RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7022
(124 letters)
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 43.8 bits (104), Expect = 2e-07
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 3 GYYCNVCDCVVKDSINFLDHINGKKHQRNL 32
G+YC +C+ D I+ H+ GKKH++N+
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNV 32
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 37.9 bits (89), Expect = 4e-05
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 4 YYCNVCDCVVKDSINFLDHINGKKH 28
+YC +C+ H+ GKKH
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 39.3 bits (91), Expect = 2e-04
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 54 KKKYE-QKKKDYDIEQRMRELKE-EEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
KK+ E +K + EQ+ RE +E E+EK KE RER +E +R E S+
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHESRMSE 635
Score = 33.5 bits (76), Expect = 0.022
Identities = 14/52 (26%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 60 KKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAA 111
KK++ +E+ RE +++ + +E +E+ KE++R E E E +++ A+
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKERER-----EREREAERAAKAS 625
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 34.9 bits (81), Expect = 5e-04
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 4 YYCNVCDCVVKDSINFLDHINGKKHQ 29
+YC CD K +H+ KKH+
Sbjct: 2 FYCVACDKYFKSENALENHLKSKKHK 27
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 33.6 bits (77), Expect = 0.015
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 53 NKKKYEQKKKDYDI--EQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLA 110
K YE+ K + D+ ++R LKE +KL++Y ++ + K E E + + L
Sbjct: 349 LTKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLK 408
Query: 111 A 111
Sbjct: 409 Q 409
>gnl|CDD|203945 pfam08439, Peptidase_M3_N, Oligopeptidase F. This domain is found
to the N-terminus of the pfam01432 domain in bacterial
and archaeal proteins including Oligoendopeptidase F. An
example of this protein is Lactococcus lactis PepF.
Length = 70
Score = 31.0 bits (71), Expect = 0.028
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 67 EQRMRELKEEEEKLKEYR---RERRKEKKRKLDDGEEE 101
E+++ L EE+ +LK YR E R++K L + EE+
Sbjct: 7 EEKLEALLEEDPELKPYRFYLEEIRRQKPHTLSEEEEK 44
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.0 bits (75), Expect = 0.030
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 37 RVERSSLDQVKKRFDMNKKKY----EQKKKDYDIEQRM-RELKEEEEKLKEYRRERRKEK 91
R +S L Q+KK DM + K K+KD Q M + LK E + ++ +EK
Sbjct: 444 RSLKSDLGQLKKENDMLQTKLNSMVSAKQKDKQSMQSMEKRLKSEADSRVNAEKQLAEEK 503
Query: 92 KRKLDDGEEEEEGDQSDLAAI 112
KRK EEEE ++ A
Sbjct: 504 KRK---KEEEETAARAAAQAA 521
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 32.4 bits (73), Expect = 0.042
Identities = 20/70 (28%), Positives = 38/70 (54%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
E D+ KK+ + KK E KKK + +++ E K+ E K+ ++ E+ +K D+
Sbjct: 1468 EAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEA 1527
Query: 99 EEEEEGDQSD 108
++ EE ++D
Sbjct: 1528 KKAEEAKKAD 1537
Score = 29.7 bits (66), Expect = 0.45
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
E D+ KK+ + KKK ++ KK + +++ E K+ EE K+ ++ E+ +K D+
Sbjct: 1481 EAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEA-KKADEAKKAEEAKKADEA 1539
Query: 99 EEEEEGDQSD 108
++ EE ++D
Sbjct: 1540 KKAEEKKKAD 1549
Score = 29.0 bits (64), Expect = 0.68
Identities = 18/70 (25%), Positives = 35/70 (50%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
E+ D+ KK+ + KK E KKK + +++ K++ E+ K+ + E + D+
Sbjct: 1300 EKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEA 1359
Query: 99 EEEEEGDQSD 108
E EE ++
Sbjct: 1360 EAAEEKAEAA 1369
Score = 27.4 bits (60), Expect = 2.2
Identities = 16/65 (24%), Positives = 29/65 (44%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
E D+ KK+ + KKK + KK + ++ E + E + E +EK +
Sbjct: 1313 EAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKK 1372
Query: 99 EEEEE 103
+EE +
Sbjct: 1373 KEEAK 1377
Score = 27.0 bits (59), Expect = 3.1
Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLK---EYRRERRKEKKRKL 95
+ +++KK + KK + KKK+ + +++ ELK+ EE+ K ++ +E K+K
Sbjct: 1618 AKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA 1677
Query: 96 DDGEEEEE 103
++ ++ EE
Sbjct: 1678 EEAKKAEE 1685
Score = 27.0 bits (59), Expect = 3.6
Identities = 19/66 (28%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEE-EEKLKEYRRERRKEKKRKLDD 97
E+ D+ KK+ + +KKK ++ KK +++ E K++ EEK K +++ E+ +K D+
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448
Query: 98 GEEEEE 103
+++ E
Sbjct: 1449 AKKKAE 1454
Score = 26.6 bits (58), Expect = 3.9
Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEE----KLKEYRRERRKEKKRK 94
E+ + + +KK + KK E KKK+ + +++ ELK+ EE K +E ++E ++KK+
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKA 1746
Query: 95 LDDGEEEEE 103
+ ++EEE
Sbjct: 1747 EEAKKDEEE 1755
Score = 26.6 bits (58), Expect = 4.9
Identities = 19/62 (30%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 44 DQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK--EKKRKLDDGEEE 101
++ KK+ D KKK E+KKK + +++ E K++ ++LK+ ++K E K+K ++ ++
Sbjct: 1374 EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKA 1433
Query: 102 EE 103
+E
Sbjct: 1434 DE 1435
Score = 26.3 bits (57), Expect = 5.9
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 26 KKHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRR 85
KK L + + ++ KK + +KKK E+ KKD + ++++ LK+EEEK E
Sbjct: 1715 KKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAE--- 1771
Query: 86 ERRKEKKRKLDDGEEEEE 103
E RKEK+ +++ +EE+
Sbjct: 1772 EIRKEKEAVIEEELDEED 1789
Score = 25.9 bits (56), Expect = 9.2
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
E+ D+ KK+ + KK E KKK + ++ K+ EE K +++ E+ +K D+
Sbjct: 1429 EKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEA 1488
Query: 99 EEEEE 103
+++ E
Sbjct: 1489 KKKAE 1493
Score = 25.9 bits (56), Expect = 9.4
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK-EKKRKLDD 97
+ D KK+ + KK E KKK + +++ ELK+ K+ ++K E+K+K D+
Sbjct: 1376 AKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADE 1435
Query: 98 GEEEEE 103
+++ E
Sbjct: 1436 AKKKAE 1441
>gnl|CDD|179310 PRK01622, PRK01622, OxaA-like protein precursor; Validated.
Length = 256
Score = 32.0 bits (73), Expect = 0.052
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 23 INGKKHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEE 76
++ K QR + M V + LD+++ + + K +QK + ++ M EL +
Sbjct: 80 VSQYKSQRGMQEKMAVMKPELDKIQAKLKVTKDLEKQK----EYQKEMMELYKS 129
>gnl|CDD|189014 cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 581
Score = 31.7 bits (73), Expect = 0.062
Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 19/84 (22%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYR---RERRKEKKRKLD 96
+SL+Q+ D KK ++D D L + E LKE+ ERR++ K L
Sbjct: 92 SASLEQLLTLLD--KKLAALSEEDLD------ALLADPE-LKEHAFFLEERRRQAKHLLS 142
Query: 97 DGEEEEEGDQSDLAAIMGFSGFGG 120
+ EEE L A + G
Sbjct: 143 EEEEE-------LIAKLSVDGLHA 159
>gnl|CDD|189015 cd09608, M3B_PepF_3, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 538
Score = 31.7 bits (73), Expect = 0.066
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 67 EQRMRELKEEEEKLKEYRR---ERRKEKKRKLDDGEEE 101
E+++ +EE +LK+YR E ++K L EEE
Sbjct: 65 EEKLESFLKEEPELKDYRHYLEEILRQKPHTLSAEEEE 102
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.4 bits (72), Expect = 0.084
Identities = 13/52 (25%), Positives = 34/52 (65%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGD 105
KK ++ KK + ++ RE +++E+K K + ++++E++ + + +EEE+ +
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEE 457
Score = 28.3 bits (64), Expect = 1.2
Identities = 18/64 (28%), Positives = 37/64 (57%)
Query: 46 VKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGD 105
V+K +++ ++KKK ++ E +EEE++ KE +E +E+ + + EEE++
Sbjct: 416 VEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKK 475
Query: 106 QSDL 109
Q+ L
Sbjct: 476 QATL 479
>gnl|CDD|135173 PRK04654, PRK04654, sec-independent translocase; Provisional.
