Query 032825
Match_columns 133
No_of_seqs 107 out of 401
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:24:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032825.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032825hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0440 Cell cycle-associated 100.0 7E-62 1.5E-66 386.0 13.6 130 2-133 112-242 (243)
2 PF03637 Mob1_phocein: Mob1/ph 100.0 4.2E-59 9.1E-64 359.3 13.5 120 2-123 55-175 (175)
3 KOG1903 Cell cycle-associated 100.0 5.2E-55 1.1E-59 335.0 13.1 130 2-131 87-217 (217)
4 KOG1852 Cell cycle-associated 99.9 3.3E-24 7.1E-29 165.0 4.6 113 2-122 96-210 (223)
5 cd00397 DNA_BRE_C DNA breaking 52.7 61 0.0013 22.2 5.8 32 44-75 84-115 (164)
6 PHA03074 late transcription fa 40.9 37 0.00081 27.4 3.5 84 27-112 59-146 (225)
7 PRK09870 tyrosine recombinase; 35.6 77 0.0017 23.7 4.4 48 24-75 78-130 (200)
8 KOG3261 Uncharacterized conser 34.0 34 0.00075 27.0 2.2 19 69-87 121-140 (202)
9 cd00800 INT_Lambda_C Lambda in 30.1 1.2E+02 0.0026 21.5 4.5 35 23-57 60-96 (162)
10 PF05029 TIMELESS_C: Timeless 27.3 93 0.002 28.3 4.2 47 25-78 9-55 (566)
11 COG4687 Uncharacterized protei 25.4 91 0.002 23.0 3.1 34 35-75 88-121 (122)
12 cd01197 INT_FimBE_C FimB and F 25.1 1.4E+02 0.003 21.5 4.1 46 24-73 70-120 (180)
13 cd01198 INT_ASSRA_C Archaeal s 24.0 1.9E+02 0.0041 20.9 4.7 29 45-73 86-115 (186)
14 PRK00811 spermidine synthase; 23.8 1.5E+02 0.0032 24.0 4.4 70 10-84 150-219 (283)
15 PF04417 DUF501: Protein of un 23.5 2.8E+02 0.0061 20.5 5.5 74 50-123 16-90 (139)
16 PF10441 Urb2: Urb2/Npa2 famil 23.1 3.6E+02 0.0079 20.9 6.7 62 33-106 28-89 (223)
17 PF12387 Peptidase_C74: Pestiv 22.7 3.2E+02 0.007 21.7 5.8 69 49-120 25-106 (200)
18 cd01186 INT_SG3_C INT_SG3, DNA 22.5 2.2E+02 0.0047 20.7 4.8 52 24-77 69-120 (180)
19 cd01049 RNRR2 Ribonucleotide R 22.5 1E+02 0.0022 24.6 3.2 30 29-58 251-280 (288)
20 COG1140 NarY Nitrate reductase 22.1 66 0.0014 28.7 2.1 34 1-65 24-59 (513)
21 TIGR01660 narH nitrate reducta 20.5 1.1E+02 0.0023 27.7 3.1 34 1-65 24-59 (492)
22 PF09454 Vps23_core: Vps23 cor 20.3 2.1E+02 0.0046 18.5 3.8 40 33-80 24-63 (65)
No 1
>KOG0440 consensus Cell cycle-associated protein Mob1-1 [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7e-62 Score=386.05 Aligned_cols=130 Identities=61% Similarity=1.050 Sum_probs=126.5
Q ss_pred CCCCCCCC-CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHH
Q 032825 2 TDKDGKLH-RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHI 80 (133)
Q Consensus 2 tcp~M~ag-~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHi 80 (133)
|||.|+|| +++|+|+|+. +||++||||||||++|+|||++++||+|||||+|.|||+||.+.||+|+||||||||||
T Consensus 112 sCp~Msag~~yeY~W~D~~--~kp~~~sApqYId~lmtw~q~~~dde~iFPtK~g~~FP~nF~~~vk~Ilr~lFrvyAHi 189 (243)
T KOG0440|consen 112 SCPHMSAGPNYEYLWADEK--GKPVRVSAPQYIDYLMTWCQNQLDDENIFPTKYGNPFPGNFESVVKKILRRLFRVYAHI 189 (243)
T ss_pred cCccccCCCcceeeeeccc--CCccccCchHHHHHHHHHHHHhccccccCccccCCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 89999999 9999999965 68999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCccccCcHHHHHHHhcccC
Q 032825 81 YHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGLIDKKELGPLQELIDSIIVPY 133 (133)
Q Consensus 81 Y~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~Li~~kel~pL~~li~~l~~~~ 133 (133)
|++||+.|.+|++++||||+||||+.|++||+|||+||++||++||+.|...+
