKECLEDADLEE 426
Y C H+++ A DDY+ E +++ E L
Sbjct: 1 YYCCKEHIEL---AIDDYVDEYETAPDLEKLEEVKKLST 36
>gnl|CDD|238201 cd00327, cond_enzymes, Condensing enzymes; Family of enzymes that
catalyze a (decarboxylating or non-decarboxylating)
Claisen-like condensation reaction. Members are share
strong structural similarity, and are involved in the
synthesis and degradation of fatty acids, and the
production of polyketides, a diverse group of natural
products.
Length = 254
Score = 30.9 bits (70), Expect = 2.1
Identities = 19/114 (16%), Positives = 34/114 (29%), Gaps = 22/114 (19%)
Query: 402 GDDYIKSNELPRVIKECLED---------ADLEEETEGEIRGIGPTPAMLGMATNQD--- 449
+++ + V+ E+ A +E E RG P ++ A D
Sbjct: 78 AVQQVQNGKADIVLAGGSEEFVFGDGAAAAVVESEEHALRRGAHPQAEIVSTAATFDGAS 137
Query: 450 ----------AERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLN 493
A + ++ A DID E + G+A A +
Sbjct: 138 MVPAVSGEGLARAARKALEGAGLTPSDIDYVEAHGTGTPIGDAVELALGLDPDG 191
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 31.4 bits (71), Expect = 2.1
Identities = 26/130 (20%), Positives = 49/130 (37%), Gaps = 17/130 (13%)
Query: 421 DADLEEETEGEIRGIGPTPA-----MLGMAT-NQDAERNDQIVDDAEDDLGDIDDEEINS 474
D EEE E ++ +L MA E+ ++ D + +++D + +
Sbjct: 1090 DDAAEEEEEIDVSSSSGVRGSDYDYLLSMAIGTLTLEKVQELCADRDKLNIEVEDLKKTT 1149
Query: 475 YI---LTEGEATNKAKLWEVLNREYLTLQAERK------AREEVEGKKEKKKRKPKANKA 525
L + +A K + L++E + R+ AR E K+ ++ PK
Sbjct: 1150 PKSLWLKDLDALEKE--LDKLDKEDAKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAP 1207
Query: 526 TSVAKTAGEA 535
K A E+
Sbjct: 1208 KKTTKKASES 1217
>gnl|CDD|235370 PRK05244, PRK05244, Der GTPase activator; Provisional.
Length = 177
Score = 30.3 bits (69), Expect = 2.2
Identities = 25/109 (22%), Positives = 38/109 (34%), Gaps = 37/109 (33%)
Query: 503 RKAREE--VEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFT 560
+K REE E ++ K+K+K K K+ S E + K
Sbjct: 18 KKTREELDAEARERKRKKKHKGLKSGSRHN------EGNTQSKGKGQA------------ 59
Query: 561 VDVNTGEMSTEQKSAPRI-----IENLEITSSIKKTRAKPTKEKREPTP 604
QK PRI I L + +K + KP +K + +P
Sbjct: 60 -----------QKKDPRIGSKKPIP-LGVEEKVKPKKKKPKSKKPKLSP 96
>gnl|CDD|227872 COG5585, COG5585, NAD+--asparagine ADP-ribosyltransferase [Signal
transduction mechanisms].
Length = 417
Score = 30.6 bits (69), Expect = 3.0
Identities = 35/205 (17%), Positives = 63/205 (30%), Gaps = 34/205 (16%)
Query: 400 VAGDDYIKSNELPRVIKEC-LEDADLEEETEGEIRGIGPTPAMLG-MATNQDAERNDQIV 457
VAG + E P V C ++E + + + P + +
Sbjct: 201 VAGVKEAEVGEFPPVHPGCRNGFGGVKENFVKDPKSLDQNPNIHDDLGKKDLKNYTKDPR 260
Query: 458 DDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKK 517
D + L D ++ + T K E KE +
Sbjct: 261 ADENEKLRQTQDRDLGKKLRK-------------------TGMPALKNGEGQIRPKEVRI 301
Query: 518 RKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVDVNTGEMST---EQKS 574
RK K A V + G ++ + + D LK + +++V+ S+ + K
Sbjct: 302 RKKKLEDAIGVDEKGGVGVDAVPFV-------SED-LKPGEGSINVHRLYRSSSSQDIKE 353
Query: 575 APRIIENLEITSSIKKTRAKPTKEK 599
IEN + T+ K + E
Sbjct: 354 LY--IENFKETNLAGKLKDAYMNEI 376
>gnl|CDD|219947 pfam08639, SLD3, DNA replication regulator SLD3. The SLD3 DNA
replication regulator is required for loading and
maintenance of Cdc45 on chromatin during DNA
replication.
