RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15016
(131 letters)
>gnl|CDD|149105 pfam07851, TMPIT, TMPIT-like protein. A number of members of
this family are annotated as being transmembrane
proteins induced by tumour necrosis factor alpha, but
no literature was found to support this.
Length = 330
Score = 39.0 bits (91), Expect = 2e-04
Identities = 16/88 (18%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQV-KTLRSEVNEMRQTRVRLIRKMKEETNKHKE 59
++KE + L + + Y++ L + Q + + ++Q V L + K T + E
Sbjct: 9 LEKEFQQLQETHRLYKQKLEEVEKLQEQCTSAIARQRKRLKQLIVSLKKLKKSLTPEDSE 68
Query: 60 QEILRNREIAKLKKESRRAQNLIRNLES 87
+ +L+++ + +N ++ES
Sbjct: 69 L-------VEQLEEQIKERKNQFFDMES 89
>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
component YidC; Validated.
Length = 429
Score = 35.6 bits (82), Expect = 0.004
Identities = 29/138 (21%), Positives = 52/138 (37%), Gaps = 22/138 (15%)
Query: 8 LTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLI-------------RKMKEET 54
LTD KE+ ++ Y + K ++ + +R+ R+R+I ++K+
Sbjct: 279 LTDEFKEHH--AEQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTR 336
Query: 55 NKHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKT-------KEVILKRKQEEWCSGY 107
K + R +EIA+ ++ + R N E V K+K S
Sbjct: 337 TAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPN 396
Query: 108 CFVPTSVLEVGGSSPSQD 125
P+ E GS P +
Sbjct: 397 EDTPSENEESKGSPPQVE 414
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.7 bits (77), Expect = 0.017
Identities = 21/96 (21%), Positives = 49/96 (51%), Gaps = 8/96 (8%)
Query: 8 LTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETN-KHKEQEILRNR 66
L A++ +L S + ++L+S++ ++++ L K+ + K K+++ +++
Sbjct: 422 LQQARQNESELRNQISLLTSLERSLKSDLGQLKKENDMLQTKLNSMVSAKQKDKQSMQSM 481
Query: 67 EIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
E +LK E+ N + L +KK ++K+EE
Sbjct: 482 E-KRLKSEADSRVNAEKQLAEEKK------RKKEEE 510
Score = 26.0 bits (57), Expect = 8.7
Identities = 28/97 (28%), Positives = 47/97 (48%), Gaps = 7/97 (7%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKT-LRSEVNEMRQ-TRVRLIRKMKEETNKHK 58
+Q ++ ++ AK QK +S S E ++K+ S VN +Q + +K +EET
Sbjct: 460 LQTKLNSMVSAK---QKDKQSMQSMEKRLKSEADSRVNAEKQLAEEKKRKKEEEETAARA 516
Query: 59 EQEILRNRE--IAKLKKESRRAQNLIRNLESDKKTKE 93
+ +RE LK+ + + I+ LE D K KE
Sbjct: 517 AAQAAASREECAESLKQAKQDLEMEIKKLEHDLKLKE 553
>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 = 33.0 bits (76), Expect = 0.026
Identities = 22/105 (20%), Positives = 50/105 (47%), Gaps = 7/105 (6%)
Query: 3 KEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEI 62
KE RN + ++ ++LL+ + + + ++++L + + + L K K K +E E
Sbjct: 72 KERRN--ELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEE 129
Query: 63 LRNREIAKLKKESRRAQN-----LIRNLESDKKTKEVILKRKQEE 102
L + +L++ S Q L+ +E + + + L ++ EE
Sbjct: 130 LIAEQREELERISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEE 174
Score = 28.4 bits (64), Expect = 1.3
Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 8 LTDAKKEYQ-----KLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRK-MKEETNKHKEQE 61
+ +AKKE + LL ++ L E+ E R RL R+ ++ E ++ E
Sbjct: 38 IEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREETLDRKME 97
Query: 62 ILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
L +E KKE N +NL+ ++ E ++ ++EE
Sbjct: 98 SLDKKEENLEKKEK-ELSNKEKNLDEKEEELEELIAEQREE 137
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 32.4 bits (75), Expect = 0.040
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 30 KTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILR-NREIAKLK----KESRRAQNLIRN 84
K +++ E + R++ + K+E K++ +L EI KL+ KE R +N ++
Sbjct: 27 KIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQK 86
Query: 85 LESDKKTKEVILKRKQEE 102
LE KE L RK E
Sbjct: 87 LEKRLLQKEENLDRKLEL 104
Score = 29.0 bits (66), Expect = 0.62
Identities = 23/107 (21%), Positives = 48/107 (44%), Gaps = 11/107 (10%)
Query: 6 RNLTDAKKEYQK----LLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQE 61
+ L + + E QK LL+ + + + +++ L E+ + L +K +E K +E E
Sbjct: 75 KELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELE 134
Query: 62 ILRNR------EIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
L I+ L E + L+ +E + + + +L ++ EE
Sbjct: 135 ELIEEQLQELERISGLTAEEAKEI-LLEKVEEEARHEAAVLIKEIEE 180
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 32.0 bits (73), Expect = 0.066
Identities = 21/91 (23%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 3 KEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQT-------RVRLIRKMKEETN 55
+E R +T +K +KL + E + L+ E+ E+++ R R+++++
Sbjct: 412 EERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVR 471
Query: 56 KHKEQEILRNREIAKLKKESRRAQNLIRNLE 86
K +E R I +L+KE + + LE
Sbjct: 472 KDREIRARD-RRIERLEKELEEKKKRVEELE 501
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 31.5 bits (72), Expect = 0.098
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 31 TLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNRE------IAK-LKKESRRAQNLIR 83
TLR+ V E+++ R RL + + E E E L+ RE I + ++ E++ I
Sbjct: 60 TLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIE 119
Query: 84 NLESDK 89
L+S++
Sbjct: 120 QLKSER 125
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 31.2 bits (71), Expect = 0.15
Identities = 21/97 (21%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 6 RNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRN 65