Length = 214
Score = 31.3 bits (70), Expect = 0.089
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 27 KHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRE----LKEEEEKLKE 82
K R G+ +R R D VK+ + + E K+ D++ +RE L+ ++++++
Sbjct: 27 KAARFAGLWVRRARMQWDSVKQELERELEAEELKRSLQDVQASLREAEDQLRNTQQQVEQ 86
Query: 83 YRRERRKEKKRKLD 96
R + R +D
Sbjct: 87 GARALHDDVSRDID 100
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 30.8 bits (70), Expect = 0.11
Identities = 11/45 (24%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 69 RMRELKEE----EEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDL 109
+M+EL++ +++ +E + +K +KL + + E DQ +L
Sbjct: 73 KMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQMEMMDDQREL 117
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 31.0 bits (70), Expect = 0.12
Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 35 SMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
M E S DQ ++R +++ E EE+ ++ R+E+ E+ +
Sbjct: 202 DMTPETSKQDQKEERRAAVERRLA--------ELVEMINWNLEERRRDLRKEQELEENVE 253
Query: 95 LDDGEEEEEGDQSD 108
D +E+E G+ S+
Sbjct: 254 RDSDDEDEHGEDSE 267
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 30.1 bits (68), Expect = 0.18
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 43 LDQVKKRFDMNKKKYEQKKKDY--------DIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
L+ +++R + + E K+D +E+R+ L+E ++L + RE R++ + +
Sbjct: 95 LEDLEERIAELESELEDLKEDLQLLRELLKSLEERLESLEESIKELAKELRELRQDLREE 154
Query: 95 LDDGEEEEEGDQSDLAAI 112
+++ EE E Q +L +
Sbjct: 155 VEELREELERLQENLQRL 172
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 30.6 bits (70), Expect = 0.20
Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRER--------RKEK 91
L+Q + + K+ E+ K++ E++ +L+EEE+KL E + +KE
Sbjct: 529 ERELEQKAEEAEALLKEAEKLKEEL--EEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEA 586
Query: 92 KRKLDDGEEEEEGDQSDLAA 111
+ + + ++G + + A
Sbjct: 587 DEIIKELRQLQKGGYASVKA 606
Score = 27.5 bits (62), Expect = 1.9
Identities = 13/54 (24%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 41 SSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
+SL+++++ + ++ E K+ E+ EL+E++EKL+E + +E +++
Sbjct: 523 ASLEELERELEQKAEEAEALLKEA--EKLKEELEEKKEKLQEEEDKLLEEAEKE 574
>gnl|CDD|185246 PRK15348, PRK15348, type III secretion system lipoprotein SsaJ;
Provisional.
Length = 249
Score = 30.3 bits (68), Expect = 0.21
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 22 HINGKKHQRNLGMSMRVERSSLDQVKKRFDMN---KKKYEQKKKDYDIEQRMRELKEEEE 78
HI+ +K Q G+++RVE+S + +N +++ K + Q + +EE++
Sbjct: 43 HIDAEKKQEEDGVTLRVEQSQFINAVELLRLNGYPHRQFTTADKMFPANQLVVSPQEEQQ 102
Query: 79 K---LKEYRRE 86
K LKE R E
Sbjct: 103 KINFLKEQRIE 113
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 30.3 bits (69), Expect = 0.25
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 37 RVERS---SLDQVKKRFDMNKKKYEQKKKDYDIEQRM-RELKEEEEKLKEYRRERRKEKK 92
R ++ +++Q KK+ + K ++E ++ R+ RE E + K+ R + K
Sbjct: 432 RQAKAEIRAIEQEKKKAEEAKARFEARQ------ARLEREKAAREARHKKAAEARAAKDK 485
>gnl|CDD|216807 pfam01956, DUF106, Integral membrane protein DUF106. This
archaebacterial protein family has no known function.
Members are predicted to be integral membrane proteins.
Length = 168
Score = 29.5 bits (67), Expect = 0.26
Identities = 13/40 (32%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKE 90
D +KY++++K+ ++R REL++ +KL + E+R+E
Sbjct: 39 DRKMEKYQKREKEI--QKRARELRKNGDKLSPKKFEKRQE 76
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 0.28
Identities = 14/60 (23%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 54 KKKYEQKKKDY--DIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAA 111
K++ + + ++ ++ +R EL++ E++L + + E K L+ EEE E + +L
Sbjct: 63 KEEIHKLRNEFEKELRERRNELQKLEKRLLQ-KEENLDRKLELLEKREEELEKKEKELEQ 121
Score = 29.4 bits (67), Expect = 0.39
Identities = 14/48 (29%), Positives = 36/48 (75%), Gaps = 1/48 (2%)
Query: 44 DQVKKRFDMNKKKYEQ-KKKDYDIEQRMRELKEEEEKLKEYRRERRKE 90
+ + ++ ++ +K+ E+ +KK+ ++EQ+ +EL+++EE+L+E E+ +E
Sbjct: 96 ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQE 143
Score = 27.4 bits (62), Expect = 2.1
Identities = 18/68 (26%), Positives = 43/68 (63%), Gaps = 5/68 (7%)
Query: 37 RVERSSLDQVKKRFDMNKKKYEQ-KKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKL 95
R R+ L +++KR +K E +K +E+R EL+++E++L++ +++ ++K+ +L
Sbjct: 78 RERRNELQKLEKR---LLQKEENLDRKLELLEKREEELEKKEKELEQ-KQQELEKKEEEL 133
Query: 96 DDGEEEEE 103
++ EE+
Sbjct: 134 EELIEEQL 141
>gnl|CDD|227000 COG4653, COG4653, Predicted phage phi-C31 gp36 major capsid-like
protein [General function prediction only].
Length = 422
Score = 29.8 bits (67), Expect = 0.29
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 59 QKKKDYDIEQRMRELKEEEEKLKEYRRER---RKEKKRKLDDGEEEEEGDQSD 108
QR + L ++ +R R +E+ R+L E GD+ D
Sbjct: 8 AGDLTGAAAQRFQALTRHATAIRAEQRRRGEEAEEENRRLLADIERVGGDKLD 60
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 30.0 bits (68), Expect = 0.33
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 23/78 (29%)
Query: 53 NKKKYEQKKKDYDIEQRMREL-------------------KEEEEKLK--EYRRERRKEK 91
E+K +YD QR+REL KEE E+LK E R RR
Sbjct: 227 PPMTPEEKDDEYD--QRVRELTFDRRAQPTDRTKTEEELAKEEAERLKKLEAERLRRMRG 284
Query: 92 KRKLDDGEEEEEGDQSDL 109
+ + D+ EE+ + DL
Sbjct: 285 EEEDDEEEEDSKESADDL 302
>gnl|CDD|114912 pfam06220, zf-U1, U1 zinc finger. This family consists of
several U1 small nuclear ribonucleoprotein C (U1-C)
proteins. The U1 small nuclear ribonucleoprotein (U1
snRNP) binds to the pre-mRNA 5' splice site (ss) at
early stages of spliceosome assembly. Recruitment of U1
to a class of weak 5' ss is promoted by binding of the
protein TIA-1 to uridine-rich sequences immediately
downstream from the 5' ss. Binding of TIA-1 in the
vicinity of a 5' ss helps to stabilise U1 snRNP
recruitment, at least in part, via a direct interaction
with U1-C, thus providing one molecular mechanism for
the function of this splicing regulator. This domain is
probably a zinc-binding. It is found in multiple copies
in some members of the family.
Length = 38
Score = 27.4 bits (61), Expect = 0.33
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 1 MLGYYCNVCDCVVKDSINFLD--HINGKKHQRN 31
M YYC+ CDC + + H G+KH+ N
Sbjct: 1 MPKYYCDYCDCYLTHDSPSVRKSHNGGRKHKDN 33
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 29.5 bits (67), Expect = 0.42
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 55 KKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
++YE++ K+Y+ E+ + E + K ++ +K K+ D+ EE
Sbjct: 72 EEYEEELKEYEAEKEIWEA-----EKKGLEKKAKKAIKKGKDEEALAEE 115
Score = 27.2 bits (61), Expect = 2.4
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 64 YDIEQRMRELKEEEEKLKEYRRERR---------KEKKRKLDDGEEEEEGDQSDLAAI 112
+IE+ +RE E EE+LKEY E+ ++K +K ++EE +L +
Sbjct: 64 EEIEEELRE--EYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLEL 119
>gnl|CDD|221049 pfam11262, Tho2, Transcription factor/nuclear export subunit
protein 2. THO and TREX form a eukaryotic complex
which functions in messenger ribonucleoprotein
metabolism and plays a role in preventing the
transcription-associated genetic instability. Tho2,
along with four other subunits forms THO.
