Query 038406
Match_columns 118
No_of_seqs 118 out of 651
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 10:42:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038406.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038406hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0834 CDK9 kinase-activating 100.0 1.1E-35 2.4E-40 231.5 10.7 116 3-118 16-181 (323)
2 KOG0835 Cyclin L [General func 100.0 9.6E-31 2.1E-35 202.1 10.6 115 4-118 2-169 (367)
3 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.2E-27 2.7E-32 185.7 11.1 107 12-118 43-192 (305)
4 COG5333 CCL1 Cdk activating ki 99.9 5.4E-24 1.2E-28 163.5 9.6 103 16-118 36-178 (297)
5 KOG0794 CDK8 kinase-activating 99.9 1.2E-23 2.5E-28 156.6 6.5 106 13-118 29-180 (264)
6 KOG2496 Cdk activating kinase 99.3 4.2E-12 9.1E-17 98.1 6.4 92 6-103 45-170 (325)
7 PRK00423 tfb transcription ini 99.0 1.5E-09 3.3E-14 84.7 9.7 93 26-118 123-245 (310)
8 PF00134 Cyclin_N: Cyclin, N-t 98.8 1.6E-08 3.5E-13 67.9 7.2 70 19-88 25-127 (127)
9 KOG0656 G1/S-specific cyclin D 97.8 9E-05 2E-09 58.7 7.9 83 24-106 77-196 (335)
10 cd00043 CYCLIN Cyclin box fold 97.4 0.00043 9.3E-09 42.4 5.2 39 25-63 2-40 (88)
11 KOG0653 Cyclin B and related k 97.3 0.0016 3.4E-08 52.5 7.9 84 23-106 156-273 (391)
12 smart00385 CYCLIN domain prese 96.7 0.0045 9.7E-08 37.4 4.6 34 30-63 1-34 (83)
13 COG1405 SUA7 Transcription ini 96.2 0.043 9.4E-07 42.7 8.6 90 27-116 99-218 (285)
14 COG5024 Cyclin [Cell division 95.7 0.069 1.5E-06 44.0 8.2 84 23-106 211-327 (440)
15 KOG0655 G1/S-specific cyclin E 94.7 0.33 7.1E-06 38.9 8.8 87 18-105 138-259 (408)
16 PF08613 Cyclin: Cyclin; Inte 94.4 0.2 4.4E-06 35.0 6.4 60 28-87 54-149 (149)
17 KOG4164 Cyclin ik3-1/CABLES [C 91.3 0.24 5.3E-06 40.4 3.5 59 32-90 389-482 (497)
18 KOG1597 Transcription initiati 89.9 6.1 0.00013 31.1 9.9 86 25-110 104-221 (308)
19 PF00382 TFIIB: Transcription 83.4 1.9 4.2E-05 26.0 3.4 28 32-59 1-28 (71)
20 KOG3975 Uncharacterized conser 50.3 45 0.00098 26.1 5.0 65 31-95 189-257 (301)
21 TIGR00873 gnd 6-phosphoglucona 48.8 52 0.0011 27.3 5.6 42 19-60 391-432 (467)
22 PF00393 6PGD: 6-phosphoglucon 28.9 1.5E+02 0.0033 23.3 5.1 50 5-54 201-253 (291)
23 COG2117 Predicted subunit of t 25.9 1.4E+02 0.0031 21.9 4.1 40 77-116 17-70 (198)
24 KOG1675 Predicted cyclin [Gene 25.8 48 0.001 26.5 1.8 33 69-103 268-300 (343)
25 COG4189 Predicted transcriptio 25.4 64 0.0014 25.1 2.3 31 25-55 33-63 (308)
26 TIGR02531 yecD_yerC TrpR-relat 25.3 39 0.00085 21.7 1.0 41 8-48 29-69 (88)
27 KOG0654 G2/Mitotic-specific cy 22.8 1.8E+02 0.0039 23.6 4.5 79 24-102 136-247 (359)
28 KOG3918 Predicted membrane pro 22.6 63 0.0014 22.0 1.7 44 53-96 26-70 (129)
29 PTZ00142 6-phosphogluconate de 22.4 2.2E+02 0.0047 23.7 5.1 39 19-57 397-435 (470)
30 PRK00423 tfb transcription ini 21.7 1.6E+02 0.0034 23.0 4.0 30 28-57 219-248 (310)
31 KOG1597 Transcription initiati 21.4 1.8E+02 0.0039 23.1 4.2 30 27-56 202-231 (308)
32 smart00497 IENR1 Intron encode 21.4 1.3E+02 0.0027 16.4 2.6 19 32-50 20-38 (53)
33 KOG2653 6-phosphogluconate deh 20.6 2.4E+02 0.0052 23.4 4.8 39 18-56 399-437 (487)
No 1
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.1e-35 Score=231.46 Aligned_cols=116 Identities=36% Similarity=0.616 Sum_probs=111.2
Q ss_pred hhhhh-hCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH------------------
Q 038406 3 LHRRE-FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD------------------ 63 (118)
Q Consensus 3 ~~~l~-~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~------------------ 63 (118)
.++++ +|||+++|++.++|...|..++.||+++|.+|++|+.++|||++||||||+.+|++
T Consensus 16 ~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKv 95 (323)
T KOG0834|consen 16 KEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKV 95 (323)
T ss_pred HHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhc
Confidence 46677 99999999999999999999999999999999999999999999999999999988
Q ss_pred ---------------------------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCCH----HHHHH
Q 038406 64 ---------------------------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLVC----DLAKS 112 (118)
Q Consensus 64 ---------------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~----~l~q~ 112 (118)
.||++|++|+..|.+||++|+|||+|+|||+||++|+++++.++ .+++.