L+ ++E ++L E +++ L+SE+ E+R +E +E L+
Sbjct: 246 EELSRLEEELEELQEELEEAEKEIEELKSELEELR----------EELEELQEELLELKE 295
Query: 66 REIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
EI +L+ E + + LE++ + E L+ +E+
Sbjct: 296 -EIEELEGEISLLRERLEELENELEELEERLEELKEK 331
Score = 30.5 bits (69), Expect = 0.28
Identities = 17/105 (16%), Positives = 48/105 (45%), Gaps = 4/105 (3%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQ 60
++ + ++E ++L E ++ L E+ E+ + + ++KEE + + +
Sbjct: 816 LESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEK----ELEELKEELEELEAE 871
Query: 61 EILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEEWCS 105
+ E+ +L++E + +R LES+ + +++ +E
Sbjct: 872 KEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEE 916
>gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
Length = 555
Score = 30.7 bits (70), Expect = 0.17
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 35 EVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKL 71
+ RV L+R E T ++E L+ R +AKL
Sbjct: 349 GDKAEIKERVELLRSQIERTTSEYDKEKLKER-LAKL 384
>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 = 29.8 bits (67), Expect = 0.44
Identities = 18/100 (18%), Positives = 44/100 (44%), Gaps = 6/100 (6%)
Query: 5 MRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILR 64
+ L+ +KE ++ + + L+ E+ + + R K E K + QE L+
Sbjct: 517 IEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEK-EAQEALK 575
Query: 65 N--REIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
+E+ + +E + + + + K+ E ++K K+ +
Sbjct: 576 ALKKEVESIIRELKEKK---IHKAKEIKSIEDLVKLKETK 612
Score = 29.0 bits (65), Expect = 0.72
Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 6/99 (6%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKT-LRSEVNE----MRQTRVRLIRKMKEETN 55
++K ++ KKE ++ + E K L E E +++ +IR++KE+
Sbjct: 534 LEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVESIIRELKEK-K 592
Query: 56 KHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKTKEV 94
HK +EI ++ KLK+ ++ N ++DK +V
Sbjct: 593 IHKAKEIKSIEDLVKLKETKQKIPQKPTNFQADKIGDKV 631
>gnl|CDD|214502 smart00068, GHB, Glycoprotein hormone beta chain homologues. Also
called gonadotropins. Glycoprotein hormones consist of
two glycosylated chains (alpha and beta) of similar
topology.
Length = 107
Score = 28.8 bits (65), Expect = 0.45
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 103 WCSGYCFVPTSVLEVGGSSPSQDI 126
C+GYC+ V + Q +
Sbjct: 29 ICAGYCYTRDPVYKSPLPPLPQRV 52
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 29.1 bits (65), Expect = 0.73
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 1 MQKEMRNLTDAKKEYQK---LLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKE-ETNK 56
+ E+R+ + Y++ L SQ+ + + L SE++E+++ RL+ +++E E
Sbjct: 34 LDSELRDAEKERDTYKQYLSKLESQNVEISNYEALDSELDELKKEEERLLDELEELEKED 93
Query: 57 HKEQEILRNREIAKLKKESRRAQ 79
L + K + E+ Q
Sbjct: 94 DDLDGELVELQEEKEQLENEELQ 116
Score = 25.6 bits (56), Expect = 8.4
Identities = 17/89 (19%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKE---ETNKH 57
+ E+ L KKE ++LL E + L E+ E+++ + +L + + E N
Sbjct: 68 LDSELDEL---KKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLF 124
Query: 58 KEQEILRNREIAKLKKESRRAQNLIRNLE 86
+ + L+ + + N + L
Sbjct: 125 DRNNLQLEDNLQSLELQYEYSLNQLDKLR 153
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 0.74
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 4/101 (3%)
Query: 2 QKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQE 61
+K+M+ K E K+ + + K ++ + + EE K +E+
Sbjct: 1604 EKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKK----KAEELKKAEEEN 1659
Query: 62 ILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
++ E AK +E ++ + E D+K LK++ EE
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEE 1700
Score = 27.0 bits (59), Expect = 4.3
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 48 RKMKEETNKHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
K E K + +E + E+ K + E ++ ++ E + K K K++ EE
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEE 1741
Score = 25.9 bits (56), Expect = 9.3
Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 2/89 (2%)
Query: 14 EYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKK 73
E +K +++K + + + + + K K + K K +E + E K +
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1454
Query: 74 ESRRAQNLIRNLESDKKTKEVILKRKQEE 102
E+++A+ + E KK E K+K EE
Sbjct: 1455 EAKKAEEAKKKAEEAKKADE--AKKKAEE 1481
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 28.9 bits (65), Expect = 0.75
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 2/95 (2%)
Query: 8 LTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNRE 67
L K + L ENQV L SE+ E+R+ R K+ ++ +E L N E
Sbjct: 40 LEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDE-RELRAL-NIE 97
Query: 68 IAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
I K+ ++ + L + + E ++ +E
Sbjct: 98 IQIAKERINSLEDELAELMEEIEKLEKEIEDLKER 132
>gnl|CDD|204405 pfam10146, zf-C4H2, Zinc finger-containing protein. This is a
family of proteins which appears to have a highly
conserved zinc finger domain at the C terminal end,
described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is
predicted to contain a coiled coil. Members are
annotated as being tumour-associated antigen HCA127 in
humans but this could not confirmed.