Length = 296
Score = 29.2 bits (66), Expect = 0.52
Identities = 12/45 (26%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDY-DIEQRMRELKEEEEKLKE 82
E L++ K D + ++KKK+ ++ +++L+EE +K E
Sbjct: 32 EIERLEKQIKELDSSSSGIDKKKKEKKRLKSLIKKLEEELKKHIE 76
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 28.9 bits (64), Expect = 0.64
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQK--KKDYDIEQRMRELKEEE--EKLKEYRRERRKEKKRK 94
E S +R N ++ Q ++ + + K+E+ KL+EY +E + E+K+
Sbjct: 161 ENQSFQPWPERLHNNVEELLQSSLSLGGSVQVKAPKPKQEQLLSKLQEYLQEHKTEEKQP 220
Query: 95 LDDGEEEEE 103
++ EEEE
Sbjct: 221 QEEQEEEEV 229
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 29.0 bits (65), Expect = 0.69
Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 41 SSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEE 100
+S D++KK F KY K + KE EEK KE E + L D ++
Sbjct: 16 ASDDEIKKAFRKLAIKYHPDKNKGN--------KEAEEKFKEI-----NEAYQVLSDPQK 62
Query: 101 EEEGDQSDLAAIMGFSGFGGG 121
+ + DQ A G GFG G
Sbjct: 63 KAQYDQFGTADFNGAGGFGSG 83
>gnl|CDD|193580 cd09891, NGN_Bact_1, Bacterial N-Utilization Substance G (NusG)
N-terminal (NGN) domain, subgroup 1. The N-Utilization
Substance G (NusG) protein is involved in transcription
elongation and termination in bacteria. NusG is
essential in Escherichia coli and associates with RNA
polymerase elongation and Rho-termination. Homologs of
the NusG gene exist in all bacteria. The NusG
N-terminal domain (NGN) is similar in all NusG
homologs, but its C-terminal domain and the linker that
separates these two domains are different. The domain
organization of NusG suggests that the common
properties of NusG and its homologs are due to their
similar NGN domains.
Length = 107
Score = 27.8 bits (63), Expect = 0.73
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 57 YEQKKKDYDIEQRMRELKEEE---------EKLKEYRRERRKEKKRKL 95
YE K K+ +E+R+ E+ E++ E + ++K K+RKL
Sbjct: 11 YENKVKEN-LEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKL 57
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 28.6 bits (65), Expect = 0.74
Identities = 11/29 (37%), Positives = 21/29 (72%)
Query: 66 IEQRMRELKEEEEKLKEYRRERRKEKKRK 94
I +R+ +LK+E EK+++ R +R+ +KR
Sbjct: 159 IRERIAQLKKELEKVEKQRERQRRRRKRA 187
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.9 bits (65), Expect = 0.75
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 37 RVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLK--EYRRERRKEKKRK 94
+ + +VKKR + + ++KKK R ++ K ++ + R R+ +K+K
Sbjct: 1301 KPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKK 1360
Query: 95 LDDGEEEEEGDQSD 108
D E+++ + D
Sbjct: 1361 SDSSSEDDDDSEVD 1374
>gnl|CDD|217838 pfam04004, Leo1, Leo1-like protein. Members of this family are
part of the Paf1/RNA polymerase II complex. The Paf1
complex probably functions during the elongation phase
of transcription. The Leo1 subunit of the yeast
Paf1-complex binds RNA and contributes to complex
recruitment. The subunit acts by co-ordinating
co-transcriptional chromain modifications and helping
recruitment of mRNA 3prime-end processing factors.
Length = 312
Score = 28.7 bits (64), Expect = 0.80
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 62 KDYDIEQRMRELKEEEEKLKEYRRE--RRKEKKRKLDDGEEEEEGDQSDLAAIMGFS 116
KD + E+R RE K+EE+KL+ RR R K K + + D + A +S
Sbjct: 233 KDPEHEKRERE-KKEEQKLRARRRRQNREKMKNKPPNRPGHGSGSDSNVAKAATTYS 288
>gnl|CDD|111006 pfam02064, MAS20, MAS20 protein import receptor.
Length = 184
Score = 28.5 bits (63), Expect = 0.80
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 50 FDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
FD ++ + +K + QR +E + EE+ E+ +E + +K R+ D E E+G SD
Sbjct: 29 FDYKRRNDPEFRKQ--LRQRAKEQAKMEEEAAEHAKEAKLQKIREFLDMEAAEDGFPSD 85
>gnl|CDD|234241 TIGR03517, GldM_gliding, gliding motility-associated protein GldM.
This protein family, GldM, is named for the member from
Flavobacterium johnsoniae, which is required for a type
of rapid gliding motility found in certain members of
the Bacteriodetes. However, members are found also in
several members of the Bacteriodetes that appear not to
be motile. The best conserved region, toward the
N-terminus, is centered on a highly hydrobobic probable
transmembrane helix. Two paralogs are found in Cytophaga
hutchinsonii.
Length = 523
Score = 28.6 bits (64), Expect = 0.81
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 52 MNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEE----EEGDQS 107
+NK + KD + ++++ + + L +Y + ++E RK D +E+ ++
Sbjct: 61 LNKAVAKAPGKDKAWSESAQKVRTKSDSLMDYMNDLKEEIIRKADGEKEDGGPKGAKEKD 120
Query: 108 DLAAIM-GFSGFGGGK 122
DL A+M G G GK
Sbjct: 121 DLEAVMVGTLGPINGK 136
>gnl|CDD|216652 pfam01698, FLO_LFY, Floricaula / Leafy protein. This family
consists of various plant development proteins which are
homologues of floricaula (FLO) and Leafy (LFY) proteins
which are floral meristem identity proteins. Mutations
in the sequences of these proteins affect flower and
leaf development.
Length = 382
Score = 28.4 bits (64), Expect = 0.90
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 70 MRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
+ + EK K+ +++RRK K +D +++E+ D
Sbjct: 174 VPGHSSDSEKKKQRKKQRRKRSKELREDDDDDEDEDDDG 212
>gnl|CDD|225962 COG3428, COG3428, Predicted membrane protein [Function unknown].
Length = 494
Score = 28.6 bits (64), Expect = 0.90
Identities = 8/49 (16%), Positives = 14/49 (28%), Gaps = 5/49 (10%)
Query: 74 KEEEEKLKEYRRERRKEKKRK-LDD----GEEEEEGDQSDLAAIMGFSG 117
E ++E R ++ + D E QS + G
Sbjct: 136 FELAALVREARVKKLDALELAEADTPEEEVAEVLARSQSSVLRYPMNKG 184
>gnl|CDD|153281 cd07597, BAR_SNX8, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 8. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX8 and the yeast counterpart Mvp1p
are involved in sorting and delivery of late-Golgi
proteins, such as carboxypeptidase Y, to vacuoles. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 246
Score = 28.0 bits (63), Expect = 0.97
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 9/49 (18%)
Query: 37 RVERSSLDQV---KKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKE 82
R E+ SL+ + KR ++NKKK E + D++ E +KL+
Sbjct: 138 RHEKLSLNNIQRLLKRIELNKKKLESLRAKPDVKG------AEVDKLEA 180
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 28.2 bits (64), Expect = 1.1
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 66 IEQRMRELKEEEEKLKEYRRERRKEKKR 93
I +R+ +L++E EK+K+ R +R +KR
Sbjct: 11 IRERIAKLRKELEKVKKQRELQRARRKR 38
>gnl|CDD|218351 pfam04961, FTCD_C, Formiminotransferase-cyclodeaminase. Members
of this family are thought to be Formiminotransferase-
cyclodeaminase enzymes EC:4.3.1.4. This domain is found
in the C-terminus of the bifunctional animal members of
the family.
Length = 176
Score = 27.9 bits (63), Expect = 1.1
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 6/34 (17%)
Query: 49 RFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKE 82
+ KKKYE D+E+ M+E+ E+ E+L+E
Sbjct: 39 NLTIGKKKYE------DVEEEMKEILEKAEELRE 66
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 27.9 bits (62), Expect = 1.4
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 13/62 (20%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKL--KEYRRERRKEKKRKLDDGEEEEEGDQSD 108
M++ +E D+ +E++ REL EKL +E RER+ E++R+ EEE+ ++D
Sbjct: 240 GMDEHSFE----DFLLEEKRREL----EKLAKEEAERERQAEEQRRR---EEEKAAMEAD 288
Query: 109 LA 110
A
Sbjct: 289 RA 290
>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 = 27.2 bits (61), Expect = 1.5
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 7/82 (8%)
Query: 13 VKDSINFLDHINGKKHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRE 72
VK SI IN K+ QR ++ S K K ++E+ K++ ++R +E
Sbjct: 55 VKVSIKKQKKINPKRLQRQAAKEVKKPGIS----TKAQQALKLEHERNKQEK--KKRSKE 108
Query: 73 LKEEEEKLK-EYRRERRKEKKR 93
KEEE++ K + +++++K K R
Sbjct: 109 KKEEEKERKRQLKQQKKKAKHR 130
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 27.9 bits (62), Expect = 1.6
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 61 KKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQ 106
K + ++ R +E++ +L++ +RE K+R L D EE E
Sbjct: 17 KGRFSADELRRRREEQQVELRKQKREELLNKRRNLADVSEEAESSF 62
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 27.7 bits (62), Expect = 1.7
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
+ + +K++ I R+ +LKEE E+ +E E ++ ++
Sbjct: 61 LLKLEVARKKERLNQIRARISQLKEEIEQKRERIEELKRALAQR 104
>gnl|CDD|184042 PRK13415, PRK13415, flagella biosynthesis protein FliZ;
Provisional.
