Query psy12976
Match_columns 87
No_of_seqs 85 out of 103
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 15:58:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12976.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12976hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3039|consensus 100.0 1.9E-34 4.2E-39 226.7 4.7 79 7-86 2-92 (303)
2 PF10186 Atg14: UV radiation r 41.8 38 0.00082 24.6 3.3 28 50-77 1-30 (302)
3 KOG0883|consensus 39.7 11 0.00025 32.6 0.4 49 18-71 11-66 (518)
4 KOG0317|consensus 28.5 30 0.00065 28.2 1.1 19 49-67 240-268 (293)
5 PF15130 DUF4566: Domain of un 20.8 27 0.00058 27.8 -0.5 35 13-58 182-217 (241)
6 KOG3507|consensus 19.2 81 0.0018 20.5 1.6 22 61-84 40-61 (62)
7 TIGR03573 WbuX N-acetyl sugar 19.2 1.4E+02 0.0029 23.6 3.1 19 50-68 3-31 (343)
8 PRK10863 anti-RNA polymerase s 19.1 1E+02 0.0022 23.9 2.3 20 67-86 164-184 (216)
9 PF13923 zf-C3HC4_2: Zinc fing 16.6 1.2E+02 0.0026 16.3 1.7 18 51-68 1-29 (39)
10 PF04641 Rtf2: Rtf2 RING-finge 16.2 1.1E+02 0.0025 23.1 2.0 30 45-74 31-71 (260)
No 1
>KOG3039|consensus
Probab=100.00 E-value=1.9e-34 Score=226.66 Aligned_cols=79 Identities=47% Similarity=0.732 Sum_probs=76.9
Q ss_pred hhhccCCCCCCccchh-hhhcchhhcCCCccceeeCCCcccCccceecccccccc----------chhHHHHHHHHHHHH
Q psy12976 7 TRVQSLKRSRCAVYTY-EKKKDAEASGYGTQNQRVGKDSVKDFDCCCLTLQHSSY----------LNQVLIFDLLILKHR 75 (87)
Q Consensus 7 t~~HSKnnTa~~vfTy-ERkk~~~~sgyGTq~~RLgkDS~k~Fd~C~LcLqpard----------~~ec~~~~ll~qk~~ 75 (87)
|| |+||||+++|||| ||++|++++|||||++|||+||+|+||||+|||||++| |+|||+..+|+||++
T Consensus 2 tR-H~kN~ta~avyTY~EkkkdaaasGYGTq~~RLgrDsiK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~ilaqKke 80 (303)
T KOG3039|consen 2 TR-HGKNCTAGAVYTYHEKKKDAAASGYGTQRERLGRDSIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYILAQKKE 80 (303)
T ss_pred Cc-cccCCccceeEeehhhcchhhhcCcchhhhhhcccccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHHHHHHH
Confidence 67 9999999999999 99999999999999999999999999999999999999 789999999999999
Q ss_pred hH-HHHhhhhhc
Q psy12976 76 IN-LINQFQSQT 86 (87)
Q Consensus 76 i~-~~~~~~~~~ 86 (87)
|+ +|++||.|.
T Consensus 81 ~arrlkayekqr 92 (303)
T KOG3039|consen 81 IARRLKAYEKQR 92 (303)
T ss_pred HHHHHHHHHHHH
Confidence 99 999999884
No 2
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins 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 []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. 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. ; GO: 0010508 positive regulation of autophagy
Probab=41.77 E-value=38 Score=24.64 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=21.9
Q ss_pred ceecccccccc--chhHHHHHHHHHHHHhH
Q psy12976 50 CCCLTLQHSSY--LNQVLIFDLLILKHRIN 77 (87)
Q Consensus 50 ~C~LcLqpard--~~ec~~~~ll~qk~~i~ 77 (87)
.|++|-.+.+. |..|+=.-|...+.+|.
T Consensus 1 ~C~iC~~~~~~~~C~~C~~~~L~~~~~~l~ 30 (302)
T PF10186_consen 1 QCPICHNSRRRFYCANCVNNRLLELRSELQ 30 (302)
T ss_pred CCCCCCCCCCCeECHHHHHHHHHHHHHHHH
Confidence 48999977666 99998887777776666
No 3
>KOG0883|consensus
Probab=39.73 E-value=11 Score=32.58 Aligned_cols=49 Identities=24% Similarity=0.278 Sum_probs=30.9
Q ss_pred ccchh-hhhcchhhcCCCccceeeC-CC--cccCccceecccccccc--ch-hHHHHHHHH
Q psy12976 18 AVYTY-EKKKDAEASGYGTQNQRVG-KD--SVKDFDCCCLTLQHSSY--LN-QVLIFDLLI 71 (87)
Q Consensus 18 ~vfTy-ERkk~~~~sgyGTq~~RLg-kD--S~k~Fd~C~LcLqpard--~~-ec~~~~ll~ 71 (87)
-..|+ |-+- -||-.+.-+- +- --+||++|+|.+.|-.+ |- .=.+|||.+
T Consensus 11 mylT~tEw~~-----~~Ggkk~~~~n~~~FkrLP~~hC~lt~~Pfe~PvC~~dg~vFd~~~ 66 (518)
T KOG0883|consen 11 MYLTTTEWKS-----IYGGKKDTGENRTQFKRLPFNHCSLTMLPFEDPVCTVDGTVFDLTA 66 (518)
T ss_pred eEEeehhhhh-----hcCCCCCCcccccccccCChhhceeccccccCcccccCCcEEeeeh
Confidence 35677 7664 3666554321 11 23699999999999999 42 333666654
No 4
>KOG0317|consensus
Probab=28.51 E-value=30 Score=28.22 Aligned_cols=19 Identities=21% Similarity=0.287 Sum_probs=15.9
Q ss_pred cceecccccccc----------chhHHHH
Q psy12976 49 DCCCLTLQHSSY----------LNQVLIF 67 (87)
Q Consensus 49 d~C~LcLqpard----------~~ec~~~ 67 (87)
.-|.|||.+-.+ |..||..