Length = 215
Score = 28.7 bits (64), Expect = 0.76
Identities = 14/76 (18%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 29 VKTLRSEVNEMRQTRVRLIRKMK--EETNKHKEQEILRNREIAKLKKESRRAQNLIRNLE 86
+K +R++ +E+ + + + + + E KH ++ ++E+ +L +E + +R +
Sbjct: 3 IKEIRNKTDELEKLKDEIKAEEEALESEEKHLKE---YDKEMEELLEEKMQHVEELRQIH 59
Query: 87 SDKKTKEVILKRKQEE 102
+D E +K+ + E
Sbjct: 60 ADINDMETEIKQSKSE 75
>gnl|CDD|180119 PRK05500, PRK05500, bifunctional orotidine 5'-phosphate
decarboxylase/orotate phosphoribosyltransferase protein;
Validated.
Length = 477
Score = 28.9 bits (65), Expect = 0.78
Identities = 13/30 (43%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 16 QKLLRSQSSYENQVKTLRSEVNEMRQTRVR 45
Q LL ++ + QVK+LR E+N++RQ V+
Sbjct: 239 QDLL-GAANLKEQVKSLREEINQIRQQIVQ 267
>gnl|CDD|217047 pfam02455, Hex_IIIa, Hexon-associated protein (IIIa). The major
capsid protein of the adenovirus strain is also known as
a hexon. This is a family of hexon-associated proteins
(protein IIIa).
Length = 491
Score = 28.9 bits (65), Expect = 0.78
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 20 RSQSSYENQVKTLRSEVNEMRQTRV 44
R Q +YE LR VNE+ Q V
Sbjct: 85 RGQENYEAFKSALRLFVNEVPQVEV 109
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 28.7 bits (64), Expect = 0.78
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 35 EVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQNLIRNLES-DKKTKE 93
++NE Q+ + L + + + KE LRN + +KK R N + +L + DKKTK+
Sbjct: 56 DLNEFYQSTLSLANQFNDCNDDDKEIAHLRNIIDSHIKKHKER--NTLPDLNNVDKKTKK 113
Query: 94 VILKRKQE 101
+I K ++E
Sbjct: 114 LINKLQKE 121
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.9 bits (65), Expect = 0.81
Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQ----SSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNK 56
+ DA K K L + ++ + ++ TL SE +Q ++ + + +++T
Sbjct: 155 LNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRA-QQAKLAQLLEERKKTLA 213
Query: 57 HKEQEIL-RNREIAKLKKESRRAQNLIRNLE 86
E+ +++ +L+ R +N I + E
Sbjct: 214 QLNSELSADQKKLEELRANESRLKNEIASAE 244
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 28.4 bits (64), Expect = 0.95
Identities = 16/77 (20%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 26 ENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQNLIRNL 85
+ +++ L+ E+ E++Q L ++++ K +E+ R + +LK+ + + L L
Sbjct: 68 KTRLEKLKKELEELKQRIAELQAQIEKL-KKGREETEERTELLEELKQLEKELKKLKAEL 126
Query: 86 ESDKKTKEVILKRKQEE 102
E +K +++ +EE
Sbjct: 127 EKYEKNDPERIEKLKEE 143
>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 = 28.5 bits (64), Expect = 0.95
Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 8 LTDAKKEYQKLLRSQSSYENQV-KTLRSEVNEMRQTRVRLIR----KMKEETNKHKEQEI 62
L + + + +LL + +V + L NE + L++ + KE N+ + +
Sbjct: 22 LYELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRARIS 81
Query: 63 LRNREIAKLKKESRRAQNLIRNLESD 88
EI + ++ + + SD
Sbjct: 82 QLKEEIEQKRERIEELKRALAQRRSD 107
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 28.5 bits (64), Expect = 1.2
Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 11/95 (11%)
Query: 16 QKLLRSQSSYENQVKTLRSEVN----EMRQTRVRLIRKMKEETNKHKEQEILRNR----- 66
+ L + S ++ + E+N E+ Q ++ + K E K +E L R
Sbjct: 98 ESLAQLSSEFQELANEIFEELNRRLAELNQQNLKQLLKPLREVL-EKFREQLEQRIHESA 156
Query: 67 -EIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQ 100
E + L +E R I+ L + LK +
Sbjct: 157 EERSTLLEEIDRLLGEIQQLAQEAGNLTAALKGNK 191
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 27.6 bits (62), Expect = 1.3
Identities = 15/75 (20%), Positives = 40/75 (53%)
Query: 7 NLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNR 66
+L +A++ ++ + YE +++ R + +E+ + + ++ EE E+E+ R +
Sbjct: 45 DLAEAERLKEEAQALLAEYEQELEEAREQASEIIEQAKKEAEQIAEEIKAEAEEELERIK 104
Query: 67 EIAKLKKESRRAQNL 81
E A+ + E+ + + L
Sbjct: 105 EAAEAEIEAEKERAL 119
>gnl|CDD|217536 pfam03403, PAF-AH_p_II, Platelet-activating factor acetylhydrolase,
isoform II. Platelet-activating factor acetylhydrolase
(PAF-AH) is a subfamily of phospholipases A2,
responsible for inactivation of platelet-activating
factor through cleavage of an acetyl group. Three known
PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose
catalytic beta and gamma subunits are aligned in
pfam02266, the extracellular, plasma PAF-AH (pPAF-AH),
and the intracellular PAF-AH isoform II (PAF-AH II).