Length = 219
Score = 27.4 bits (61), Expect = 1.9
Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 4/91 (4%)
Query: 13 VKDSINFLDHINGKKHQRNLGMSMRVER--SSLDQVKKRFDMNKKKYEQKKKDYDIEQRM 70
V +SI L I +K + ++ ER S + + + + + K+
Sbjct: 130 VGESIQLLKEIEDEK-EIEEILAQHEERLESKAEWSRWGQKLRDQWKGKSKQKQTTLPSF 188
Query: 71 RE-LKEEEEKLKEYRRERRKEKKRKLDDGEE 100
LKEE ++LKE R E K K+K +E
Sbjct: 189 SALLKEELKELKEKRSEGLKRLKKKGTAHDE 219
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 27.7 bits (61), Expect = 1.9
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 58 EQKKKDYDIEQRMRELKEEEEKLKE---YRRERRKEKKRKLDDGEEEEEGDQSDLAAIMG 114
E KKK E+R + L+EEE++ K+ R+ R +E+KR+L + E + ++ +
Sbjct: 218 ELKKKR---EERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVP 274
Query: 115 FSGFGGGKK 123
G KK
Sbjct: 275 EDGLSEDKK 283
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 27.3 bits (60), Expect = 1.9
Identities = 28/95 (29%), Positives = 53/95 (55%), Gaps = 14/95 (14%)
Query: 23 INGKKHQRNLGMSMRVERSSLDQVKKRFDMNKKKY---------EQKKKDYDIEQRMREL 73
IN + + +++R+ R L VKK D+ KKK + +++ ++E+RM E
Sbjct: 88 INRAAYDTGVPLAIRI-RDQLRSVKKD-DIKKKKSLIIRQEQIEKARQEREELEERM-EW 144
Query: 74 KEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
+ EEK+ E RE ++E++R+ ++ EE+ D S+
Sbjct: 145 ERREEKIDE--REDQEEQEREREEQTIEEQSDDSE 177
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 27.6 bits (62), Expect = 1.9
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 45 QVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
+V ++ D +++ E+K I + E ++EE + K + E++KE++ EE
Sbjct: 256 EVLRKVDKTREEEEEK-----ILKAAEEERQEEAQEK--KEEKKKEEREAKLAKLSPEE 307
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 27.5 bits (61), Expect = 1.9
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 50 FDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK-----EKKRKLDDGEEEEEG 104
F++ + + + +++ + +QR + E E K KE ++R+ ++ R+LD E + +
Sbjct: 3 FELRRAREKLEREQRERKQRAKLKLERERKAKEEAAKQREAIEAAQRSRRLDAIEAQIKA 62
Query: 105 DQ 106
DQ
Sbjct: 63 DQ 64
>gnl|CDD|118668 pfam10140, YukC, WXG100 protein secretion system (Wss), protein
YukC. Members of this family of proteins include
predicted membrane proteins homologous to YukC in B.
subtilis. The YukC protein family would participate to
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria, the
WXG100 protein secretion system (Wss). This family
includes EssB in Staphylococcus aureus.
Length = 359
Score = 27.6 bits (62), Expect = 1.9
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 55 KKYEQKKKDYDI--EQRMRELKEEEEKLKEYRRER 87
K EQ K D D+ ++R +L E E++L EY +ER
Sbjct: 325 KYREQVKNDDDLSGDERQEKLDELEDELDEYWKER 359
>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the
first step in fucose metabolism, and has been
characterized in Escherichia coli and Bacteroides
thetaiotaomicron [Energy metabolism, Sugars].
Length = 587
Score = 27.6 bits (61), Expect = 2.1
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 9/70 (12%)
Query: 34 MSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKR 93
+ MR E + ++++R D +K YD E+ L ++ K E KE +R
Sbjct: 198 LGMRNEAVDMTEIRRRID---------QKIYDEEELEMALAWADKYCKYGEDENNKEYQR 248
Query: 94 KLDDGEEEEE 103
+ E
Sbjct: 249 NAEQSRAVWE 258
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 27.6 bits (62), Expect = 2.1
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 54 KKKYEQKKKDYDIE--QRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLA 110
K++ + + + + E +R EL+ E +L + R E K LD EE E + +L+
Sbjct: 57 KEEVHKLRAELERELKERRNELQRLERRLLQ-REETLDRKMESLDKKEENLEKKEKELS 114
Score = 26.8 bits (60), Expect = 3.3
Identities = 15/47 (31%), Positives = 31/47 (65%)
Query: 47 KKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKR 93
+K ++KK+ +KK+ ++ + + L E+EE+L+E E+R+E +R
Sbjct: 94 RKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELER 140
>gnl|CDD|148701 pfam07246, Phlebovirus_NSM, Phlebovirus nonstructural protein NS-M.
This family consists of several Phlebovirus
nonstructural NS-M proteins which represent the
N-terminal region of the M polyprotein precursor. The
function of this family is unknown.
Length = 264
Score = 27.2 bits (59), Expect = 2.2
Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 28 HQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRER 87
RN+ + R +++KK + ++K K+ + + R + E ++ K ++
Sbjct: 128 FIRNITTGEQSPRVDYEKLKKNAEEKDATIQRKTKEMEEDSRNQIAHHEIQQKKNEIQKL 187
Query: 88 RKEKKRKLDDGEEEEEGDQ 106
R + KR G+E +
Sbjct: 188 RNDLKR----GQEHRDAKL 202
>gnl|CDD|220535 pfam10037, MRP-S27, Mitochondrial 28S ribosomal protein S27.
Members of this family of small ribosomal proteins
possess one of three conserved blocks of sequence found
in proteins that stimulate the dissociation of guanine
nucleotides from G-proteins, leaving open the
possibility that MRP-S27 might be a functional partner
of GTP-binding ribosomal proteins.
Length = 417
Score = 27.4 bits (61), Expect = 2.2
Identities = 11/44 (25%), Positives = 25/44 (56%)
Query: 60 KKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
+++ IE+ EL E+ ++L + + ++K+KL + +EE
Sbjct: 365 EERLPTIEKEDLELYEQRQQLWFFENRKLWQRKKKLREQADEEY 408
>gnl|CDD|221489 pfam12252, SidE, Dot/Icm substrate protein. This family of proteins
is found in bacteria. Proteins in this family are
typically between 397 and 1543 amino acids in length.
This family is the SidE protein in the Dot/Icm pathway of
Legionella pneumophila bacteria. There is little
literature describing the family.
Length = 1443
Score = 27.5 bits (61), Expect = 2.3
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 40 RSSLDQVK-KRFDMNKKKYEQK-------KKDYDIEQRMRELKEEEEKLKEYRRERRK 89
RSSL+Q+K K F+M +K+ +Q +K D +L+E+ KLK+ ++K
Sbjct: 1266 RSSLNQMKPKTFEMQEKEIQQNFELLAKLEKTLDKSDTAEKLREDIPKLKDLLIAKQK 1323
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 27.2 bits (61), Expect = 2.3
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 83 YRR--ERRKEKKRKLDDGEEEEEGDQSDLAAI 112
YRR +R+ ++ +G E E L +
Sbjct: 748 YRRALAKRQNLVKEGAEGAEPVEEPTLALEQV 779
>gnl|CDD|146486 pfam03879, Cgr1, Cgr1 family. Members of this family are
coiled-coil proteins that are involved in pre-rRNA
processing.
Length = 105
Score = 26.6 bits (59), Expect = 2.4
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
+K+ E++ + I+ R +ELK+E+E ++ R + KE++ ++ E E+
Sbjct: 31 EKRMEKRLEQQAIKAREKELKDEKEAERQRRIQAIKERRAAKEEKERYEK 80
>gnl|CDD|112836 pfam04037, DUF382, Domain of unknown function (DUF382). This
domain is specific to the human splicing factor 3b
subunit 2 and it's orthologues. Splicing factor 3b
subunit 2 or SAP145 is a suppressor of U2 snRNA
mutations. Pre-mRNA splicing is catalyzed by a large
ribonucleoprotein complex called the spliceosome.
Spliceosomes are multi-component enzymes that catalyze
pre-mRNA splicing and form step-wise by the ordered
interaction of UsnRNPs and non-snRNP proteins with
short conserved regions of the pre-mRNA at the 5' and
3' splice sites and branch site.