Length = 437
Score = 30.6 bits (69), Expect = 3.0
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 12/77 (15%)
Query: 486 AKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKI 545
+L +L E L L+ +R + E E KK+ KR ++ K K KK
Sbjct: 105 TQLQIILILELLALELDRFTKFEKEYKKKLLKRSQNLDR---------SKRRKRRKRKKN 155
Query: 546 STKINYDVLKSLDFTVD 562
+ D+ LD +D
Sbjct: 156 KKQ---DLPVLLDLHLD 169
>gnl|CDD|227545 COG5220, TFB3, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH, subunit TFB3 [Cell division and chromosome
partitioning / Transcription / DNA replication,
recombination, and repair].
Length = 314
Score = 30.4 bits (68), Expect = 3.0
Identities = 26/135 (19%), Positives = 48/135 (35%), Gaps = 5/135 (3%)
Query: 475 YILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGE 534
++ K K +E +N++ + ER EV K+K + + + E
Sbjct: 122 ELIDVSLTEEKVKKYEEMNQDSILNNLER-PTPEVMPGKQKNVLQKRMKLKKRQLERQIE 180
Query: 535 AIEKMLKEKKISTKINYDVLKSLDFTVDVNTGEMST--EQKSAPRIIENLEITSSIKKTR 592
E+M KE N S D + G +S + + PRI+ + I +
Sbjct: 181 EEERMNKEWTKKEIGNRLGTASEDGNKTIKIGIISDKFDPEELPRIVVEPTRNNKIYLSN 240
Query: 593 AKPTKEKREPTPKTP 607
+ + + P P
Sbjct: 241 VQGFLK--DLQPFAP 253
>gnl|CDD|218148 pfam04557, tRNA_synt_1c_R2, Glutaminyl-tRNA synthetase,
non-specific RNA binding region part 2. This is a
region found N terminal to the catalytic domain of
glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes
but not in Escherichia coli. This region is thought to
bind RNA in a non-specific manner, enhancing
interactions between the tRNA and enzyme, but is not
essential for enzyme function.
Length = 83
Score = 28.1 bits (63), Expect = 3.1
Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 5/37 (13%)
Query: 512 KKEKKKRKPKANKATSVAKTAGEAIE-----KMLKEK 543
KK+KKK+K KA + AK E M E
Sbjct: 24 KKKKKKKKKKAEDTAATAKAKKATAEDVSEGAMFMEG 60
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 30.8 bits (70), Expect = 3.3
Identities = 24/133 (18%), Positives = 39/133 (29%), Gaps = 4/133 (3%)
Query: 494 REYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDV 553
E + +R + K K RKPK K K + K S +++ D
Sbjct: 1148 EEKEIAKEQRL--KSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDE 1205
Query: 554 LKSLDFTVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPKVAGD 613
+ LD N S+ E R K K + + + + D
Sbjct: 1206 KRKLD-DKPDNKKSNSSGSDQEDD-EEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSD 1263
Query: 614 NYIKSNELPRVIK 626
+ K + K
Sbjct: 1264 DLSKEGKPKNAPK 1276
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This
domain is found to the N-terminus of bacterial signal
peptidases of the S49 family (pfam01343).