This family aligns pPAF-AH and PAF-AH II, whose
similarity was previously noted.
Length = 372
Score = 28.1 bits (63), Expect = 1.3
Identities = 7/40 (17%), Positives = 21/40 (52%)
Query: 56 KHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKTKEVI 95
+E+ +RN ++ + +E +A ++I ++ + V+
Sbjct: 166 NAEEEFHIRNEQVGQRAQECSKALSIILQIDLGTPVENVL 205
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 28.3 bits (63), Expect = 1.4
Identities = 15/68 (22%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 38 EMRQTRVRLIRKMKEETNKHK---------EQEILRNREIAKLKKESRRAQNLIRNLESD 88
E+R+ R +L R+ +E + K ++E + RE + + SRR + +++D
Sbjct: 4 ELRRAREKLEREQRERKQRAKLKLERERKAKEEAAKQREAIEAAQRSRRLDAIEAQIKAD 63
Query: 89 KKTKEVIL 96
++ +E +
Sbjct: 64 QQMQESLQ 71
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.9 bits (63), Expect = 1.5
Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 16/98 (16%)
Query: 11 AKKEYQK-------LLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEIL 63
AKK + L+ S E +++ E + + +L +++E+ K +E+E
Sbjct: 507 AKKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEE-- 564
Query: 64 RNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQE 101
++ + + +KE AQ I+ KK + I+K ++
Sbjct: 565 -DKLLEEAEKE---AQQAIKEA---KKEADEIIKELRQ 595
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.1 bits (63), Expect = 1.7
Identities = 11/84 (13%), Positives = 27/84 (32%), Gaps = 1/84 (1%)
Query: 10 DAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIA 69
+EY++ + + N++ L + +L R + E +
Sbjct: 103 SLDEEYRERFEGERHFVNELY-LTILYRPLPSLIGKLERYKNKLRAAQANTENDLKEILR 161
Query: 70 KLKKESRRAQNLIRNLESDKKTKE 93
L+ ++ R L+R +
Sbjct: 162 NLEDKTARVLALLRKYGPELLGNY 185
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 27.6 bits (62), Expect = 1.7
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 5 MRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILR 64
MR A++ +L + E + + L V E+ + ++ +EE + +E
Sbjct: 112 MRKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEE---RQIEEKRH 168
Query: 65 NREIAKLKKESRRAQNLIRNL 85
EIA LKK++++ ++ + +
Sbjct: 169 ADEIAFLKKQNQQLKSQLEQI 189
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This
family includes outer membrane proteins such as OmpH
among others. Skp (OmpH) has been characterized as a
molecular chaperone that interacts with unfolded
proteins as they emerge in the periplasm from the Sec
translocation machinery.
Length = 140
Score = 27.2 bits (61), Expect = 1.7
Identities = 13/90 (14%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQ 60
+QK ++ K ++L + + +++ L E+ ++++ + + E + KE+
Sbjct: 6 VQKILQESPAGKAAQKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEK 65
Query: 61 EIL-RNREIAKLKKESRRAQNLIRNLESDK 89
E+ + +E + +++ ++ + E K
Sbjct: 66 ELQKKVQEFQRKQQKLQQDLQKRQQEELQK 95
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 27.2 bits (61), Expect = 1.8
Identities = 15/86 (17%), Positives = 40/86 (46%), Gaps = 2/86 (2%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQ 60
+QK + K ++L + + +++ E+ + Q + + EE K K+Q
Sbjct: 23 VQKVLSESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQ 82
Query: 61 EILRNREIAKLKKESRRAQNLIRNLE 86
E+ ++ +L+++ + AQ ++ +
Sbjct: 83 EL--QQKQQELQQKQQAAQQELQQKQ 106
>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 = 27.7 bits (62), Expect = 2.2
Identities = 16/89 (17%), Positives = 36/89 (40%)
Query: 2 QKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQE 61
Q E+ L + + LR N++ + + + Q +KE+ +++
Sbjct: 797 QAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEI 856
Query: 62 ILRNREIAKLKKESRRAQNLIRNLESDKK 90
N + +L++E + +R+LES
Sbjct: 857 ENLNGKKEELEEELEELEAALRDLESRLG 885
>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 = 27.3 bits (61), Expect = 2.5
Identities = 14/97 (14%), Positives = 41/97 (42%), Gaps = 1/97 (1%)
Query: 7 NLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKH-KEQEILRN 65
+ + +K +L + E +++ LR E+ E+ + L + + + + +E +
Sbjct: 692 KIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQ 751
Query: 66 REIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
+ E+ + R E++++ E + ++ E
Sbjct: 752 LSKELTELEAEIEELEERLEEAEEELAEAEAEIEELE 788
Score = 25.8 bits (57), Expect = 9.0
Identities = 18/101 (17%), Positives = 45/101 (44%), Gaps = 4/101 (3%)
Query: 2 QKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQE 61
++ L + +E +L + ++++L +E+ E+ L +++E + +