Length = 129
Score = 26.8 bits (60), Expect = 2.4
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 45 QVKKRFDMNKKKYEQKK-------KDYDIEQRMREL---KEEEEKLKEYRRERRKEKKRK 94
K+++ K+ E+ + I + MR+ KE E+ LK+ +RER + K K
Sbjct: 37 SQKRKYLSGKRGIEKPPFELPDFIEATGIAE-MRDALLEKEAEKTLKQKQRERVQPKMGK 95
Query: 95 LD 96
LD
Sbjct: 96 LD 97
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly
related to archaeal Holliday junction resolvase
[Nucleotide transport and metabolism].
Length = 175
Score = 27.0 bits (60), Expect = 2.4
Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 39 ERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRE---LKEEEEKLKEYRRERRKEKKR 93
R+ + ++ + + ++ E+ + + E+ + E KEEE KLKE+ ++ +E +
Sbjct: 20 LRAYIRSLQGKVESKARELEETLQKAERERLVNEAQARKEEEWKLKEWIEKKIEEARE 77
>gnl|CDD|227666 COG5374, COG5374, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 27.1 bits (60), Expect = 2.5
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKE 82
+K E+ K D +RE ++E K+
Sbjct: 163 QKNQEELFKLLDKYNELREQVQKESSKKK 191
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 27.0 bits (60), Expect = 2.6
Identities = 12/50 (24%), Positives = 33/50 (66%)
Query: 57 YEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQ 106
E KKK ++ + + ++K+E E+ ++++ +++K KK+K D +++++
Sbjct: 58 TEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKD 107
>gnl|CDD|148285 pfam06584, DIRP, DIRP. DIRP (Domain in Rb-related Pathway) is
postulated to be involved in the Rb-related pathway,
which is encoded by multiple eukaryotic genomes and is
present in proteins including lin-9 of Caenorhabditis
elegans, aly of fruit fly and mustard weed. Studies of
lin-9 and aly of fruit fly proteins containing DIRP
suggest that this domain might be involved in
development. Aly, lin-9, act in parallel to, or
downstream of, activation of MAPK by the RTK-Ras
signalling pathway.
Length = 109
Score = 26.5 bits (59), Expect = 2.6
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 73 LKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
LKEE EKL+ R + R+ ++ KL E
Sbjct: 54 LKEEREKLERKREKIRQLQQLKLHYKELNVG 84
>gnl|CDD|197850 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 26.2 bits (58), Expect = 2.9
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
+ E+K + +E ++ + E++KE RR ++K +RKL G
Sbjct: 16 AENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPG 60
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 27.1 bits (60), Expect = 3.0
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 59 QKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
+ +D D + E + EE+ +E +E+RK K+ ++D +E+EE
Sbjct: 266 DEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEE 310
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 27.1 bits (60), Expect = 3.0
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 46 VKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKE 82
K D++ +KK D+E ++ +E LK+
Sbjct: 221 AKTDRDVSTSTAASQKKSSDLESKLEAQSKELWSLKD 257
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 27.2 bits (60), Expect = 3.0
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 34 MSMRVERSSLDQVKKRF-DMNKKKYEQKKKDYDIEQRM----RELKEEEEKLKEYRRERR 88
M+M L QV+KR + KK+ E+ +++Y + ++M +EL E ++ E +R
Sbjct: 197 MAMMESEIDLLQVEKRIRNRVKKQMEKSQREYYLNEQMKAIQKELGEMDDAPDENEALKR 256
Query: 89 K-EKKRKLDDGEEEEEGDQSDL 109
K + + + +E+ E + L
Sbjct: 257 KIDAAKMPKEAKEKAEAELQKL 278
>gnl|CDD|149875 pfam08941, USP8_interact, USP8 interacting. This domain
interacts with the UBP deubiquitinating enzyme USP8.
Length = 179
Score = 26.7 bits (59), Expect = 3.1
Identities = 14/38 (36%), Positives = 17/38 (44%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERR 88
D + E K D E ++ E K E E LK Y R R
Sbjct: 8 DQATEIAELKHTQVDHEIQINEQKRELELLKYYIRALR 45
>gnl|CDD|188441 TIGR03926, T7_EssB, type VII secretion protein EssB. Members of
this family are associated with type VII secretion of
WXG100 family targets in the Firmicutes, but not in the
Actinobacteria. This protein is designated YukC in
Bacillus subtilis and EssB is Staphylococcus aureus
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 377
Score = 26.9 bits (60), Expect = 3.3
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 55 KKYEQKKKDYDI--EQRMRELKEEEEKLKEYRRE 86
K EQ K D D+ ++R +L E E++L EY ++
Sbjct: 344 KYREQVKNDTDLSGDERQEKLDELEKELDEYLKK 377
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 26.9 bits (60), Expect = 3.3
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 36 MRVERSSLDQVKKRF-----DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKE 90
+ S +++++ + + K K ++K K +I++ ++ELKEE +L + E
Sbjct: 39 RKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALEAE 98
Query: 91 KKRKL 95
+ KL
Sbjct: 99 LQDKL 103
>gnl|CDD|222366 pfam13764, E3_UbLigase_R4, E3 ubiquitin-protein ligase UBR4. This
is a family of E## ubiquitin ligase enzymes.
Length = 794
Score = 26.9 bits (60), Expect = 3.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 67 EQRMRELKEEE---EKLKEYRRERRKEKKRK 94
E + L E+E +K+ E R E R EK+R
Sbjct: 394 ENLLETLAEKEGVAKKIDEVRDETRAEKRRL 424
>gnl|CDD|215532 PLN02982, PLN02982, galactinol-raffinose
galactosyltransferase/ghydrolase, hydrolyzing O-glycosyl
compounds.
Length = 865
Score = 27.1 bits (60), Expect = 3.4
Identities = 32/132 (24%), Positives = 51/132 (38%), Gaps = 34/132 (25%)
Query: 16 SINFLDHINGKKHQRNL---GMSMRVERSSLDQVKK---------------RFDMNKKK- 56
SINF D N + +NL G M D+ +K FD K K
Sbjct: 266 SINF-DGDNPNEDAKNLVLGGTQMTARLYRFDECEKFRNYKGGSMLGPDPPHFDPKKPKM 324
Query: 57 ---------YEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQS 107
+ +K + IE + +L E + K+K+ ++E + DGEE+ +S
Sbjct: 325 LIYKAIEREHAEKARKKAIESGVTDLSEFDAKIKQLKKEL-----DAMFDGEEKSVSSES 379
Query: 108 DLAAIMGFSGFG 119
+ + SG G
Sbjct: 380 ESSGSCKVSGSG 391
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 27.0 bits (60), Expect = 3.4
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 47 KKRFDMN--KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKR 93
K+ N K E K D E+ ++ K+E++K +EY+RE EK R
Sbjct: 721 MKKIFRNWNGKDAEFKISDSVEEKTKKKKKKEKKKEEEYKRE---EKAR 766
Score = 25.8 bits (57), Expect = 9.1
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 64 YDIEQRMREL------KEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
+DI M+++ K+ E K+ + E+ K+KK+K EEE +
Sbjct: 715 FDISGLMKKIFRNWNGKDAEFKISDSVEEKTKKKKKKEKKKEEEYK 760
>gnl|CDD|234350 TIGR03766, TIGR03766, conserved hypothetical integral membrane
protein. Models TIGR03110, TIGR03111, and TIGR03112
describe a three-gene system found in several
Gram-positive bacteria, where TIGR03110 (XrtG) is
distantly related to a putative transpeptidase,
exosortase (TIGR02602). This model describes a small
clade that correlates by both gene clustering and
phyletic pattern, although imperfectly, to the three
gene system. Both this narrow clade, and the larger set
of full-length homologous integral membrane proteins,
have an especially well-conserved region near the
C-terminus with an invariant tyrosine. The function is
unknown.
Length = 483
Score = 26.9 bits (60), Expect = 3.5
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKE 75
+ +K Y I++ R LKE
Sbjct: 325 ATLSLPTKAEKNKYSIKEIKRRLKE 349
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 26.9 bits (59), Expect = 3.6
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 75 EEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
EEEK ++ R+RRK KK D ++ E + SD
Sbjct: 128 VEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVSD 161
>gnl|CDD|216096 pfam00749, tRNA-synt_1c, tRNA synthetases class I (E and Q),
catalytic domain. Other tRNA synthetase sub-families
are too dissimilar to be included. This family includes
only glutamyl and glutaminyl tRNA synthetases. In some
organisms, a single glutamyl-tRNA synthetase
aminoacylates both tRNA(Glu) and tRNA(Gln).