T Consensus 190 Y~~Hf~~i~~L~l~ahlNt~F~Hf~~f~~eF~LiD~kE~aPl~~Li~~l~~~d 242 (243)
T KOG0440|consen 190 YHSHFDEIVALQLEAHLNTSFKHFILFAREFQLLDKKETAPLLELIESLLSQD 242 (243)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccCHHhhhhHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999987653
No 2
>PF03637 Mob1_phocein: Mob1/phocein family; InterPro: IPR005301 Mob1 is an essential Saccharomyces cerevisiae (Baker's yeast) protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature []. This family also includes phocein Q9QYW3 from SWISSPROT, a rat protein that by yeast two hybrid interacts with striatin [].; PDB: 2HJN_A 1PI1_A 1R3B_A.
Probab=100.00 E-value=4.2e-59 Score=359.27 Aligned_cols=120 Identities=63% Similarity=1.116 Sum_probs=109.8
Q ss_pred CCCCCCCC-CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHH
Q 032825 2 TDKDGKLH-RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHI 80 (133)
Q Consensus 2 tcp~M~ag-~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHi 80 (133)
|||.|+|| +|+|+|+|++ ++|++||||+||+++|+|++++|+||++|||+.|++||++|.++|++||||||||||||
T Consensus 55 tCP~Msag~~~~Ylw~d~~--~kp~~~~A~~Yi~~~l~w~~~~l~d~~iFPt~~~~~fp~~f~~~v~~I~rrLfRvyaHi 132 (175)
T PF03637_consen 55 TCPTMSAGPNWEYLWADHK--KKPVKCSAPQYIDHLLDWIQSQLNDEKIFPTKPGVPFPKNFKKTVKKIFRRLFRVYAHI 132 (175)
T ss_dssp TTSSEESSTTCEE-BSSST--TS-BS--HHHHHHHHHHHHHHHHTSTTTSSSSTTS-TTTTHHHHHHHHHHHHHHHHHHH
T ss_pred cCcCccCCccceeeeeccC--CCCcccCHHHHHHHHHHHHHHHccCcccCCCccccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999 9999999965 57999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCccccCcHH
Q 032825 81 YHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGLIDKKELGPLQ 123 (133)
Q Consensus 81 Y~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~Li~~kel~pL~ 123 (133)
|++|++.|.++|+++|||++||||++|++||+||++||++||+
T Consensus 133 Y~~H~~~~~~l~~~~hln~~F~hF~~f~~eF~Li~~~el~pL~ 175 (175)
T PF03637_consen 133 YHHHFEQFVELELEAHLNTCFKHFVLFAREFDLIDEKELEPLQ 175 (175)
T ss_dssp HHHCHHHHHHTT-HHHHHHHHHHHHHHHHHHT-S-GGGGGGGH
T ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCCHHHhcccC
Confidence 9999999999999999999999999999999999999999996
No 3
>KOG1903 consensus Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=5.2e-55 Score=335.05 Aligned_cols=130 Identities=51% Similarity=0.974 Sum_probs=128.3
Q ss_pred CCCCCCCC-CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHH
Q 032825 2 TDKDGKLH-RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHI 80 (133)
Q Consensus 2 tcp~M~ag-~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHi 80 (133)
|||.|++| +|||+|+|+..||||+.+|||+||+++||||+.+||||.+|||..|+|||+||.+++++|..||||||.|+
T Consensus 87 sCP~MsGG~rYEY~WqD~~~ykkPt~L~Ap~Ym~lLMDWIE~~INnE~vFPt~~~vpFPKnF~qi~~KILtRLFRVFVHV 166 (217)
T KOG1903|consen 87 SCPVMSGGPRYEYRWQDERKYKKPTALSAPRYMALLMDWIEVQINNEEVFPTSVGVPFPKNFLQICKKILTRLFRVFVHV 166 (217)
T ss_pred CCCcccCCCcceeEecccccccCCccCCcHHHHHHHHHHHHHhccccccccccCCCCCcHhHHHHHHHHHHHHHHHHhhh
Confidence 89999999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCccccCcHHHHHHHhcc
Q 032825 81 YHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGLIDKKELGPLQELIDSIIV 131 (133)
Q Consensus 81 Y~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~Li~~kel~pL~~li~~l~~ 131 (133)
|.|||+.+.++|+|+|+|||+|||.+|++||+|||.|||+||+++.+.++.