T Consensus 96 Eetp~kl~dIi~~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~ 175 (323)
T KOG0834|consen 96 EETPRKLEDIIKVSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQA 175 (323)
T ss_pred ccCcccHHHHHHHHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHH
Confidence 58899999999999999999999999999999999999999985 59999
Q ss_pred HhhhcC
Q 038406 113 SMEFHK 118 (118)
Q Consensus 113 Aw~~~N 118 (118)
||+|+|
T Consensus 176 Aw~~~n 181 (323)
T KOG0834|consen 176 AWNFVN 181 (323)
T ss_pred HHHHhc
Confidence 999998
No 2
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.97 E-value=9.6e-31 Score=202.09 Aligned_cols=115 Identities=28% Similarity=0.482 Sum_probs=108.0
Q ss_pred hhhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------
Q 038406 4 HRREFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------- 63 (118)
Q Consensus 4 ~~l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------- 63 (118)
+.+.+|||..||++.+.|..+|..||+|||++|++|+|||.++||++++|+|||..+|+.
T Consensus 2 ~~i~~~~s~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE 81 (367)
T KOG0835|consen 2 EKIDSTPSLQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEE 81 (367)
T ss_pred CcccCchhhhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhcc
Confidence 357899999999999999999999999999999999999999999999999999999877
Q ss_pred -------------------------------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC--HHHH
Q 038406 64 -------------------------------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV--CDLA 110 (118)
Q Consensus 64 -------------------------------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~--~~l~ 110 (118)
.|..++..++.+|..||++||||++|+|||+.++.|++.|++. .+|.
T Consensus 82 ~Prr~rdVinVFh~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~ 161 (367)
T KOG0835|consen 82 EPRRIRDVINVFHYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLL 161 (367)
T ss_pred ccccHhHHHHHHHHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHH
Confidence 3446788999999999999999999999999999999999998 5579
Q ss_pred HHHhhhcC
Q 038406 111 KSSMEFHK 118 (118)
Q Consensus 111 q~Aw~~~N 118 (118)
|.||+|.|
T Consensus 162 Q~~wNfmN 169 (367)
T KOG0835|consen 162 QAAWNFMN 169 (367)
T ss_pred HHHHHhhh
Confidence 99999998
No 3
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.95 E-value=1.2e-27 Score=185.69 Aligned_cols=107 Identities=24% Similarity=0.337 Sum_probs=96.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHHHHhhhcchH--------------------------
Q 038406 12 KKDGISFKKDSELWKLYCSFLQELGTKLK--LPQVIVACAMMLCHQFYMHQLHD-------------------------- 63 (118)
Q Consensus 12 ~~~gi~~~~E~~~r~~~~~~I~~~g~~L~--lp~~~~aTA~~~~hRFy~~~S~~-------------------------- 63 (118)
...++|+++|..+|.+||.+|+++|.+|+ +|+.|+|||++||||||+++|++
T Consensus 43 ~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~ 122 (305)
T TIGR00569 43 KPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSID 122 (305)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHH
Confidence 34699999999999999999999999999 99999999999999999999998
Q ss_pred --------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC-------CHHHHHHHhhhcC
Q 038406 64 --------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL-------VCDLAKSSMEFHK 118 (118)
Q Consensus 64 --------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~-------~~~l~q~Aw~~~N 118 (118)
....+++.|+++|+.||++||||+.|+|||+++.+|+.+++. .+.+.|.||+|+|
T Consensus 123 ~fv~~~~~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~ln 192 (305)
T TIGR00569 123 QFVGNLKETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLN 192 (305)
T ss_pred HHHhhccCCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHH
Confidence 122367999999999999999999999999999999976642 2679999999997
No 4
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.91 E-value=5.4e-24 Score=163.53 Aligned_cols=103 Identities=24% Similarity=0.410 Sum_probs=96.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH--------------------------------
Q 038406 16 ISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-------------------------------- 63 (118)
Q Consensus 16 i~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-------------------------------- 63 (118)
++-++|..+|.+++.+|+++|.+|++|+.+.|||+.||+|||.++|.+
T Consensus 36 l~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~ 115 (297)