Length = 314
Score = 26.5 bits (59), Expect = 3.6
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 48 KRFDMNKKKYEQKKK------DYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEE 101
RFD+ K E+ + + + + E +EE+E L R R E+ +L EEE
Sbjct: 76 DRFDIYYKYAEELIEKGLAYVCFCTPEELEEEREEQEALGSPERPRYDEECLRL--FEEE 133
Query: 102 EE 103
Sbjct: 134 MR 135
>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 = 26.6 bits (59), Expect = 3.6
Identities = 18/56 (32%), Positives = 26/56 (46%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDL 109
K K + + E +L E+KLKE E E+ K ++ EEEEE + D
Sbjct: 134 KFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDF 189
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 26.8 bits (60), Expect = 3.7
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 58 EQKKKDYD--IEQRMRELKEEEEKLKEYRRERRKEKKRK 94
E + + I +R+ +LK E E +++ R RRK++ R
Sbjct: 152 ETQLETDRRRIRRRIAKLKRELENVEKAREPRRKKRSRS 190
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 26.8 bits (59), Expect = 3.7
Identities = 15/54 (27%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 58 EQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAA 111
E K K ++R+++L E+E+LK ++++ E+ K E++++ +Q+ AA
Sbjct: 91 ELKPKQAAEQERLKQL--EKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAA 142
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 26.6 bits (58), Expect = 3.8
Identities = 13/65 (20%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 34 MSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMREL-KEEEEKLKEYRRERRKEKK 92
+S R+E + +++ ++ + +++ KD + ++RM L + +EE++ + +ER + +
Sbjct: 999 VSRRIELPVPPECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEEIGKKEKEREQRIR 1058
Query: 93 RKLDD 97
+ + D
Sbjct: 1059 KTIHD 1063
Score = 25.9 bits (56), Expect = 8.6
Identities = 12/82 (14%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 22 HINGKKHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLK 81
R + + +++ S+ V +R ++ + ++ ++I+ R+ + + ++++ K
Sbjct: 975 AEEDYSLPREIESKLPLDKRSIAVVSRRIELPVP--PECREKHEIKDRIVKERIKDQEEK 1032
Query: 82 EYRRERRKEKKRKLDDGEEEEE 103
E ++ K+ ++ E+E E
Sbjct: 1033 ERMESLQRAKEEEIGKKEKERE 1054
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 26.3 bits (59), Expect = 3.9
Identities = 19/38 (50%), Positives = 24/38 (63%), Gaps = 7/38 (18%)
Query: 72 ELKEEE-EKLKEYRRERRKEKKRKLDDGEEEEEGDQSD 108
ELK E EK RRERR+E + KL+ E +EEGD +
Sbjct: 86 ELKSGELEK----RRERREEAEEKLE--EAKEEGDAEE 117
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 26.7 bits (59), Expect = 4.0
Identities = 7/38 (18%), Positives = 20/38 (52%)
Query: 65 DIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEE 102
+I++ K E + K+ ++R+ +R+++ +E
Sbjct: 331 EIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQE 368
>gnl|CDD|172594 PRK14104, PRK14104, chaperonin GroEL; Provisional.
Length = 546
Score = 26.5 bits (58), Expect = 4.1
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 62 KDYDIEQRMRELKEE-EEKLKEYRRERRKEKKRKLDDG 98
K DIE R+ ++K + EE +Y RE+ +E+ KL G
Sbjct: 338 KKADIEARVAQIKAQIEETTSDYDREKLQERLAKLAGG 375
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 26.8 bits (59), Expect = 4.2
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 47 KKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE--- 103
KK+ + K+ E KK ++ +L+ ++ ++ ++K RK D +E E
Sbjct: 21 KKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRDVEDENPEDFI 80
Query: 104 ------GDQSDLAAIM 113
G + L++ M
Sbjct: 81 DPDTPFGQKKRLSSQM 96
>gnl|CDD|237147 PRK12586, PRK12586, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 145
Score = 25.9 bits (57), Expect = 4.8
Identities = 7/39 (17%), Positives = 13/39 (33%)
Query: 52 MNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKE 90
M +K + + E + + R E RK+
Sbjct: 102 MYRKNDAHTHASILLSSNEQNSTEALQLRAKKREEHRKK 140
>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 = 26.0 bits (58), Expect = 4.8
Identities = 5/54 (9%), Positives = 19/54 (35%), Gaps = 3/54 (5%)
Query: 43 LDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLD 96
+ +Y+++K Y +EL+ + ++ + + + +
Sbjct: 65 AAAPRAELQAKIARYKKEKARY--RSEAKELEAKAKEAEA-ESDHALHQHHRFA 115
>gnl|CDD|178195 PLN02583, PLN02583, cinnamoyl-CoA reductase.
Length = 297
Score = 26.2 bits (58), Expect = 4.9
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 59 QKKKDYDIEQRMRELKEEEEKLKEYR 84
QK + +IE+ +R L EEE+LK +
Sbjct: 38 QKNGETEIEKEIRGLSCEEERLKVFD 63
>gnl|CDD|219627 pfam07897, DUF1675, Protein of unknown function (DUF1675). The
members of this family are sequences derived from
hypothetical plant proteins of unknown function. One
member of this family is annotated as a putative
RNA-binding protein, but no evidence was found to
support this.
Length = 283
Score = 26.1 bits (57), Expect = 5.0
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 71 RELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAAIMGFSGFGGGKKK 124
E +EE K KE + RR E KRK + E + D+ +I +G G G+ K
Sbjct: 66 VETEEEWRKRKEMQSLRRLEAKRKRSEKEYNGVSNGDDMDSINAANGGGSGRDK 119
>gnl|CDD|152107 pfam11671, Apis_Csd, Complementary sex determiner protein. This
family of proteins represents the complementary sex
determiner in the honeybee. In the honeybee, the
mechanism of sex determination depends on the csd gene
which produces an SR-type protein. Males are homozygous
while females are homozygous for the csd gene.
Heterozygosity generates an active protein which
initiates female development.
Length = 146
Score = 25.8 bits (56), Expect = 5.0
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 58 EQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKL 95
E+++K Y E RE +E + R ER + ++ K+
Sbjct: 11 EREQKSYKNENSYREYRETSRERSRDRTERERSREHKI 48
>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812). This is
a family of fungal proteins whose function is not known.
Length = 126
Score = 25.7 bits (57), Expect = 5.0
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK 89
+++++ Q+ +D + + E K + E+ KE RE++K
Sbjct: 88 EIDERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126
>gnl|CDD|217360 pfam03087, DUF241, Arabidopsis protein of unknown function. This
family represents a number of Arabidopsis proteins.
Their functions are unknown.
Length = 230
Score = 26.2 bits (58), Expect = 5.1
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 35 SMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRR 85
S+R E S LD+ K+R + K K+ ++E + EL++E E L +RR
Sbjct: 173 SIRSELSRLDEEKRRDNEEVKD--ILKRLEELENSIEELEDELESL--FRR 219
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 26.4 bits (59), Expect = 5.3
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 55 KKYEQKKKDYDIE----QRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEE 101
KK ++ + + E + +RE+KEE E++++ R +E K EE
Sbjct: 198 KKLGFERLELEEEGTPSELIREIKEELEEIEKERESLLEELKELAKKYLEE 248
Score = 26.0 bits (58), Expect = 7.3
Identities = 14/52 (26%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 47 KKRFDMNKKKYEQKKKDYD-----IEQRMRELKEEEEKLKEYRRERRKEKKR 93
+++ ++ K E+ KD + IE+ ++EL+EE +L+ +E +E +R
Sbjct: 74 EEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIER 125
>gnl|CDD|218735 pfam05760, IER, Immediate early response protein (IER). This
family consists of several eukaryotic immediate early
response (IER) 2 and 5 proteins. The role of IER5 is
unclear although it play an important role in mediating
the cellular response to mitogenic signals. Again,
little is known about the function of IER2 although it
is thought to play a role in mediating the cellular
responses to a variety of extracellular signals.
Length = 272
Score = 26.0 bits (57), Expect = 5.3
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 84 RRERRKEKKRKL----DDGEEEEEGDQSDLAAIMGFSGFGG 120
+R RR++ + + +D EE E G+ S+L +I G SGF G
Sbjct: 195 KRARREDFEPESGGESEDAEEMETGNISNLISIFG-SGFSG 234
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 26.2 bits (58), Expect = 5.8
Identities = 12/37 (32%), Positives = 25/37 (67%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKE 90
++ E+ KK ++ +R ++ ++ ++EYRRERR+E
Sbjct: 616 RRAIEEWKKRFEERERRQKEEDILRIIEEYRRERRRE 652
>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 = 26.2 bits (58), Expect = 5.9
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 35 SMRVERSSLDQVKKRFDMNKKKYEQKKKDY-----DIEQRMRELKEEEEKLKEYRRERRK 89
++ E SSL +R + + Q+ D +IE+ + +L++EEEKLKE R E +
Sbjct: 685 GLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKE-RLEELE 743
Query: 90 EKKRKLDDGEEEEEGDQSDLAA 111
E L+ E + + +L A
Sbjct: 744 EDLSSLEQEIENVKSELKELEA 765
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 25.9 bits (58), Expect = 6.1
Identities = 4/39 (10%), Positives = 25/39 (64%)
Query: 65 DIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
++++ ++ ++++LK + + ++K++K++ + + +
Sbjct: 51 EMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSK 89
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 26.1 bits (58), Expect = 6.3
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 11/52 (21%)
Query: 43 LDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
+++ KR + K+KY + K K+ EEK + R++++K KK+
Sbjct: 365 KEELNKRIEEIKEKYPKPPK-----------KKREEKKPQKRKKKKKRKKKG 405
>gnl|CDD|235040 PRK02463, PRK02463, OxaA-like protein precursor; Provisional.