T Consensus 167 YIHHFDri~~mGaE~HvNtcYKHFYyFv~Ef~li~~kELEpLkeMT~R~c~ 217 (217)
T KOG1903|consen 167 YIHHFDRILSMGAEAHVNTCYKHFYYFVTEFGLIDTKELEPLKEMTERICH 217 (217)
T ss_pred hhhhhHHHHHhccHHHHHHHHHHHHHHhhhccccchhhcchHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999874
No 4
>KOG1852 consensus Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning]
Probab=99.89 E-value=3.3e-24 Score=164.95 Aligned_cols=113 Identities=21% Similarity=0.405 Sum_probs=104.6
Q ss_pred CCCCCCCC-CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHH
Q 032825 2 TDKDGKLH-RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHI 80 (133)
Q Consensus 2 tcp~M~ag-~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHi 80 (133)
||.+|+|+ +|.|+|+.+ |.|.+|||++|..+++|.+.-+||+.+.|||+.+. .......+..++||.||||+|.
T Consensus 96 tctqmtateqwiflcaah---ktpkecpaidytrhtldgaacllnsnkyfpsrvsi--kessv~klgsvcrrvyrifsha 170 (223)
T KOG1852|consen 96 TCTQMTATEQWIFLCAAH---KTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSI--KESSVAKLGSVCRRVYRIFSHA 170 (223)
T ss_pred HhhhhhhHhHHHhhhhhc---CCcccCCcccchhhccccccccccCCccCCcccch--hhhhHHHHHHHHHHHHHHHHHH
Confidence 89999999 999999988 58999999999999999999999999999999876 6888999999999999999999
Q ss_pred hhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCcccc-CcH
Q 032825 81 YHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGLIDKKEL-GPL 122 (133)
Q Consensus 81 Y~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~Li~~kel-~pL 122 (133)
|+||+..|.+.+.|+||+ ++|..|+..|+|++.+.| .|+
T Consensus 171 ~fhhr~ifdefe~etylc---~rft~~v~kynlms~e~livpi 210 (223)
T KOG1852|consen 171 YFHHRKIFDEFENETYLC---HRFTKFVSKYNLMSKENLIVPI 210 (223)
T ss_pred HHHHHHHHHHhhhhhHHH---HHHHHHHHhhhhccccceeeec
Confidence 999999999999999998 566778889999998875 554
No 5
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=52.67 E-value=61 Score=22.20 Aligned_cols=32 Identities=38% Similarity=0.526 Sum_probs=21.6
Q ss_pred cCCCCCCCCCCCCCCCcchHHHHHHHHHHHHH
Q 032825 44 LDDESIFPQKLGAPFPSNFKEVVKTIFKRLFR 75 (133)
Q Consensus 44 l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfR 75 (133)
.+++.+|++..+.+........+.++++++-.