Sbjct: 326 EELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETL- 384
Query: 62 ILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
++A+L+ + N I LE+ + E +R Q+E
Sbjct: 385 ---RSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQE 422
Score = 25.8 bits (57), Expect = 9.4
Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 9/104 (8%)
Query: 6 RNLTDAKKEYQK--LLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKE-----ETNKHK 58
+ L +E + L+ +++ L+ E+ E + L +++E E + +
Sbjct: 216 KELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLE 275
Query: 59 EQEILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
E EI +L+KE N I LE K+ L + +
Sbjct: 276 VSE--LEEEIEELQKELYALANEISRLEQQKQILRERLANLERQ 317
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 27.3 bits (61), Expect = 2.9
Identities = 19/94 (20%), Positives = 42/94 (44%), Gaps = 17/94 (18%)
Query: 21 SQSSYENQVKTLRSEVNEMRQ--TRVRLIRKMKEETNKHK--------EQEILRNREIAK 70
++ Q K VNE+R+ R +RK++ + K + ++ ++E
Sbjct: 16 NEDVSAFQRKF----VNEVRRCDEVERKLRKLESKIKKLGIPLKDTGGKPDVPPSKEFLD 71
Query: 71 LKKESRRAQNLIRNLE-SDKKTKEVILKRKQEEW 103
L++E + I+ +E + + ++ I + EEW
Sbjct: 72 LEEEILDLEAEIKEVEENLESLEKEI--NELEEW 103
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 27.0 bits (60), Expect = 2.9
Identities = 25/107 (23%), Positives = 41/107 (38%), Gaps = 9/107 (8%)
Query: 3 KEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKE--ETNKHKEQ 60
EM D KE + L + + Q+ L S + E+ L K+K+ E Q
Sbjct: 256 AEMDTEEDRTKEREAEL---EALQEQIDELESSIEEVLSEIKALASKIKQVNEELTTVRQ 312
Query: 61 EILRNREIAKLKKES----RRAQNLIRNLESDKKTKEVILKRKQEEW 103
E E K+KK + A+N + L++ L ++W
Sbjct: 313 ENEELEEEYKIKKRTVELLPDAENNVAKLQALVVASSERLLELAQQW 359
>gnl|CDD|233149 TIGR00845, caca, sodium/calcium exchanger 1. The Ca2+:Cation
Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA
family are found ubiquitously, having been identified in
animals, plants, yeast, archaea and widely divergent
bacteria.All of the characterized animal proteins
catalyze Ca2+:Na+ exchange although some also transport
K+. The NCX1 plasma membrane protein exchanges 3 Na+ for
1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+
antiport but may also catalyze Na+:H+ antiport. All
remaining well-characterized members of the family
catalyze Ca2+:H+ exchange.This model is specific for the
eukaryotic sodium ion/calcium ion exchangers of the Caca
family [Transport and binding proteins, Other].
Length = 928
Score = 27.1 bits (60), Expect = 3.1
Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 11/99 (11%)
Query: 32 LRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKT 91
L EV E + R +IR +KE KH ++++ + E+A + SR+ ++ R + T
Sbjct: 305 LVLEVKEFDEARREMIRILKELKQKHPDKDLEQLEEMANYQVLSRQQKS--RAFYRIQAT 362
Query: 92 KEV-----ILKRKQEEWCSGYCFVPTSVLEVGGSSPSQD 125
+ + ILK+ + S+ EV D
Sbjct: 363 RLMTGAGNILKKHAADAARK----AVSMHEVATDDEEND 397
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 26.8 bits (60), Expect = 3.5
Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 2 QKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEV-NEMRQTRVRLIRKMKEETNKHKEQ 60
+ L + ++E ++L + +K L + ++ + + K+ E K E
Sbjct: 330 PELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSE- 388
Query: 61 EILRNREIAKLKKESRRAQNLIRNLESDKKTK 92
E+ +L++E + + + +L S+ K
Sbjct: 389 ------ELEELEEELKELKEELESLYSEGKIS 414
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 26.9 bits (60), Expect = 4.0
Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 18/89 (20%)
Query: 3 KEMRNLTDA------KKEYQ-KLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETN 55
+E+ L + K + + L +S +N V + S + ++ ++ + E +N
Sbjct: 630 EELDALANNLPNGKLKVALKNEALDLRSIQQNFVPPMESLLEKLNSN----VKTLDESSN 685
Query: 56 KHKEQEILRNREIAKLKKESRRAQNLIRN 84
+ + + E + AQ + N
Sbjct: 686 DLQN-------AVKDVLAEVQAAQGFLNN 707
>gnl|CDD|239460 cd03344, GroEL, GroEL_like type I chaperonin. Chaperonins are
involved in productive folding of proteins. They share a
common general morphology, a double toroid of 2 stacked
rings, each composed of 7-9 subunits. The symmetry of
type I is seven-fold and they are found in eubacteria
(GroEL) and in organelles of eubacterial descent (hsp60
and RBP). With the aid of cochaperonin GroES, GroEL
encapsulates non-native substrate proteins inside the
cavity of the GroEL-ES complex and promotes folding by
using energy derived from ATP hydrolysis.