Length = 154
Score = 29.4 bits (67), Expect = 3.5
Identities = 17/51 (33%), Positives = 20/51 (39%), Gaps = 10/51 (19%)
Query: 492 LNREYLTLQ----------AERKAREEVEGKKEKKKRKPKANKATSVAKTA 532
LN EY L+ E KA E+ E K EK K K + KA
Sbjct: 47 LNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKAKKEEPKP 97
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 30.6 bits (69), Expect = 3.8
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 490 EVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTK 548
E ++ Y LQ ER+ REE K +K + KA E EK LK +S K
Sbjct: 430 EEEHQIYRKLQEERRLREEAIRAKAEKTARMKA-----------EMKEKTLKMFLLSQK 477
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 30.3 bits (69), Expect = 3.9
Identities = 14/133 (10%), Positives = 35/133 (26%), Gaps = 4/133 (3%)
Query: 514 EKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTVD----VNTGEMS 569
K + K + K + I+ + + L+S T + V
Sbjct: 2 TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61
Query: 570 TEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPKVAGDNYIKSNELPRVIKECL 629
+ + ++ + +A K + K + K+ +
Sbjct: 62 MVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYV 121
Query: 630 EDADLEEDMGGEI 642
+D D+ +
Sbjct: 122 KDIDVLNQADDDD 134
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 28.8 bits (65), Expect = 4.2
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 15/75 (20%)
Query: 486 AKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPK-----ANKATSVAKT---AGEAI- 536
++ E + + TL+ +V KK+KK PK A K A +A+
Sbjct: 36 PEILEFILKHLSTLK--FTEAVKVSIKKQKKIN-PKRLQRQAAKEVKKPGISTKAQQALK 92
Query: 537 ---EKMLKEKKISTK 548
E+ +EKK +K
Sbjct: 93 LEHERNKQEKKKRSK 107
>gnl|CDD|217206 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 29.2 bits (66), Expect = 4.5
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 20/60 (33%)
Query: 486 AKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKI 545
AKL E L AERKAREEV + E +++ + EK KE+K+
Sbjct: 108 AKLSEALY------IAERKAREEVRQRAELQRQLAEK--------------EKQEKEEKL 147
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 29.0 bits (65), Expect = 4.6
Identities = 13/48 (27%), Positives = 16/48 (33%), Gaps = 1/48 (2%)
Query: 503 RKAREEVEGKKEKKKRKPKAN-KATSVAKTAGEAIEKMLKEKKISTKI 549
K EE E K KK++K K K KK + K
Sbjct: 103 SKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKT 150
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 29.9 bits (67), Expect = 5.0
Identities = 20/111 (18%), Positives = 40/111 (36%), Gaps = 10/111 (9%)
Query: 500 QAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDF 559
+ + + +EE + KKEK K +PK K AK EK +++K V + D
Sbjct: 108 KEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEK-------KVEEPRDR 160
Query: 560 TVDVNTGEM--STEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPP 608
+ + + K P+ + ++ + + + K
Sbjct: 161 EEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAA-REAVKGKPEE 210
>gnl|CDD|224174 COG1254, AcyP, Acylphosphatases [Energy production and
conversion].
Length = 92
Score = 27.9 bits (63), Expect = 5.3
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 2 NFDDDEKQKLIEEV-----HAVVT-VRDAKHTNFVEFRNFKIVY 39
D+ +K IE + A V V + EF +F I Y
Sbjct: 49 EGPDEAVEKFIEWLRKGPPAAKVERVEVEEEEYTGEFPDFSIRY 92
>gnl|CDD|183147 PRK11465, PRK11465, putative mechanosensitive channel protein;
Provisional.
Length = 741
Score = 29.7 bits (67), Expect = 5.4
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 432 IRGIGPTPAMLGMATNQDAERNDQIVDDAEDDLGDIDDEEINSYILTE 479
+RGIG A + ++DA++ +Q + DA +L +++EEI I+ E
Sbjct: 621 VRGIGSVVANYDVDRHEDADKANQALKDAVAEL--MENEEIRGLIIGE 666
>gnl|CDD|215840 pfam00291, PALP, Pyridoxal-phosphate dependent enzyme. Members of
this family are all pyridoxal-phosphate dependent
enzymes. This family includes: serine dehydratase
EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16,
tryptophan synthase beta chain EC:4.2.1.20, threonine
synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8
P11096, cystathionine beta-synthase EC:4.2.1.22,
1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.