T COG5333 36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEA 115 (297)
T ss_pred cchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHh
Confidence 677999999999999999999999999999999999999999999988
Q ss_pred ------HHHHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC--HHHHHHHhhhcC
Q 038406 64 ------VYYKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV--CDLAKSSMEFHK 118 (118)
Q Consensus 64 ------~~~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~--~~l~q~Aw~~~N 118 (118)
..+..|++|+++|+.+|++|+||++|+|||+++.++++++... .++.+.||+++|
T Consensus 116 ~~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~in 178 (297)
T COG5333 116 RDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIIN 178 (297)
T ss_pred hccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 2345789999999999999999999999999999999999876 359999999987
No 5
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.89 E-value=1.2e-23 Score=156.62 Aligned_cols=106 Identities=23% Similarity=0.360 Sum_probs=96.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------------
Q 038406 13 KDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------------------- 63 (118)
Q Consensus 13 ~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------------------- 63 (118)
..|++.++-..++.+..++|+.+|.+|+++|+|+|||++||+|||.++|++
T Consensus 29 ~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l 108 (264)
T KOG0794|consen 29 LRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLL 108 (264)
T ss_pred hhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHH
Confidence 348999999999999999999999999999999999999999999999988
Q ss_pred -----------HHHH-----HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC-CHHHHHHHhhhcC
Q 038406 64 -----------VYYK-----QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL-VCDLAKSSMEFHK 118 (118)
Q Consensus 64 -----------~~~~-----~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~-~~~l~q~Aw~~~N 118 (118)
.|+. -+..|+++|+.+|+.|++.+.|+|||++|.+++++.|. +.++.+.||+++|
T Consensus 109 ~~~a~~L~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivN 180 (264)
T KOG0794|consen 109 VNEAKVLKTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVN 180 (264)
T ss_pred HHHHHHHhhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhc
Confidence 0111 13789999999999999999999999999999999999 5779999999998
No 6
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.31 E-value=4.2e-12 Score=98.06 Aligned_cols=92 Identities=21% Similarity=0.418 Sum_probs=74.2
Q ss_pred hhhCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------------
Q 038406 6 REFSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------- 63 (118)
Q Consensus 6 l~~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------- 63 (118)
+.-+|+..--++-++|..+-.++..|-. .+|..|++||+.||.|||+.+|.+
T Consensus 45 ~~v~~~ee~tl~k~~E~~l~~f~~k~~p------~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ 118 (325)
T KOG2496|consen 45 VFVLEAEELTLTKEEELSLVNFYSKFKP------NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFY 118 (325)
T ss_pred hhccccccccccHHHHHHHHHHHHHhcC------CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhe
Confidence 3445555555666666666666555544 899999999999999999999988
Q ss_pred ----HH--------HHHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHc
Q 038406 64 ----VY--------YKQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRL 103 (118)
Q Consensus 64 ----~~--------~~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l 103 (118)
.| |+-.+.|+..|+.+|+.|.|++.|++||+++-+++.++
T Consensus 119 ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~ 170 (325)
T KOG2496|consen 119 ISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDM 170 (325)
T ss_pred ecHHHHHhhccCcccccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHH
Confidence 11 24468999999999999999999999999999998887
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.05 E-value=1.5e-09 Score=84.65 Aligned_cols=93 Identities=17% Similarity=0.217 Sum_probs=82.9
Q ss_pred HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HH-------------------HHHHHHHHHH
Q 038406 26 KLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VY-------------------YKQKELILTA 75 (118)
Q Consensus 26 ~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~-------------------~~~~~~Il~~ 75 (118)
..+.+.|.++|..|++|+.++.+|..+|++++..+.++ .| .-.+.+|-..