Length = 520
Score = 26.7 bits (60), Expect = 4.0
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 43 RVRLIRKMKEETNKHKEQEILRNREIAKL 71
R+ IRK EET ++E L+ R +AKL
Sbjct: 342 RIAQIRKQIEETTSDYDKEKLQER-LAKL 369
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 509
Score = 26.7 bits (60), Expect = 4.7
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 45 RLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQN-LIRNLESDKKTKEVILKRKQEEW 103
L+ ++K+E E E R ++++E + + LE + K K L R
Sbjct: 95 ELVEELKKEIPAAFESEEYEAR-KEEIEEEFQEKREEAFEELEEEAKEKGFALVRTP--- 150
Query: 104 CSGYCFVP 111
G+ F P
Sbjct: 151 -GGFVFAP 157
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 26.6 bits (60), Expect = 5.0
Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 21/82 (25%)
Query: 24 SYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQNLI- 82
+ + + L++E+ E++ R N ++EI + K++ A+ LI
Sbjct: 32 ELDEERRELQTELEELQAER-----------NA-------LSKEIGQAKRKGEDAEALIA 73
Query: 83 --RNLESDKKTKEVILKRKQEE 102
+ L+ + K E L + E
Sbjct: 74 EVKELKEEIKALEAELDELEAE 95
>gnl|CDD|212672 cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1
and similar proteins. This subgroup includes human
HYOU1 (also known as human hypoxia up-regulated 1,
GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human
HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces
cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian
HYOU1 functions as a nucleotide exchange factor (NEF)
for HSPA5 (alos known as BiP, Grp78 or HspA5) and may
also function as a HSPA5-independent chaperone. S.
cerevisiae Lhs1p, does not have a detectable endogenous
ATPase activity like canonical HSP70s, but functions as
a NEF for Kar2p; it's interaction with Kar2p is
stimulated by nucleotide-binding. In addition, Lhs1p has
a nucleotide-independent holdase activity that prevents
heat-induced aggregation of proteins in vitro. This
subgroup belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as NEFs, to
remove ADP from their HSP70 chaperone partners during
the ATP hydrolysis cycle. HSP70 chaperones assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 388
Score = 26.4 bits (59), Expect = 5.0
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 45 RLIRKMKEE-TNKHKEQEILRN--REIAKLKKESRRA 78
RL + +E KHK + +R R +AKL KE+ RA
Sbjct: 244 RLADHLAKEFEEKHKAKVDVRTNPRAMAKLLKEANRA 280
>gnl|CDD|109076 pfam00007, Cys_knot, Cystine-knot domain. The family comprises
glycoprotein hormones and the C-terminal domain of
various extracellular proteins. It is believed to be
involved in disulfide-linked dimerisation.
Length = 105
Score = 25.8 bits (57), Expect = 5.1
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 103 WCSGYCFVPTSVLEVGGSSPSQDI 126
C+GYC+ V + G + SQ +
Sbjct: 28 ICAGYCYTRDPVYKDGRRAVSQRV 51
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the CF(0)
(base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the ab
CF(1) proteins (in the head of the ATP synthase) which
are found in pfam00006.
Length = 132
Score = 26.1 bits (58), Expect = 5.2
Identities = 17/80 (21%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 7 NLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNR 66
N+ +A++ ++ + E Q+ R+E +E+ + +K+KEE +++ R
Sbjct: 38 NIKEAEERLKQAAALLAEAEQQLAQARAEASEIINNAKKEAQKLKEEILAEAQKDAERLL 97
Query: 67 EIAK--LKKESRRAQNLIRN 84
E A+ +++E +A +R
Sbjct: 98 ESARAEIEQEKEQALAELRQ 117
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 26.4 bits (59), Expect = 5.2
Identities = 7/35 (20%), Positives = 12/35 (34%)
Query: 50 MKEETNKHKEQEILRNREIAKLKKESRRAQNLIRN 84
K+ Q RE +L+K + I +
Sbjct: 98 NKQPNIAELAQGEKERREQERLEKLKQELDQAIES 132
>gnl|CDD|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.