Length = 295
Score = 29.3 bits (66), Expect = 5.7
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 429 EGEIRGIGPTPAMLGMATNQDAERNDQIVDDAEDDLGDIDDEEI 472
G T A LG D E +++D+ D+ + DEE
Sbjct: 206 AGRRVPKPTTIAGLGPGIPLDGELALELIDEYVGDVYAVSDEEA 249
>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
Length = 117
Score = 28.2 bits (64), Expect = 5.9
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 512 KKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKIST 547
+K+ + NK AK G+ I + K K I
Sbjct: 56 EKDVRAGLKGGNKE--AAKKVGKLIAERAKAKGIKQ 89
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 29.4 bits (67), Expect = 6.2
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 10/46 (21%)
Query: 492 LNREYLTLQ----------AERKAREEVEGKKEKKKRKPKANKATS 527
LN +Y ++ E KA + + KKEK++ K K+
Sbjct: 45 LNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSKP 90
>gnl|CDD|176204 cd08242, MDR_like, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family, including threonine dehydrogenase.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 29.1 bits (66), Expect = 6.4
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 7/41 (17%)
Query: 169 VLKELRVLRSRCGPSPW-------RHILEDSVIVSEMQFEE 202
V+ E+ ++ SRCGP + D +I + EE
Sbjct: 259 VVNEITLVGSRCGPFAPALRLLRKGLVDVDPLITAVYPLEE 299
>gnl|CDD|212091 cd11522, SLC6sbd_SBAT1, Sodium-coupled branched-chain amino-acid
transporter 1; solute-binding domain. SBAT1 (also
called B0AT2, v7-3, NTT7-3) is a high-affinity
Na(+)-dependent transporter for large neutral amino
acids, including leucine, isoleucine, valine, proline
and methionine. Human SBAT1 is encoded by the SLC6A15
gene, a susceptibility gene for major depression. SBAT1
is expressed in brain, and may have a role in
transporting neurotransmitter precursors into neurons.
This subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 580
Score = 29.5 bits (66), Expect = 7.0
Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 22/86 (25%)
Query: 360 VTMTALRILQRMKKDMLHSGRRPNGLIGKYSCDSHVDISRVAGDDY---------IKSNE 410
+ + +I++ +K L P+ H++ S + +DY +K E
Sbjct: 308 IIQNSEKIIKLLKMGNLSQDIIPH----------HINFSSITAEDYNLVYDIIQKVKEEE 357
Query: 411 LPRVIKECLEDADLEEETEGEIRGIG 436
P + L+ +E+E ++G G
Sbjct: 358 FPAL---GLKSCQIEDELNKAVQGTG 380
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 29.7 bits (66), Expect = 7.2
Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 5/109 (4%)
Query: 442 LGMATNQDAERNDQIVDDAED-DLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQ 500
AT E ++++ D E + D++DEE +S E + + + + +
Sbjct: 581 QKDATLDSIEGEEELIQDDEKGNFEDLEDEENSSDNEMEESRGSSVTAENEESADEVDYE 640
Query: 501 AER----KAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKI 545
ER + +EE+ G E ++R K IE+ LK +
Sbjct: 641 TEREENARKKEELRGNFELEERGDPEKKDVDWYTEEKRKIEEQLKINRS 689
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 29.3 bits (66), Expect = 7.7
Identities = 14/105 (13%), Positives = 38/105 (36%), Gaps = 3/105 (2%)
Query: 537 EKMLKEKKISTKINYDVLKSLDFTVDVNTGEMSTEQ---KSAPRIIENLEITSSIKKTRA 593
E + + KK+ I+ + S+++ ++ + K E+L S+I
Sbjct: 928 ELIARLKKLLNNIDLEEGPSIEYVKLPELNKLHEVESKLKETSEEYEDLLKKSTILVREG 987
Query: 594 KPTKEKREPTPKTPPKVAGDNYIKSNELPRVIKECLEDADLEEDM 638
+ + K +++ ++ + +E A+L+
Sbjct: 988 NKANSELKNFKKELAELSKQYGALQESTKQLKELPVEVAELQSAS 1032
>gnl|CDD|234846 PRK00844, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 407
Score = 29.0 bits (66), Expect = 8.1
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 598 EKREPTPKTPPKVAGD---------NYI-KSNELPRVIKECLEDADLEEDMGGEI 642
EK P PP + D NY+ ++ L ++ D D DMGG+I
Sbjct: 178 EK----PADPPGLPDDPDEALASMGNYVFTTDALVDALRRDAADEDSSHDMGGDI 228
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 29.1 bits (66), Expect = 8.2
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 396 DISRVAGDDYIKSNELPRVIKECLEDADLEEETEGEIRGI---GPTPAMLGMATNQDAER 452
++ + G D EL KE LE L +E + + G + + +
Sbjct: 390 ELLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGIKT 449
Query: 453 NDQIVDDAEDDLGDIDDEE 471
+ + + A D+L DI+ +E
Sbjct: 450 LEDLAEQAVDELIDIEGDE 468
>gnl|CDD|218230 pfam04724, Glyco_transf_17, Glycosyltransferase family 17. This
family represents beta-1,4-mannosyl-glycoprotein
beta-1,4-N-acetylglucosaminyltransferase (EC:2.4.1.144).