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~ 202 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRC 202 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHH
Confidence 56889999999999999999999999999999987766 11 1236788999
Q ss_pred HHHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhhcC
Q 038406 76 ERLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEFHK 118 (118)
Q Consensus 76 E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~~N 118 (118)
++.|++.|++++.+.+|+.++..++..|++++++.+.||.+++
T Consensus 203 ~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~ 245 (310)
T PRK00423 203 YRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQ 245 (310)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999998764
No 8
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=98.83 E-value=1.6e-08 Score=67.93 Aligned_cols=70 Identities=23% Similarity=0.332 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH---------------------------HH------
Q 038406 19 KKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD---------------------------VY------ 65 (118)
Q Consensus 19 ~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~---------------------------~~------ 65 (118)
+-....|...++||.+++..++++..+.++|+.|++||+.+.++. .+
T Consensus 25 ~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~ 104 (127)
T PF00134_consen 25 EITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDN 104 (127)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTT
T ss_pred hcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcC
Confidence 445588999999999999999999999999999999999988755 00
Q ss_pred HHHHHHHHHHHHHHHHHcCccee
Q 038406 66 YKQKELILTAERLLPATIAFDFD 88 (118)
Q Consensus 66 ~~~~~~Il~~E~~iL~~L~Fdl~ 88 (118)
.--+++|+++|+.||++|+||++
T Consensus 105 ~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 105 TFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp SSHHHHHHHHHHHHHHHTTT---
T ss_pred CCCHHHHHHHHHHHHHHCCCCcC
Confidence 01368999999999999999974
No 9
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=97.84 E-value=9e-05 Score=58.68 Aligned_cols=83 Identities=12% Similarity=0.157 Sum_probs=74.0
Q ss_pred HHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------------------------H---HH
Q 038406 24 LWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------------------------V---YY 66 (118)
Q Consensus 24 ~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------------------------~---~~ 66 (118)
-|..+..||.+++...+....+..-|+.|+=||-..+++. + |-
T Consensus 77 ~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~ 156 (335)
T KOG0656|consen 77 MRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNV 156 (335)
T ss_pred HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccc
Confidence 3899999999999999999999999999999998766655 1 12
Q ss_pred HHHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406 67 KQKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV 106 (118)
Q Consensus 67 ~~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~ 106 (118)
--.+.|..+|.+||.+|+-+++--.||.++-.++.+++..
T Consensus 157 feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~ 196 (335)
T KOG0656|consen 157 FEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQK 196 (335)
T ss_pred ccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcc
Confidence 2368999999999999999999999999999999999874
No 10
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=97.42 E-value=0.00043 Score=42.36 Aligned_cols=39 Identities=18% Similarity=0.168 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH
Q 038406 25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD 63 (118)
Q Consensus 25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~ 63 (118)
|...++||.+++..+++|..+..+|..++.||+..+++.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~ 40 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVL 40 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccc
Confidence 456789999999999999999999999999999887765
No 11
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.26 E-value=0.0016 Score=52.54 Aligned_cols=84 Identities=20% Similarity=0.272 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------HHH-----------------HH
Q 038406 23 ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------VYY-----------------KQ 68 (118)
Q Consensus 23 ~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------~~~-----------------~~ 68 (118)
..|..-++|+.++-...++...|+..|+-++-||-...+.. -|+ --
T Consensus 156 ~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s 235 (391)
T KOG0653|consen 156 KMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYS 235 (391)
T ss_pred HHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccc
Confidence 56888899999999999999999999999999998876543 122 13
Q ss_pred HHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406 69 KELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV 106 (118)
Q Consensus 69 ~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~ 106 (118)
+++|+.+|..||.+|+|++.+.+|+.+|..+.+..+.+
T Consensus 236 ~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d 273 (391)
T KOG0653|consen 236 REEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYD 273 (391)
T ss_pred hHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcc
Confidence 69999999999999999999999999999999988754
No 12
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=96.66 E-value=0.0045 Score=37.35 Aligned_cols=34 Identities=21% Similarity=0.223 Sum_probs=29.6
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH
Q 038406 30 SFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD 63 (118)
Q Consensus 30 ~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~ 63 (118)
+||.+++..+++|..+..+|..++.||...+++.