HSP70 (70-kDa heat shock protein) family chaperones
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some HSP70 family members are not
chaperones but instead, function as NEFs to remove ADP
from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 26.4 bits (59), Expect = 5.3
Identities = 23/104 (22%), Positives = 33/104 (31%), Gaps = 31/104 (29%)
Query: 46 LIRKMKEETNKHKEQEILRNREIAKLKKESRRAQ---------NLIRNLESDKKTKEVIL 96
L K KE K L R + +LK+ + +A+ + EV L
Sbjct: 233 LAEKFKE---KGGIDLRLDPRALRRLKEAAEKAKIALSSSEEATITLPGLGSGGDLEVEL 289
Query: 97 KRKQ-EEWCSG--YCFVP--TSVLE--------------VGGSS 121
R++ EE + VL VGGSS
Sbjct: 290 TREEFEELIRPLLERTIDLVERVLADAGLKPEDIDAVLLVGGSS 333
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 26.6 bits (59), Expect = 5.3
Identities = 21/106 (19%), Positives = 44/106 (41%), Gaps = 22/106 (20%)
Query: 13 KEYQKLLRSQSSYEN---QVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRN---- 65
K+Y L + SS E+ QV +L +++++ ++ V EIL++
Sbjct: 36 KKYSDFLPNMSSAEDLLEQVSSLSEDISDLLKSEV--------------SNEILQDLNDA 81
Query: 66 -REIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEEWCSGYCFV 110
E+A+LK++ ++ L+ K E + + + Y
Sbjct: 82 VEELAELKRQLEEKILGLKILQKLLKIHEALEETNEALSGKDYLKA 127
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 26.5 bits (59), Expect = 5.8
Identities = 9/48 (18%), Positives = 21/48 (43%)
Query: 52 EETNKHKEQEILRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRK 99
EE + + Q +E+ KL+++ + + I E + + + K
Sbjct: 88 EENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDK 135
>gnl|CDD|185747 cd09234, V_HD-PTP_like, Protein-interacting V-domain of mammalian
His-Domain type N23 protein tyrosine phosphatase and
related domains. This family contains the V-shaped (V)
domain of mammalian His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23) and related
domains. It belongs to the V_Alix_like superfamily which
includes the V domains of Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, mammalian Alix
(apoptosis-linked gene-2 interacting protein X/ also
known as apoptosis-linked gene-2 interacting protein 1,
AIP1), and related domains. HD_PTP interacts with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system, and participates in cell migration
and endosomal trafficking. The related Alix V-domain
(belonging to a different family in this superfamily)
contains a binding site, partially conserved in the
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. The Alix V-domain is also a dimerization
domain. In addition to the V-domain, HD_PTP also has an
N-terminal Bro1-like domain, a proline-rich region
(PRR), a catalytically inactive tyrosine phosphatase
domain, and a region containing a PEST motif. Bro1-like
domains bind components of the ESCRT-III complex,
specifically to CHMP4 in the case of HD-PTP. The
Bro1-like domain of HD-PTP can also bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
HD-PTP is encoded by the PTPN23 gene, a tumor suppressor
gene candidate frequently absent in human kidney,
breast, lung, and cervical tumors. This family also
contains Drosophila Myopic, which promotes epidermal
growth factor receptor (EGFR) signaling, and
Caenorhabditis elegans (enhancer of glp-1) EGO-2 which
promotes Notch signaling.
Length = 337
Score = 26.1 bits (58), Expect = 6.3
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 8 LTDAKKEYQKLLRSQSSYEN--------QVKTLRSEVNEMRQTRVRLIRKMKEETNK 56
L E QK L S S + ++K + ++VNEMR+ R L +++++ ++
Sbjct: 164 LAGPLDELQKKLPSPSLLDRPEDEAIEKELKRILNKVNEMRKQRRSLEQQLRDAIHE 220
>gnl|CDD|226824 COG4389, COG4389, Site-specific recombinase [DNA replication,
recombination, and repair].
Length = 677
Score = 26.4 bits (58), Expect = 6.4
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 33 RSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNRE 67
S + R + L R + E + H E I R+R+
Sbjct: 313 YSTRHLRRSSIRMLARSITENKSHHGEHYITRDRK 347
>gnl|CDD|153342 cd07658, F-BAR_NOSTRIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Nitric Oxide Synthase
TRaffic INducer (NOSTRIN). F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Nitric Oxide Synthase TRaffic
INducer (NOSTRIN) is expressed in endothelial and
epithelial cells and is involved in the regulation,
trafficking and targeting of endothelial NOS (eNOS).
NOSTRIN facilitates the endocytosis of eNOS by
coordinating the functions of dynamin and the
Wiskott-Aldrich syndrome protein (WASP). Increased
expression of NOSTRIN may be correlated to preeclampsia.
NOSTRIN contains an N-terminal F-BAR domain and a
C-terminal SH3 domain. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
The F-BAR domain of NOSTRIN is necessary and sufficient
for its membrane association and is responsible for its
subcellular localization.
Length = 239
Score = 25.8 bits (57), Expect = 6.6
Identities = 20/101 (19%), Positives = 45/101 (44%), Gaps = 5/101 (4%)
Query: 3 KEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEI 62
K + LTD + E K+ + + + L+ +V + +Q+ + K + + +
Sbjct: 113 KAAKLLTDWRSEQIKVKKKLHGLARENEKLQDQVEDNKQSCTKQKMLNKLKKSAEVQD-- 170
Query: 63 LRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEEW 103
+E KL+ + ++ + E++ T V L+R + EW
Sbjct: 171 ---KEDEKLEAKRKKGEESRLKAENEYYTCCVRLERLRLEW 208
>gnl|CDD|131952 TIGR02906, spore_CotS, spore coat protein, CotS family. Members of
this family include the spore coat proteins CotS and
YtaA from Bacillus subtilis and, from other
endospore-forming bacteria, homologs that are more
closely related to these two than to the spore coat
proteins YutH and YsxE. The CotS family is more broadly
distributed than YutH or YsxE, but still is not
universal among spore-formers [Cellular processes,
Sporulation and germination].
Length = 313
Score = 26.1 bits (58), Expect = 6.6
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 49 KMKEETNKHKEQEILRNREIAKLKKESRRAQNLI-----RNLESDKKTKEVILKRKQEEW 103
K ++ K + E+ R ++IA KK L LE KK E++ K K +
Sbjct: 121 KWPKQFEKRLK-ELERFKKIALEKKYKDEFDKLYLKEVDYFLERGKKALELLNKSKYYDL 179
Query: 104 CS 105
C
Sbjct: 180 CK 181
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 26.2 bits (58), Expect = 6.9
Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 1/76 (1%)
Query: 2 QKEMRNLTDAKKEYQKLLRSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQE 61
+ L + +EY+ LL+ + + SE+ ++ + K + +Q
Sbjct: 960 HEVESKLKETSEEYEDLLKKSTILVREGNKANSELKNFKKELAE-LSKQYGALQESTKQL 1018
Query: 62 ILRNREIAKLKKESRR 77
E+A+L+ S+
Sbjct: 1019 KELPVEVAELQSASKI 1034
>gnl|CDD|114015 pfam05266, DUF724, Protein of unknown function (DUF724). This
family contains several uncharacterized proteins found
in Arabidopsis thaliana and other plants. This region is
often found associated with Agenet domains and may
contain coiled-coil.