T Consensus 84 ~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (164)
T cd00397 84 GDEEYLFPSRRGGPAATLSRRNVKRIFKAAGR 115 (164)
T ss_pred CCCCceeecCCCCCccCCcHHHHHHHHHHHHH
Confidence 46788999988775554555666666666554
No 6
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=40.90 E-value=37 Score=27.45 Aligned_cols=84 Identities=15% Similarity=0.294 Sum_probs=57.3
Q ss_pred cChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHH----HHHHHHHHHHHHHHhhhhHHHHHhhchhhHHHHHHH
Q 032825 27 VSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVV----KTIFKRLFRVYAHIYHSHFQKIVSLKEEAHLNTCFK 102 (133)
Q Consensus 27 ~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v----~~I~rrLfRvyaHiY~~H~~~~~~l~~~~hlNt~fk 102 (133)
++-.|=.+.+.+-..+++++..+=+......|-.+|.+.= ++=+|..|-+.-|+=-.-.. + .-+--.-++-.|+
T Consensus 59 lls~qcs~~ii~ell~lm~kn~i~~~didan~vs~fLK~~~~inkKdYklvfeiiN~~~~e~ln-L-ttekInei~eIFk 136 (225)
T PHA03074 59 LLSNQCSGEIISELLELMNKNQISTKDVDANFVSSFLKAKERINKKDYKLVFEIINQVKDEKLN-L-TTEKINEVVEIFK 136 (225)
T ss_pred HHHhHhhHHHHHHHHHHHHHccCChhhhhHHHHHHHHHHHHhcCchhHHHHHHHHHHhhhhccc-c-cHHHHHHHHHHHH
Confidence 4445667777888888899999988888887888887665 44477777766655333222 1 1111234567899
Q ss_pred HHHHHHHHhC
Q 032825 103 HFILFTCEFG 112 (133)
Q Consensus 103 hF~~F~~eF~ 112 (133)
||+.|++|..
T Consensus 137 ~lvfF~qent 146 (225)
T PHA03074 137 HLVFFCQENT 146 (225)
T ss_pred HHHHHHhccC
Confidence 9999999854
No 7
>PRK09870 tyrosine recombinase; Provisional
Probab=35.59 E-value=77 Score=23.73 Aligned_cols=48 Identities=17% Similarity=0.297 Sum_probs=30.3
Q ss_pred CcccChHHHHHHHHHHHHHh-----cCCCCCCCCCCCCCCCcchHHHHHHHHHHHHH
Q 032825 24 PIEVSAPKYVEYLMDWIESQ-----LDDESIFPQKLGAPFPSNFKEVVKTIFKRLFR 75 (133)
Q Consensus 24 p~~~sA~~YI~~~m~wi~~~-----l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfR 75 (133)
.++++ ++-++.+-.|+... .+++-+||+..|.+..+ ..+.++++++.+
T Consensus 78 ~vpl~-~~~~~~l~~~~~~~~~~~~~~~~~lf~~~~g~~~s~---~~~~~~~k~~~~ 130 (200)
T PRK09870 78 THPLL-NKEIQALKNWLSIRTSYPHAESEWVFLSRKGNPLSR---QQFYHIISTSGG 130 (200)
T ss_pred EEECC-HHHHHHHHHHHHhcccCCCCCCCceeeCCCCCcCCH---HHHHHHHHHHHH
Confidence 45554 34577777887643 35678999988875543 445566666544
No 8
>KOG3261 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.98 E-value=34 Score=26.99 Aligned_cols=19 Identities=47% Similarity=0.856 Sum_probs=13.8
Q ss_pred HHHHHHHHH-HHHhhhhHHH
Q 032825 69 IFKRLFRVY-AHIYHSHFQK 87 (133)
Q Consensus 69 I~rrLfRvy-aHiY~~H~~~ 87 (133)
=|||-|||. |-.|..||..