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~ 34 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFL 34 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 3789999999999999999999999998855443
No 13
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=96.21 E-value=0.043 Score=42.73 Aligned_cols=90 Identities=18% Similarity=0.197 Sum_probs=74.3
Q ss_pred HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------HH-------------------HHHHHHHHHHH
Q 038406 27 LYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------VY-------------------YKQKELILTAE 76 (118)
Q Consensus 27 ~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------~~-------------------~~~~~~Il~~E 76 (118)
.+.+.|..++..|++|..+.-+|+.+|.+-+..+-.. .| .-.+.+|-.+.
T Consensus 99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rty 178 (285)
T COG1405 99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTY 178 (285)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHH
Confidence 5778899999999999999999999999887655433 11 12358899999
Q ss_pred HHHHHHcCcceeecCChHHHHHHHHHcCCCHHHHHHHhhh
Q 038406 77 RLLPATIAFDFDIQLPYEPLVAAFTRLDLVCDLAKSSMEF 116 (118)
Q Consensus 77 ~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~~~l~q~Aw~~ 116 (118)
+.+.+.|+=.+....|..|+..|+.+|+++.+....|-.+
T Consensus 179 r~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei 218 (285)
T COG1405 179 RLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEI 218 (285)
T ss_pred HHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 9999999999999999999999999999996666555444
No 14
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=95.74 E-value=0.069 Score=43.98 Aligned_cols=84 Identities=18% Similarity=0.230 Sum_probs=70.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------HHH-----------------HHH
Q 038406 23 ELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------VYY-----------------KQK 69 (118)
Q Consensus 23 ~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------~~~-----------------~~~ 69 (118)
..|.--.+||.++=..+++-..|.-.|+.+.-||-..+... -|+ --+
T Consensus 211 ~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~ 290 (440)
T COG5024 211 SMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTR 290 (440)
T ss_pred hHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccH
Confidence 45777889999999999999999999999999998877654 122 126
Q ss_pred HHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCCC
Q 038406 70 ELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDLV 106 (118)
Q Consensus 70 ~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~~ 106 (118)
++|+.+|+.+|.+|+|++..-.|+-++..+-+.-+-+
T Consensus 291 ~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd 327 (440)
T COG5024 291 DDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYD 327 (440)
T ss_pred HHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccc
Confidence 9999999999999999999999999988877766554
No 15
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=94.71 E-value=0.33 Score=38.92 Aligned_cols=87 Identities=14% Similarity=0.104 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH------------------HHHH------------
Q 038406 18 FKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD------------------VYYK------------ 67 (118)
Q Consensus 18 ~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~------------------~~~~------------ 67 (118)
+.-+-+.|+--..|+.++|.--+|-..|..-|+-||-||.... .+ -+++
T Consensus 138 pdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~-~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyv 216 (408)
T KOG0655|consen 138 PDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQ-VEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYV 216 (408)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH-HHhhhhhHHHhhHHHHHHHHHHhhccCccccceeee
Confidence 3344556777889999999999999999999999999997644 22 1111
Q ss_pred -----HHHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHcCC
Q 038406 68 -----QKELILTAERLLPATIAFDFDIQLPYEPLVAAFTRLDL 105 (118)
Q Consensus 68 -----~~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l~~ 105 (118)
--++|+.+|.+||+.|+.++..-.--.-|--|++...+
T Consensus 217 TDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~ 259 (408)
T KOG0655|consen 217 TDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDAL 259 (408)
T ss_pred ccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhc
Confidence 24899999999999999999855444555555555433
No 16
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=94.38 E-value=0.2 Score=34.98 Aligned_cols=60 Identities=8% Similarity=0.076 Sum_probs=42.7
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhh---hcchH----------------------------HHHH-----HHHH
Q 038406 28 YCSFLQELGTKLKLPQVIVACAMMLCHQFYM---HQLHD----------------------------VYYK-----QKEL 71 (118)