Length = 307
Score = 25.8 bits (57), Expect = 6.4
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 54 KKKYEQKKKDY------DIEQRMRELKEEEEKL 80
K Y+ +K Y I +R++ +EEK+
Sbjct: 85 KATYQSEKMAYLKPVFEPINERLKNATTQEEKM 117
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 25.7 bits (57), Expect = 6.6
Identities = 10/39 (25%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 53 NKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEK 91
N YE++ +E R+ +++E E+++ + +++ +KEK
Sbjct: 165 NTGVYEKEDLKERVE-RLEQIEELEKEIAKLKKKLKKEK 202
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 26.0 bits (58), Expect = 6.6
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDL 109
+KK +K++ E++ E+EE K +++ + +K + E + D
Sbjct: 411 RKKLRKKQRK--AEKK----AEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPDP 460
>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 = 25.9 bits (57), Expect = 6.9
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 44 DQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKL 95
+ +K + K EQ+K ++EQ M ELKE E K + +E + L
Sbjct: 526 ELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKAL 577
Score = 25.9 bits (57), Expect = 8.2
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 54 KKKYEQKKKDYD-----IEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
K Y + K++ + + +EL+++ E L++ +E+ K KK + EE +E
Sbjct: 503 KTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKE 557
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 25.8 bits (57), Expect = 7.0
Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKKDYD-IEQRMRELKEEEEKLKEYRRERRKEKKRKLDDG 98
+ L+++++R + K+K E K++ + E + EL++ +L+E + E ++ L++
Sbjct: 315 ENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEEL 374
Query: 99 EEEEEGDQSDLAAIM 113
EE E + +LA +
Sbjct: 375 EELFEALREELAELE 389
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 25.4 bits (56), Expect = 7.1
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 67 EQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
E++ E K E E+ +E E +EKK++ ++ +E EE
Sbjct: 30 ERKKLEEKREGERKEEEELEEEREKKKEEEERKEREE 66
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 25.8 bits (57), Expect = 7.2
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEK-LKEYRRERRKEKKRKLDDGEEE 101
D + KK E +++ + E++ EL ++ E L + + E + E++R LD+ EE
Sbjct: 47 DADTKKREAEQERREYEEKNEELDQQREVLLTKAKEEAQAERQRLLDEAREE 98
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 25.7 bits (56), Expect = 7.3
Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)
Query: 37 RVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEK--LKEYRRERRKEKKRK 94
+ + LD+ + D ++K + + + D ++ K++E K K KE K+
Sbjct: 216 QQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQV 275
Query: 95 LDDGEEEEEGDQ 106
++ + E E Q
Sbjct: 276 AENQKREIEKAQ 287
>gnl|CDD|217701 pfam03732, Retrotrans_gag, Retrotransposon gag protein. Gag or
Capsid-like proteins from LTR retrotransposons. There is
a central motif QGXXEXXXXXFXXLXXH that is common to
Retroviridae gag-proteins, but is poorly conserved.
Length = 97
Score = 25.0 bits (55), Expect = 7.3
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 44 DQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEE 103
D++K F K++ + +E +R L++ E ++EY ER K R+L +EE
Sbjct: 30 DELKDAF---LKRFFPSIRKDLLENELRSLRQGTESVREY-VERFKRLARQLPHHGFDEE 85
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 26.1 bits (57), Expect = 7.4
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 48 KRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKR-----KLDDGEEEE 102
+ M K EQ+K + E R ++++ +E + + KK +L DG EE
Sbjct: 417 TKAQMAKLSKEQRKAYLE-EYDYRVKLLQKKQWREELKRMKMMKKFGKEIGELPDGYSEE 475
Query: 103 EGDQS 107
+++
Sbjct: 476 VDEEN 480
>gnl|CDD|119241 pfam10721, DUF2514, Protein of unknown function (DUF2514). This
family is conserved in bacteria and some viruses. The
function is not known.
Length = 162
Score = 25.5 bits (56), Expect = 7.6
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 57 YEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAAI 112
++QK D D + E+ E R +E++R+ E ++ Q + AA
Sbjct: 30 WQQKWADRDAADALAEVIAE-------TAARAEEQRRQAAQNEAAKDA-QEEAAAA 77
>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p
homolog [Translation, ribosomal structure and
biogenesis].
Length = 395
Score = 25.8 bits (57), Expect = 7.7
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 65 DIEQRMRELKEEEEKL--------KEYRRERRKEKKRKLDDGEEEEEGDQS 107
++E+R+ +LKE+ K + R R +K+K + E G Q+
Sbjct: 345 ELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQN 395
>gnl|CDD|219788 pfam08314, Sec39, Secretory pathway protein Sec39. Mnaimneh et al
identified Sec39p as a protein involved in ER-Golgi
transport in a large scale promoter shut down analysis
of essential yeast genes. Kraynack et al. (2005) showed
that Sec39p (Dsl3p) is required for Golgi-ER retrograde
transport and is part of a very stable protein complex
that also includes Dsl1p (in mammals ZW10), Tip20p
(Rint-1) and the ER localized Q-SNARE proteins Ufe1p
(syntaxin-18), Sec20p and Use1p. This was confirmed in a
genome-wide analysis of protein complexes by Gavin et al
(2006).
Length = 675
Score = 25.9 bits (57), Expect = 8.1
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 22 HINGKKHQRNLGMSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMREL----KEEE 77
+ K + + +RV L + K + N K Y K DI + + E EEE
Sbjct: 499 SLVLKPGEPFKPVQIRVHDDPLSLISKVLEQNPKAYTDLDKLLDILKNLVEAGQPDSEEE 558
Query: 78 EKLKEYRR 85
+ RR
Sbjct: 559 QVETAERR 566
>gnl|CDD|238038 cd00085, HNHc, HNH nucleases; HNH endonuclease signature which is
found in viral, prokaryotic, and eukaryotic proteins.
The alignment includes members of the large group of
homing endonucleases, yeast intron 1 protein, MutS, as
well as bacterial colicins, pyocins, and anaredoxins.
Length = 57
Score = 24.4 bits (53), Expect = 8.1
Identities = 5/26 (19%), Positives = 6/26 (23%)
Query: 3 GYYCNVCDCVVKDSINFLDHINGKKH 28
C C +DHI
Sbjct: 11 DGLCPYCGKPGGTEGLEVDHIIPLSD 36
>gnl|CDD|215349 PLN02647, PLN02647, acyl-CoA thioesterase.
Length = 437
Score = 25.5 bits (56), Expect = 8.1
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 75 EEEEKLKEYRRERRKEKKRKLDDGEEE-EEGDQSDLAAIM 113
EEE+ L E R K +K+K + + E E G+ L A++
Sbjct: 227 EEEKLLFEEAEARNKLRKKKRGEQKREFENGEAERLEALL 266
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 25.6 bits (57), Expect = 8.2
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 62 KDYDIEQRMRELKEE-EEKLKEYRRERRKEKKRKL 95
K +IE+R RE++EE EEK +E + E E+ RK
Sbjct: 40 KAEEIEER-REVREEAEEKYEEAKEEGDLEEARKY 73
>gnl|CDD|217337 pfam03050, DDE_Tnp_IS66, Transposase IS66 family. Transposase
proteins are necessary for efficient DNA transposition.
This family includes IS66 from Agrobacterium
tumefaciens.
Length = 277
Score = 25.6 bits (57), Expect = 8.2
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 68 QRMRELKEEEEKLK----EYRRERRKEKKRKLDDGEEE 101
+R+ EL E + + E R R+E R L D E
Sbjct: 170 RRIGELYAIEREARGLPPEERLALRQEYSRPLLDALEA 207
>gnl|CDD|163506 TIGR03794, NHLM_micro_HlyD, NHLM bacteriocin system secretion
protein. Members of this protein family are homologs of
the HlyD membrane fusion protein of type I secretion
systems. Their occurrence in prokaryotic genomes is
associated with the occurrence of a novel class of
microcin (small bacteriocins) with a leader peptide
region related to nitrile hydratase. We designate the
class of bacteriocin as Nitrile Hydratase Leader
Microcin, or NHLM. This family, therefore, is designated
as NHLM bacteriocin system secretion protein. Some but
not all NHLM-class putative microcins belong to the TOMM
(thiazole/oxazole modified microcin) class as assessed
by the presence of the scaffolding protein and/or
cyclodehydratase in the same gene clusters [Transport
and binding proteins, Amino acids, peptides and amines,
Cellular processes, Biosynthesis of natural products].