This enzyme transfers the bisecting GlcNAc to the core
mannose of complex N-glycans. The addition of this
residue is regulated during development and has
functional consequences for receptor signalling, cell
adhesion, and tumour progression.
Length = 357
Score = 28.9 bits (65), Expect = 8.2
Identities = 22/63 (34%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 380 RRPNGLIGKYSCDSHVDISRVAGDDYIKSNELPRVIK--ECLEDADLEEETEGEIRG-IG 436
RR G + K SH D R DY+ + +I L D EE T EI G +G
Sbjct: 266 RRIEGFVFKMKAYSHGDRVRW--GDYLNPKRIQDLICKGGDLFDMLPEEYTFKEIIGKMG 323
Query: 437 PTP 439
P P
Sbjct: 324 PIP 326
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 29.1 bits (65), Expect = 8.3
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 503 RKAREEVEGKKEKKKRKPKAN-------KATSVAKTAGEAIEKMLKEKKI 545
R+ARE++E +E+++RK +A KA A EAIE + +++
Sbjct: 6 RRAREKLE--REQRERKQRAKLKLERERKAKEEAAKQREAIEAAQRSRRL 53
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 29.0 bits (65), Expect = 8.8
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 477 LTEGEATNKAKLWEVLNREYLTLQAERKAREEVE--GKKEKKKRKPKANKATSVAKTAGE 534
L + +A + +L + L +E L Q ++K EE ++K+ + A KA + AK E
Sbjct: 92 LQQKQAAEQERLKQ-LEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAE 150
Query: 535 AIEKMLKE 542
A K
Sbjct: 151 AEAKRAAA 158
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 28.9 bits (65), Expect = 8.8
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 16/74 (21%)
Query: 458 DDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKK 517
D E + D +DEE + EA KAK E + E+ E E+++
Sbjct: 123 SDKEIESSDSEDEEE------KDEAAKKAKE----------DSDEELSEEDEEEAAEEEE 166
Query: 518 RKPKANKATSVAKT 531
+ + KA+ +A T
Sbjct: 167 AEAEKEKASELATT 180
>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62.
Length = 217
Score = 28.6 bits (64), Expect = 8.9
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 19/75 (25%)
Query: 504 KAREEVEGKKEKKKRKPKA-------NKATSVAK---TAGEAIE---------KMLKEKK 544
+A E + K K K P+ +KA K A A K K+K
Sbjct: 14 RALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKP 73
Query: 545 ISTKINYDVLKSLDF 559
K+ V + F
Sbjct: 74 KKKKVPLQVNPAQLF 88
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 28.6 bits (64), Expect = 8.9
Identities = 31/169 (18%), Positives = 55/169 (32%), Gaps = 35/169 (20%)
Query: 322 RTYLRLSQALCISI-----------PSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQR 370
R L S+ S DP + RYS++ K L+
Sbjct: 52 RYQASLYIEFRASLRDGPFYTGSESLSQDPKDGIERYSDKYQKKRKIGPSIKEHPFDLEL 111
Query: 371 MKKDMLHSGRRPNGLIGKYSCDSH---VDISRVAG-DDYIKSNELPRVIKECLEDADLEE 426
K++ K + V + D K + L + +KE LE D++E
Sbjct: 112 FPKELYSVMGINKKAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKE-LEAEDVDE 170
Query: 427 ETEGEIRGIGPTPAMLGMATNQDAERNDQIVDDAEDDLGDIDDEEINSY 475
E E + E ++ ++ ++D D DD++ + Y
Sbjct: 171 EDEKD-------------------EEEEEEEEEEDEDFDDDDDDDDDDY 200
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 27.0 bits (60), Expect = 9.0
Identities = 11/50 (22%), Positives = 19/50 (38%)
Query: 509 VEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLD 558
++ KK+KKK+K K V E + + + + D K
Sbjct: 17 IDVKKKKKKKKKKNKSKEEVVTEKEEEEKSSAESDLKEGEEDEDNEKIEQ 66
>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
Length = 470
Score = 28.9 bits (65), Expect = 9.4
Identities = 21/119 (17%), Positives = 41/119 (34%), Gaps = 26/119 (21%)