Q Consensus 28 ~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~---~~S~~----------------------------~~~~-----~~~~ 71 (118)
-.+|+.++....+++..+.-.|.+|+.|+.. ...+. .+|. -.++
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e 133 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE 133 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence 4567888888999999999999999999988 22221 1121 2579
Q ss_pred HHHHHHHHHHHcCcce
Q 038406 72 ILTAERLLPATIAFDF 87 (118)
Q Consensus 72 Il~~E~~iL~~L~Fdl 87 (118)
+-.+|+..|..|+|+|
T Consensus 134 ln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 134 LNELEREFLKLLDYNL 149 (149)
T ss_dssp HHHHHHHHHHHTTT--
T ss_pred HHHHHHHHHHHCCCcC
Confidence 9999999999999986
No 17
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=91.30 E-value=0.24 Score=40.42 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=47.9
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------------------HHHHHHHHHHHHH
Q 038406 32 LQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------------------VYYKQKELILTAE 76 (118)
Q Consensus 32 I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------------------~~~~~~~~Il~~E 76 (118)
|.++|.-.++...|+|+|-|||-+--+..-+. .|..-|.+++..|
T Consensus 389 Mr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~E 468 (497)
T KOG4164|consen 389 MRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAFE 468 (497)
T ss_pred HHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhhh
Confidence 66777777888899999999999888765544 2334578999999
Q ss_pred HHHHHHcCcceeec
Q 038406 77 RLLPATIAFDFDIQ 90 (118)
Q Consensus 77 ~~iL~~L~Fdl~v~ 90 (118)
+-||-.|.|-|++.
T Consensus 469 f~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 469 FPVLVALEFALHLP 482 (497)
T ss_pred hhHHHhhhhhccCC
Confidence 99999999999754
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=89.85 E-value=6.1 Score=31.14 Aligned_cols=86 Identities=15% Similarity=0.106 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH-----------------------HHHH-------HHHHHHH
Q 038406 25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD-----------------------VYYK-------QKELILT 74 (118)
Q Consensus 25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~-----------------------~~~~-------~~~~Il~ 74 (118)
-..+..-|..++.+++||..+.-+|.-+|+++...++++ .|.+ .+++|=.
T Consensus 104 ~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr 183 (308)
T KOG1597|consen 104 LKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGR 183 (308)
T ss_pred HHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHH
Confidence 345778899999999999999999999999999766655 1222 2567777
Q ss_pred HHHHHHHHcCcceeec--CChHHHHHHHHHcCCCHHHH
Q 038406 75 AERLLPATIAFDFDIQ--LPYEPLVAAFTRLDLVCDLA 110 (118)
Q Consensus 75 ~E~~iL~~L~Fdl~v~--hP~~~l~~~~~~l~~~~~l~ 110 (118)
+=..|++.|+=.+... |--.++..|+..|+++++..
T Consensus 184 ~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q 221 (308)
T KOG1597|consen 184 CVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQ 221 (308)
T ss_pred HHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHH
Confidence 7788888877766544 46778899999999985443
No 19
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=83.42 E-value=1.9 Score=26.00 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=21.0
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHhhh
Q 038406 32 LQELGTKLKLPQVIVACAMMLCHQFYMH 59 (118)
Q Consensus 32 I~~~g~~L~lp~~~~aTA~~~~hRFy~~ 59 (118)
|.++|..|+||..+.-+|.-++++-...
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~ 28 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQER 28 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHc
Confidence 5678899999999999999988876543
No 20
>KOG3975 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.29 E-value=45 Score=26.15 Aligned_cols=65 Identities=14% Similarity=0.151 Sum_probs=43.6
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHH----HcCcceeecCChHH
Q 038406 31 FLQELGTKLKLPQVIVACAMMLCHQFYMHQLHDVYYKQKELILTAERLLPA----TIAFDFDIQLPYEP 95 (118)
Q Consensus 31 ~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~~~~~~~~~Il~~E~~iL~----~L~Fdl~v~hP~~~ 95 (118)
+|+-.+...+.|+....||+-+.|++..+|+.-.-.+--++|...-..+++ .+-|-+....|..+
T Consensus 189 Li~~~l~~~n~p~e~l~tal~l~h~~v~rn~v~la~qEm~eV~~~d~e~~een~d~l~Fyygt~DgW~p 257 (301)
T KOG3975|consen 189 LIKFMLCGSNGPQEFLSTALFLTHPQVVRNSVGLAAQEMEEVTTRDIEYCEENLDSLWFYYGTNDGWVP 257 (301)
T ss_pred HHHHhcccCCCcHHHHhhHHHhhcHHHHHHHhhhchHHHHHHHHhHHHHHHhcCcEEEEEccCCCCCcc
Confidence 344455667889999999999999999999987333333333333333333 46677777777666
No 21
>TIGR00873 gnd 6-phosphogluconate dehydrogenase, decarboxylating. This model does not specify whether the cofactor is NADP only (EC 1.1.1.44), NAD only, or both. The model does not assign an EC number for that reason.