Length = 421
Score = 25.6 bits (56), Expect = 8.3
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 49 RFDMNKKKYEQK---KKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKL 95
+ K+ ++ K +E+ + L+EE L ++R R L
Sbjct: 117 NYTGRLKEGRERHFQKSKEALEETIGRLREELAALSREVGKQRGLLSRGL 166
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 25.6 bits (56), Expect = 8.3
Identities = 11/64 (17%), Positives = 24/64 (37%)
Query: 34 MSMRVERSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKR 93
+ +E ++ ++ K E+ K+ IE + E+ E L+ ++ KK
Sbjct: 415 FRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFLRSILKDEEVIKKV 474
Query: 94 KLDD 97
Sbjct: 475 AERP 478
>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
transduction. This family is a four helix bundle that
operates as a ubiquitous sensory module in prokaryotic
signal-transduction. The 4HB_MCP is always found between
two predicted transmembrane helices indicating that it
detects only extracellular signals. In many cases the
domain is associated with a cytoplasmic HAMP domain
suggesting that most proteins carrying the bundle might
share the mechanism of transmembrane signalling which is
well-characterized in E coli chemoreceptors.
Length = 181
Score = 25.3 bits (56), Expect = 8.4
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 41 SSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK 89
+++++ D KKYE+ + ++ E K E+LK YR+ R K
Sbjct: 82 KDIEELRAEIDKLLKKYEKTILTEEEKKLFNEFK---EQLKAYRKVRNK 127
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 25.5 bits (56), Expect = 8.6
Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKE-KKRKLDDG 98
RS ++ ++R + + ++ + + ++R +E K+++ RR R ++D+
Sbjct: 314 RSRVELRRRRVNDVIRPLVREHNNDQLNVKLRNPSTKESKMRDKRRARLDPIDFEEVDED 373
Query: 99 EEEEEGDQSD 108
E+EEE +SD
Sbjct: 374 EDEEEEQRSD 383
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 25.8 bits (57), Expect = 8.7
Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 52 MNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGEEEEEGDQSDLAA 111
++ ++Y + K ++EE ++LK KE K +L + + ++
Sbjct: 453 IDDERYARFLKK------KENIEEEIQRLKSTWLTPSKEVKEELKNHLQSPLKREASGED 506
Query: 112 IMGFSGF 118
++
Sbjct: 507 LLRRPEM 513
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial 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. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 25.8 bits (57), Expect = 8.7
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGE 99
S LD++ + ++K E+ K+ EL+ E +L+E E +E + +L++ E
Sbjct: 329 ESKLDELAEELAELEEKLEELKE---------ELESLEAELEELEAE-LEELESRLEELE 378
Query: 100 EEEEGDQSDLAAI 112
E+ E +S +A +
Sbjct: 379 EQLETLRSKVAQL 391
>gnl|CDD|233229 TIGR00999, 8a0102, Membrane Fusion Protein cluster 2 (function
with RND porters). [Transport and binding proteins,
Other].
Length = 265
Score = 25.5 bits (56), Expect = 8.8
Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 40 RSSLDQVKKRFDMNKKKYEQKKK--------DYDIEQRMRELKEEEEKLK 81
+ L +KR ++ +K YE++KK + E L+E + +++
Sbjct: 22 AAELKVAQKRVELARKTYEREKKLFEQGVIPRQEFESAEYALEEAQAEVQ 71
>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 = 24.9 bits (55), Expect = 8.8
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 62 KDYDIEQRMRELKEEEEKLKEYRRERRKEKKRK 94
KDY EQ +ELK++ ++ ++++K K +K
Sbjct: 26 KDYLEEQEEKELKQKADEGNNSGKKKKKRKAKK 58
>gnl|CDD|227684 COG5397, COG5397, Uncharacterized conserved protein [Function
unknown].
Length = 349
Score = 25.6 bits (56), Expect = 9.3
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 54 KKKYEQKKKDYDIEQRMRELKEEEEKLKEYRRERRK 89
K++Y D +I QR+ K +K+ R RR+
Sbjct: 58 KRRYVGPADDPEIAQRVERHK----AVKDDLRARRR 89
>gnl|CDD|233509 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase,
flippase. This model describes the P-type ATPase
responsible for transporting phospholipids from one
leaflet of bilayer membranes to the other. These ATPases
are found only in eukaryotes.
Length = 1057
Score = 25.4 bits (56), Expect = 9.3
Identities = 8/32 (25%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 51 DMNKKKYEQKKKDYDIEQRMRELKEEEEKLKE 82
++++++YE+ ++Y+ L + EEKL
Sbjct: 582 ELSEEEYEEWNEEYNEASTA--LTDREEKLDV 611
>gnl|CDD|131739 TIGR02692, tRNA_CCA_actino, tRNA adenylyltransferase. The enzyme
tRNA adenylyltransferase, also called
tRNA-nucleotidyltransferase and CCA-adding enzyme, can
add or repair the required CCA triplet at the 3'-end of
tRNA molecules. Genes encoding tRNA include the CCA tail
in some but not all bacteria, and this enzyme may be
required for viability. Members of this family represent
a distinct clade within the larger family pfam01743
(tRNA nucleotidyltransferase/poly(A) polymerase family
protein). The example from Streptomyces coelicolor was
shown to act as a CCA-adding enzyme and not as a poly(A)
polymerase [Protein synthesis, tRNA and rRNA base
modification].
Length = 466
Score = 25.5 bits (56), Expect = 9.4
Identities = 10/27 (37%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 53 NKKKYEQKKKDYD-IEQRMRELKEEEE 78
NK+K + + YD +E+R+ EL +E+
Sbjct: 384 NKRKAARLQAAYDDLEERIAELAAQED 410
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 25.4 bits (56), Expect = 9.7
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 65 DIEQRMRELKEEEEKLKEYRR 85
DI +M +L + E L EY+R
Sbjct: 284 DIYCKMCDLNFDGELLLEYKR 304
>gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6. RNA
polymerases catalyze the DNA dependent polymerisation
of RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 6, represents a mobile module of the RNA
polymerase. Domain 6 forms part of the shelf module.
This family appears to be specific to the largest
subunit of RNA polymerase II.
Length = 187
Score = 25.1 bits (56), Expect = 9.7
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 9/58 (15%)
Query: 49 RFDMNKKKYEQKKK--DYDIEQRMR-------ELKEEEEKLKEYRRERRKEKKRKLDD 97
R D+ D D+ + + L EE E+L E RR R+E D
Sbjct: 26 RVDLMDPDEGFLPGVLDEDVVKELLGDAEVQKLLDEEYEQLLEDRRLLREEIFPDGDS 83
>gnl|CDD|131941 TIGR02895, spore_sigI, RNA polymerase sigma-I factor. Members of
this sigma factor protein family are strictly limited to
endospore-forming species in the Firmicutes lineage of
bacteria, but are not universally present among such
species. Sigma-I was shown to be induced by heat shock
(PMID:11157964) in Bacillus subtilis and is suggested by
its phylogenetic profile to be connected to the program
of sporulation (PMID:16311624) [Transcription,
Transcription factors, Cellular processes, Sporulation
and germination].
Length = 218
Score = 25.1 bits (55), Expect = 9.8
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 52 MNKKKYEQKKKDYDIEQRMRELKEEEEKLKEY 83
K E+ + + + E R E+ E ++ LK++
Sbjct: 102 EFNKSMEEYRNEIENENRRLEILEYKKLLKQF 133
>gnl|CDD|219589 pfam07808, RED_N, RED-like protein N-terminal region. This
family contains sequences that are similar to the
N-terminal region of Red protein. This and related
proteins contain a RED repeat which consists of a
number of RE and RD sequence elements. The region in
question has several conserved NLS sequences and a
putative trimeric coiled-coil region, suggesting that
these proteins are expressed in the nucleus. The
function of Red protein is unknown, but efficient
sequestration to nuclear bodies suggests that its
expression may be tightly regulated of that the protein
self-aggregates extremely efficiently.
Length = 238
Score = 25.2 bits (55), Expect = 9.9
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 59 QKKKDYDIEQRMRELKEEEEKLKEYRRERRKEKKRKLDDGE 99
+KK Y +Q KE K ++ RERRK + D
Sbjct: 3 KKKYAYLRKQEENAEKEINPKYRDRARERRKGINKDYDPSS 43
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
0.314 0.134 0.375
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,647,961
Number of extensions: 632649
Number of successful extensions: 4359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3345
Number of HSP's successfully gapped: 1073
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.0 bits)