T Consensus 121 ~frRkFRVI~a~~y~k~faS 140 (202)
T KOG3261|consen 121 EFRRKFRVIHAPLYFKHFAS 140 (202)
T ss_pred HHHhheeeeccHHHHHHhhc
Confidence 578999875 6677777743
No 9
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.
Probab=30.06 E-value=1.2e+02 Score=21.45 Aligned_cols=35 Identities=3% Similarity=0.100 Sum_probs=19.9
Q ss_pred CCcccChHHHHHHHHHHHHHhc--CCCCCCCCCCCCC
Q 032825 23 KPIEVSAPKYVEYLMDWIESQL--DDESIFPQKLGAP 57 (133)
Q Consensus 23 kp~~~sA~~YI~~~m~wi~~~l--~de~iFPt~~~~~ 57 (133)
++..+|-++.+..++......- +++-+||+..|.+
T Consensus 60 ~~r~vpl~~~~~~~l~~~~~~~~~~~~~vf~~~~~~~ 96 (162)
T cd00800 60 AKLAIPLSPSLREVIERCRDLSRVSSPYLVHTRPGGK 96 (162)
T ss_pred CeeEEECCHHHHHHHHHHHhhcccCCceEEEcCCCCC
Confidence 3445555555444444333332 6788999987653
No 10
>PF05029 TIMELESS_C: Timeless protein C terminal region; InterPro: IPR007725 The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2) []. mTim has been shown to be essential for embryonic development, but does not have substantiated circadian function []. Some family members contain a SANT domain in this region.
Probab=27.26 E-value=93 Score=28.27 Aligned_cols=47 Identities=19% Similarity=0.340 Sum_probs=41.5
Q ss_pred cccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHH
Q 032825 25 IEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYA 78 (133)
Q Consensus 25 ~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvya 78 (133)
.+|++.=|=-.++.-.+++|+|+...|+ +.+...++.|+|++|+...
T Consensus 9 ~~~~~mLfqlsl~~lF~~il~~~~~~~~-------kEl~~f~~~ilrkffk~~~ 55 (566)
T PF05029_consen 9 LKMSVMLFQLSLFRLFQRILKDPKSLDS-------KELEEFVKYILRKFFKKAE 55 (566)
T ss_pred CCCceeeHHHHHHHHHHHHHhCcccCCH-------HHHHHHHHHHHHHHHHHHh
Confidence 5788888888999999999999987776 8899999999999998764
No 11
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.42 E-value=91 Score=22.98 Aligned_cols=34 Identities=21% Similarity=0.433 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHH
Q 032825 35 YLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFR 75 (133)
Q Consensus 35 ~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfR 75 (133)
.++.|+..-++++++-- .++|..++++-||++|+
T Consensus 88 ~iLk~ir~yvg~~~vV~-------spsl~d~~kr~fk~~f~ 121 (122)
T COG4687 88 KILKKIREYVGNEKVVK-------SPSLLDTFKRAFKSLFK 121 (122)
T ss_pred hHHHHHHHHhCccceec-------chHHHHHHHHHHHHHhc
Confidence 36888999999888743 37889999999999885
No 12
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI.
Probab=25.12 E-value=1.4e+02 Score=21.49 Aligned_cols=46 Identities=26% Similarity=0.507 Sum_probs=24.8
Q ss_pred CcccChHHHHHHHHHHHHH-----hcCCCCCCCCCCCCCCCcchHHHHHHHHHHH
Q 032825 24 PIEVSAPKYVEYLMDWIES-----QLDDESIFPQKLGAPFPSNFKEVVKTIFKRL 73 (133)
Q Consensus 24 p~~~sA~~YI~~~m~wi~~-----~l~de~iFPt~~~~~fp~~F~~~v~~I~rrL 73 (133)
.++++..- ++.+-.|.+. .-+++-+||+..|.++.+ +.+.+++|++
T Consensus 70 ~~pi~~~~-~~~l~~~~~~~~~~~~~~~~~lf~~~~g~~~~~---~~~~~~~~~~ 120 (180)
T cd01197 70 THPLRDDE-LEALKNWLEIRAWKGLPDSDWIFLSRRGGPLSR---QQVYKLIRRL 120 (180)
T ss_pred eeECCHHH-HHHHHHHHHHhccCCCCCCCeEEeCCCCCcCCH---HHHHHHHHHH
Confidence 44554322 3444455544 235667999988876543 3444455544
No 13
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. Members of this CD are archael in origin. No biochemical characterization is available for the proteins of this subgroup at this point.