Length = 190
Score = 25.9 bits (57), Expect = 7.0
Identities = 25/102 (24%), Positives = 51/102 (50%), Gaps = 8/102 (7%)
Query: 7 NLTDAKKEYQKLLRSQSSYENQ---VKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEIL 63
+ D+ E++ L + S E V+ L+S +N++ + +K++E K E+EI
Sbjct: 63 QIDDSISEFESLSKCFSELEKHGFNVQALQSRLNKLLSLKDDQTKKLEER--KGLEKEIA 120
Query: 64 RNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEEWCS 105
+EI++ + +S A+ + LE + + +LK K+E
Sbjct: 121 E-KEISRQELDSEIAELERKILE--LQRQAALLKEKKEAEDK 159
>gnl|CDD|233395 TIGR01396, FlgB, flagellar basal-body rod protein FlgB. This model
represents FlgB, one of several components of bacterial
flagella that share a domain described by Pfam model
pfam00460. FlgB is part of the basal body [Cellular
processes, Chemotaxis and motility].
Length = 131
Score = 25.4 bits (56), Expect = 7.6
Identities = 6/31 (19%), Positives = 10/31 (32%)
Query: 1 MQKEMRNLTDAKKEYQKLLRSQSSYENQVKT 31
+ EM L + YQ L + +
Sbjct: 98 IDSEMAELAQNQMHYQALTNFLNGKIKGLNY 128
>gnl|CDD|129660 TIGR00569, ccl1, cyclin ccl1. All proteins in this family for
which functions are known are cyclins that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription initiation.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, StanfordUniversity) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 305
Score = 26.0 bits (57), Expect = 7.7
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 20 RSQSSYENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQ 79
R+ + E+ + S V R+ +LI M+E K+ E R+ ++A LKK+
Sbjct: 219 RAGLNMESYLTEQLS-VPGNREELPQLIDIMRELRILVKKYEEPRSEKVAALKKKLDECH 277
Query: 80 NLIRNLESDKKTKEVILKRKQEE 102
++ NL S K I KRK E
Sbjct: 278 SIEENLSSVK-----IRKRKGYE 295
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 25.8 bits (58), Expect = 8.3
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 13/52 (25%)
Query: 58 KEQEI-------LRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
KEQ I L + EI ++ K+ A+ N E DKK KE++ R Q +
Sbjct: 488 KEQSITITASSGLSDEEIERMVKD---AE---ANAEEDKKRKELVEARNQAD 533
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 25.7 bits (57), Expect = 8.8
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 13/52 (25%)
Query: 58 KEQEI-------LRNREIAKLKKESRRAQNLIRNLESDKKTKEVILKRKQEE 102
KEQ I L EI ++ KE+ N E DKK KE I R +
Sbjct: 486 KEQSITITASSGLSEEEIERMVKEAEA------NAEEDKKRKEEIEARNNAD 531
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 25.7 bits (57), Expect = 8.9
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 49 KMKEETNKHKEQEILR-NREIAKLKKESRRAQNLIRNLES--DKKTKEVILK--RKQEEW 103
+ E+ R +E+ KL+KE R + + N E K +EV+ K K E+
Sbjct: 803 FLPLAGLIDLAAELARLEKELEKLEKEIDRIEKKLSN-EGFVAKAPEEVVEKEKEKLAEY 861
>gnl|CDD|221283 pfam11875, DUF3395, Domain of unknown function (DUF3395). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 147 to 176 amino acids in length. This domain
is found associated with pfam00226.
Length = 144
Score = 25.4 bits (56), Expect = 9.2
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 54 TNKHKEQEILRNRE-----IAKLKKESRRAQNLIRNLESDKKTKE 93
K++E R RE IAK K+E+ A +L+ ++ K T+E
Sbjct: 3 NKAQKKKEQERQREKNKTEIAKKKQEAESAVSLMGDVVERKLTRE 47
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 25.6 bits (57), Expect = 9.2
Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 25 YENQVKTLRSEVNEMRQTRVRLIRKMKEETNKHKEQEILRNREIAKLKKESRRAQNLIRN 84
+ ++ E++ R+M EE +I +E+ LK++ + L+
Sbjct: 217 LKELQNEFPDQLEELKAG----YREMTEEGYHFDHLDI--EKELQDLKEQIDQNLALLEE 270
Query: 85 LESDKKTKEV 94
L+ D+ +E
Sbjct: 271 LDLDEAEEEN 280
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family is
long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 25.9 bits (57), Expect = 9.9
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 17 KLLRSQSSYENQVKTLRSEVNEMRQTR 43
+LL S NQ+K L+ E+N +R
Sbjct: 1103 ELLSGHSDNANQIKQLKQELNALRDKT 1129
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
0.312 0.126 0.340
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,205,743
Number of extensions: 532739
Number of successful extensions: 1421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1260
Number of HSP's successfully gapped: 480
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (24.3 bits)