T Consensus 240 ~kC~LCLe~~~~pSaTpCGHiFCWsCI~~ 268 (293)
T KOG0317|consen 240 RKCSLCLENRSNPSATPCGHIFCWSCILE 268 (293)
T ss_pred CceEEEecCCCCCCcCcCcchHHHHHHHH
Confidence 579999999877 7888765
No 5
>PF15130 DUF4566: Domain of unknown function (DUF4566)
Probab=20.80 E-value=27 Score=27.79 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=23.2
Q ss_pred CCCCCccchh-hhhcchhhcCCCccceeeCCCcccCccceecccccc
Q psy12976 13 KRSRCAVYTY-EKKKDAEASGYGTQNQRVGKDSVKDFDCCCLTLQHS 58 (87)
Q Consensus 13 nnTa~~vfTy-ERkk~~~~sgyGTq~~RLgkDS~k~Fd~C~LcLqpa 58 (87)
||...+||+| .|+.. ||-+.. .--|-=|+|||---
T Consensus 182 nNP~QsvFlfidrq~l------~tpk~k-----a~~fkLs~lCL~lp 217 (241)
T PF15130_consen 182 NNPEQSVFLFIDRQQL------QTPKNK-----ATMFKLSSLCLFLP 217 (241)
T ss_pred cCCCceEEEEEeHhhh------CCcchh-----hHHHHHhhhheecc
Confidence 7888999999 88864 443221 11266789998543
No 6
>KOG3507|consensus
Probab=19.24 E-value=81 Score=20.54 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=18.3
Q ss_pred chhHHHHHHHHHHHHhHHHHhhhh
Q psy12976 61 LNQVLIFDLLILKHRINLINQFQS 84 (87)
Q Consensus 61 ~~ec~~~~ll~qk~~i~~~~~~~~ 84 (87)
|+||-+-=|. |++++.+.|||+
T Consensus 40 CReCG~RIly--KkRtkrlvqfea 61 (62)
T KOG3507|consen 40 CRECGYRILY--KKRTKRLVQFEA 61 (62)
T ss_pred hhhcchHHHH--HHHHhhhheeec
Confidence 9999988765 688888888875
No 7
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=19.21 E-value=1.4e+02 Score=23.55 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=16.2
Q ss_pred ceecccccccc----------chhHHHHH
Q psy12976 50 CCCLTLQHSSY----------LNQVLIFD 68 (87)
Q Consensus 50 ~C~LcLqpard----------~~ec~~~~ 68 (87)
-|..|+.|..+ |+.|..+.
T Consensus 3 ~C~~C~~~~t~p~i~fd~~GvC~~C~~~~ 31 (343)
T TIGR03573 3 FCKRCVMPTTRPGITFDEDGVCSACRNFE 31 (343)
T ss_pred cCCCCCCCCCCCCeeECCCCCchhhhhHH
Confidence 49999999877 99999875
No 8
>PRK10863 anti-RNA polymerase sigma factor SigE; Provisional
Probab=19.10 E-value=1e+02 Score=23.89 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=17.0
Q ss_pred HHHHHHHHHhH-HHHhhhhhc
Q psy12976 67 FDLLILKHRIN-LINQFQSQT 86 (87)
Q Consensus 67 ~~ll~qk~~i~-~~~~~~~~~ 86 (87)
.-+..|++||+ .|..||.|.
T Consensus 164 ~q~~eq~~RIna~lqd~elQ~ 184 (216)
T PRK10863 164 QQVQEQRRRINAMLQDYELQR 184 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 35889999999 999999873
No 9
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=16.65 E-value=1.2e+02 Score=16.26 Aligned_cols=18 Identities=11% Similarity=0.111 Sum_probs=11.2
Q ss_pred eecccccccc-----------chhHHHHH
Q psy12976 51 CCLTLQHSSY-----------LNQVLIFD 68 (87)
Q Consensus 51 C~LcLqpard-----------~~ec~~~~ 68 (87)
|.+|+...++ |.+|+..-
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~ 29 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKY 29 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHH
Confidence 5566666555 78996553
No 10
>PF04641 Rtf2: Rtf2 RING-finger
Probab=16.17 E-value=1.1e+02 Score=23.13 Aligned_cols=30 Identities=20% Similarity=0.160 Sum_probs=23.9
Q ss_pred ccCccceecccccccc----c-------hhHHHHHHHHHHH
Q psy12976 45 VKDFDCCCLTLQHSSY----L-------NQVLIFDLLILKH 74 (87)
Q Consensus 45 ~k~Fd~C~LcLqpard----~-------~ec~~~~ll~qk~ 74 (87)
..+|.+|+|+++|-.+ | +|=||.=||...+
T Consensus 31 ~~~w~~CaLS~~pL~~PiV~d~~G~LynKeaile~Ll~~~~ 71 (260)
T PF04641_consen 31 EARWTHCALSQQPLEDPIVSDRLGRLYNKEAILEFLLDKKK 71 (260)
T ss_pred hCCcCcccCcCCccCCCeeeCCCCeeEcHHHHHHHHHhcCc
Confidence 3579999999999888 2 5888888887643
Done!