Probab=23.98 E-value=1.9e+02 Score=20.87 Aligned_cols=29 Identities=14% Similarity=0.036 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCCCCCc-chHHHHHHHHHHH
Q 032825 45 DDESIFPQKLGAPFPS-NFKEVVKTIFKRL 73 (133)
Q Consensus 45 ~de~iFPt~~~~~fp~-~F~~~v~~I~rrL 73 (133)
+++.+||+..+.+.+. .+...++++.+++
T Consensus 86 ~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~ 115 (186)
T cd01198 86 PADALFIGTQDGWGCRRLVYEMVTGMARRH 115 (186)
T ss_pred CCCceEEecCCCcccchhHHHHHHHHHHHh
Confidence 5678999987765533 3345555655554
No 14
>PRK00811 spermidine synthase; Provisional
Probab=23.76 E-value=1.5e+02 Score=24.04 Aligned_cols=70 Identities=16% Similarity=0.370 Sum_probs=51.4
Q ss_pred CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHHhhhh
Q 032825 10 RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHIYHSH 84 (133)
Q Consensus 10 ~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHiY~~H 84 (133)
.|...+.|.. .|...+..-|-...+..+.+.|++..+|=...+.++-. ...++.|.++|=.+|.|++.-+
T Consensus 150 ~yDvIi~D~~---dp~~~~~~l~t~ef~~~~~~~L~~gGvlv~~~~~~~~~--~~~~~~i~~tl~~~F~~v~~~~ 219 (283)
T PRK00811 150 SFDVIIVDST---DPVGPAEGLFTKEFYENCKRALKEDGIFVAQSGSPFYQ--ADEIKDMHRKLKEVFPIVRPYQ 219 (283)
T ss_pred cccEEEECCC---CCCCchhhhhHHHHHHHHHHhcCCCcEEEEeCCCcccC--HHHHHHHHHHHHHHCCCEEEEE
Confidence 6777777753 34444445677788889999999999998876665432 5678888999999988876533
No 15
>PF04417 DUF501: Protein of unknown function (DUF501); InterPro: IPR007511 This is a family of uncharacterised bacterial proteins.
Probab=23.47 E-value=2.8e+02 Score=20.54 Aligned_cols=74 Identities=20% Similarity=0.170 Sum_probs=51.4
Q ss_pred CC-CCCCCCCCcchHHHHHHHHHHHHHHHHHHhhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCccccCcHH
Q 032825 50 FP-QKLGAPFPSNFKEVVKTIFKRLFRVYAHIYHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGLIDKKELGPLQ 123 (133)
Q Consensus 50 FP-t~~~~~fp~~F~~~v~~I~rrLfRvyaHiY~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~Li~~kel~pL~ 123 (133)
.| ...|.|||..|-=++..+.+..-|+=+.=.-.-.+...+-+.+----..-.|--+-..+-.|+++++.+=++
T Consensus 16 ~P~l~~g~PFPTlfwLtcP~L~~~isrLE~~G~i~~l~~~l~~d~~l~~~~~~aH~~y~~~R~~ll~~~~~~~~~ 90 (139)
T PF04417_consen 16 APRLVDGKPFPTLFWLTCPYLVKAISRLEAEGGIAELEERLAEDEELAEAYRRAHRRYAALRWSLLSEEEREFLE 90 (139)
T ss_pred ccCCCCCccCCccHhhcCHHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhcchhHHHHHH
Confidence 45 566899999998888888888888877777766666554443311111236777888899999877755443
No 16
>PF10441 Urb2: Urb2/Npa2 family; InterPro: IPR018849 This entry represents a conserved domain found towards the C terminus of proteins involved in ribosome biogenesis, such as the Urb2 protein from yeast [].