Query: 504 KAREEVEGKKEKKKRKPKANKAT--------------SVAKTAGEAIEKMLKEKKISTKI 549
+++ + K++ K+K K +K + + +K K+KK K
Sbjct: 10 VKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKKKKKK 69
Query: 550 NYDVLKSLDFTVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPP 608
N L + + V + + S R + N P +E ++ P T P
Sbjct: 70 NLGEAYDLAYDLPVVWSSAAFQDNSHIRKLGN------------WPEQEWKQTQPPTIP 116
>gnl|CDD|176498 cd08555, PI-PLCc_GDPD_SF, Catalytic domain of
phosphoinositide-specific phospholipase C-like
phosphodiesterases superfamily. The PI-PLC-like
phosphodiesterases superfamily represents the catalytic
domains of bacterial phosphatidylinositol-specific
phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11), glycerophosphodiester phosphodiesterases
(GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D)
(sphingomyelin phosphodiesterase D, EC 3.1.4.41) from
spider venom, SMases D-like proteins, and phospholipase
D (PLD) from several pathogenic bacteria, as well as
their uncharacterized homologs found in organisms
ranging from bacteria and archaea to metazoans, plants,
and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing
the membrane lipid phosphoinositides to yield two
important second messengers, inositol phosphates and
diacylglycerol (DAG). GP-GDEs play essential roles in
glycerol metabolism and catalyze the hydrolysis of
glycerophosphodiesters to sn-glycerol-3-phosphate (G3P)
and the corresponding alcohols that are major sources of
carbon and phosphate. Both, PI-PLCs and GP-GDEs, can
hydrolyze the 3'-5' phosphodiester bonds in different
substrates, and utilize a similar mechanism of general
base and acid catalysis with conserved histidine
residues, which consists of two steps, a phosphotransfer
and a phosphodiesterase reaction. This superfamily also
includes Neurospora crassa ankyrin repeat protein NUC-2
and its Saccharomyces cerevisiae counterpart, Phosphate
system positive regulatory protein PHO81,
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs). The residues
essential for enzyme activities and metal binding are
not conserved in these sequence homologs, which might
suggest that the function of catalytic domains in these
proteins might be distinct from those in typical
PLC-like phosphodiesterases.
Length = 179
Score = 28.2 bits (63), Expect = 9.4
Identities = 28/134 (20%), Positives = 39/134 (29%), Gaps = 27/134 (20%)
Query: 97 YRRYAGLYFCICVDVNDNNLCYLEAIHNFVE------VLNEYFHNVCELDLVFNFYKVYT 150
YR + +DV L H +L V EL + YT
Sbjct: 20 YRALDAGARGLELDVRLTKDGELVVYHGPTLDRTTAGILPPTLEEVLELIADYLKNPDYT 79
Query: 151 VVDEMFLAGEIRETS------QTKVLKELR-----------VLRSRCGPSPWRHILEDSV 193
++ L+ EI++ S KVLKELR VL S + +
Sbjct: 80 II----LSLEIKQDSPEYDEFLAKVLKELRVYFDYDLRGKVVLSSFNALGVDYYNFSSKL 135
Query: 194 IVSEMQFEENAHGG 207
I G
Sbjct: 136 IKDTELIASANKLG 149
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 0.136 0.397
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,527,655
Number of extensions: 3334860
Number of successful extensions: 4079
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3927
Number of HSP's successfully gapped: 147
Length of query: 661
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 558
Effective length of database: 6,369,140
Effective search space: 3553980120
Effective search space used: 3553980120
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 (21.7 bits)
S2: 62 (27.5 bits)