Probab=23.11 E-value=3.6e+02 Score=20.91 Aligned_cols=62 Identities=15% Similarity=0.219 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHHhhhhHHHHHhhchhhHHHHHHHHHHH
Q 032825 33 VEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHIYHSHFQKIVSLKEEAHLNTCFKHFIL 106 (133)
Q Consensus 33 I~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHiY~~H~~~~~~l~~~~hlNt~fkhF~~ 106 (133)
|+.++..+.....+.. +....+....||.++.++..+|-.+|+..+.. -.+++..++...+.
T Consensus 28 ie~~l~~~~~~~~~~~----------~~~~~~~~~~if~~~~~ll~~il~~hr~~l~~--r~hll~~~l~~LL~ 89 (223)
T PF10441_consen 28 IEQILSILSTLFSSLR----------NTLSADSSPSIFISLCRLLSSILRHHRFKLSG--RFHLLLSVLQRLLR 89 (223)
T ss_pred HHHHHHHHHHHHcccc----------cccccchhHHHHHHHHHHHHHHHHHhHHHHcC--CChHHHHHHHHHHH
Confidence 4455555555554433 33445566778888999999999999998865 45677777776654
No 17
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=22.73 E-value=3.2e+02 Score=21.68 Aligned_cols=69 Identities=19% Similarity=0.304 Sum_probs=46.8
Q ss_pred CCCCCCCCCCCcch-HHHHHHH-----------HHHHHHHHHHHhhhhHHHHHhhchhhHHHHHHHHHHHHHHHhCC-CC
Q 032825 49 IFPQKLGAPFPSNF-KEVVKTI-----------FKRLFRVYAHIYHSHFQKIVSLKEEAHLNTCFKHFILFTCEFGL-ID 115 (133)
Q Consensus 49 iFPt~~~~~fp~~F-~~~v~~I-----------~rrLfRvyaHiY~~H~~~~~~l~~~~hlNt~fkhF~~F~~eF~L-i~ 115 (133)
+|||+.....-.++ .+.++.+ +=.+|-+.--.|+-|...+.++.-.+.+= .+++.--.|-|- +|
T Consensus 25 lfPS~qk~~~~~~~~lpllra~LIsCiSS~Wq~~Yl~yL~ie~~Yy~H~kIIeEiaGgtN~i---SR~iAaliElNW~~d 101 (200)
T PF12387_consen 25 LFPSRQKGGSCTGFLLPLLRAILISCISSKWQCFYLLYLIIELSYYMHRKIIEEIAGGTNFI---SRLIAALIELNWAMD 101 (200)
T ss_pred EccccccCCCCccchHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHcCcchHH---HHHHHHHHHhhcccc
Confidence 69999877665555 6666654 34677788899999999999986555432 456655555443 45
Q ss_pred ccccC
Q 032825 116 KKELG 120 (133)
Q Consensus 116 ~kel~ 120 (133)
++|..
T Consensus 102 ~eE~k 106 (200)
T PF12387_consen 102 EEESK 106 (200)
T ss_pred chhhc
Confidence 55554
No 18
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available.
Probab=22.50 E-value=2.2e+02 Score=20.67 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=30.8
Q ss_pred CcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHH
Q 032825 24 PIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVY 77 (133)
Q Consensus 24 p~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvy 77 (133)
.++++ ++-+..+..|+...-+++-+||+..|..- +=....+.++++++.+-.
T Consensus 69 ~vpl~-~~l~~~l~~~~~~~~~~~~lf~~~~~~~~-~~~~~~~~~~~k~~~~~~ 120 (180)
T cd01186 69 RIYLN-PILKEELLYYIKDLEENEYLFQSRKGGNR-PITRQQAYRILKKAAEQV 120 (180)
T ss_pred EEEEC-HHHHHHHHHHHHhCCCcCceEEecCCCCC-CccHHHHHHHHHHHHHHc
Confidence 35554 23345555666655678999999876531 223455666777666533
No 19
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-
Probab=22.50 E-value=1e+02 Score=24.62 Aligned_cols=30 Identities=27% Similarity=0.462 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 032825 29 APKYVEYLMDWIESQLDDESIFPQKLGAPF 58 (133)
Q Consensus 29 A~~YI~~~m~wi~~~l~de~iFPt~~~~~f 58 (133)
-.+||.++.+..-..|.-+++||++...|+
T Consensus 251 ~~~yi~y~an~~l~~lG~~~~f~~~~~nP~ 280 (288)
T cd01049 251 MKQYIEYVANRRLENLGLEKLFNVEDKNPF 280 (288)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
Confidence 458999999999999999999999644433
No 20
>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]
Probab=22.13 E-value=66 Score=28.66 Aligned_cols=34 Identities=26% Similarity=0.531 Sum_probs=24.1
Q ss_pred CCCCCCCCC--CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHH
Q 032825 1 MTDKDGKLH--RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEV 65 (133)
Q Consensus 1 ~tcp~M~ag--~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~ 65 (133)
.||++-=-+ +.||.|-.+.. ||+|+.||+++...
T Consensus 24 vTCKnvWTnR~G~EY~WfNNVE-------------------------------TkPGvGyPk~WEdQ 59 (513)
T COG1140 24 VTCKNVWTNREGMEYAWFNNVE-------------------------------TKPGVGYPKQWEDQ 59 (513)
T ss_pred eeecccccCCCCceeeeecccc-------------------------------cCCCCCCCCcccch
Confidence 367665433 67899987642 77889999888654
No 21
>TIGR01660 narH nitrate reductase, beta subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following: NarH and NarY, both E.Coli, sequences from B. Subtilis, Pseudomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans. This model also matches PFAM pfam00037 for 4Fe-4S binding domain.
Probab=20.48 E-value=1.1e+02 Score=27.74 Aligned_cols=34 Identities=26% Similarity=0.497 Sum_probs=25.8
Q ss_pred CCCCCCCCC--CceEEeccCCCCCCCcccChHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHH
Q 032825 1 MTDKDGKLH--RYEYRWADGVQIKKPIEVSAPKYVEYLMDWIESQLDDESIFPQKLGAPFPSNFKEV 65 (133)
Q Consensus 1 ~tcp~M~ag--~~~YlW~d~~~~kkp~~~sA~~YI~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~ 65 (133)
+||++.=-. +.||.|-.+.. ||+|..||+++...
T Consensus 24 vtCK~~WT~r~G~Eymw~NNVE-------------------------------TkPg~GyP~~we~q 59 (492)
T TIGR01660 24 VTCKNVWTSREGVEYAWFNNVE-------------------------------TKPGIGYPKDWENQ 59 (492)
T ss_pred ccCcCccccCCCcEEEEeeccc-------------------------------cCCCCCCCCChhhh
Confidence 578876433 67899987642 78899999998775
No 22
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=20.35 E-value=2.1e+02 Score=18.48 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHH
Q 032825 33 VEYLMDWIESQLDDESIFPQKLGAPFPSNFKEVVKTIFKRLFRVYAHI 80 (133)
Q Consensus 33 I~~~m~wi~~~l~de~iFPt~~~~~fp~~F~~~v~~I~rrLfRvyaHi 80 (133)
|+-++..+.+.+++.+| + ...|.+.|+.+-|.-|-.-||+
T Consensus 24 ieDtiy~L~~al~~g~I-------~-~d~~lK~vR~LaReQF~~Ral~ 63 (65)
T PF09454_consen 24 IEDTIYYLDRALQRGSI-------D-LDTFLKQVRSLAREQFLKRALI 63 (65)
T ss_dssp HHHHHHHHHHHHHTTSS---------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCC-------C-HHHHHHHHHHHHHHHHHHHHHh
Confidence 66677788888888775 2 3789999999999999988876
Done!