Probab=48.77 E-value=52 Score=27.35 Aligned_cols=42 Identities=10% Similarity=0.052 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhc
Q 038406 19 KKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQ 60 (118)
Q Consensus 19 ~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~ 60 (118)
..+..-...+.+.+...+...++|..++++|..||-+|-..+
T Consensus 391 ~~~i~~~~~~~r~vV~~a~~~gip~P~ls~aL~y~~~~~s~~ 432 (467)
T TIGR00873 391 KDALKDAQSGWRRVVALAIEYGIPVPAFSAALSFYDGYRTAR 432 (467)
T ss_pred HHHHHHhhHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcCc
Confidence 556667778889999999999999999999999999986633
No 22
>PF00393 6PGD: 6-phosphogluconate dehydrogenase, C-terminal domain; InterPro: IPR006114 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequences are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This entry represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. The NAD-binding domain is described in IPR006115 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0050661 NADP binding, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 2ZYD_A 2ZYA_A 3FWN_A 2JKV_E 2ZYG_B 4E21_A 1PGJ_A 1PGP_A 1PGN_A 2PGD_A ....
Probab=28.94 E-value=1.5e+02 Score=23.28 Aligned_cols=50 Identities=10% Similarity=0.092 Sum_probs=32.9
Q ss_pred hhhhCCCCCCC-CC--HHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 038406 5 RREFSPSKKDG-IS--FKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCH 54 (118)
Q Consensus 5 ~l~~tPS~~~g-i~--~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~h 54 (118)
..+..|....= ++ ..++..-.....+.+...|...++|..++++|..||.
T Consensus 201 af~~~p~l~nLll~~~f~~~l~~~~~~lR~vV~~ai~~gipvPalsaaL~Y~d 253 (291)
T PF00393_consen 201 AFKENPDLENLLLDPYFAEELKDNQPSLRRVVSLAIEAGIPVPALSAALSYFD 253 (291)
T ss_dssp HHHH-TT-STGGGSHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHH
T ss_pred HHHhCCChhccccCHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Confidence 34555653321 22 3456666777888899999999999999999998886
No 23
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=25.93 E-value=1.4e+02 Score=21.88 Aligned_cols=40 Identities=8% Similarity=0.227 Sum_probs=26.8
Q ss_pred HHHHHHcCccee-------ecCChHHHHHHHHHcCCC-------HHHHHHHhhh
Q 038406 77 RLLPATIAFDFD-------IQLPYEPLVAAFTRLDLV-------CDLAKSSMEF 116 (118)
Q Consensus 77 ~~iL~~L~Fdl~-------v~hP~~~l~~~~~~l~~~-------~~l~q~Aw~~ 116 (118)
-.||+-|||+.. |..-|++..+..+.++.+ .++...|..+
T Consensus 17 A~iL~klgyev~LVTvnFGv~d~~k~A~~tA~~lgF~h~vl~Ldr~ile~A~em 70 (198)
T COG2117 17 ALILDKLGYEVELVTVNFGVLDSWKYARETAAILGFPHEVLQLDREILEDAVEM 70 (198)
T ss_pred HHHHHHhCCCcEEEEEEeccccchhhHHHHHHHhCCCcceeccCHHHHHHHHHH
Confidence 367888888754 445677777777777654 6666666554
No 24
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=25.75 E-value=48 Score=26.54 Aligned_cols=33 Identities=15% Similarity=0.290 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHcCcceeecCChHHHHHHHHHc
Q 038406 69 KELILTAERLLPATIAFDFDIQLPYEPLVAAFTRL 103 (118)
Q Consensus 69 ~~~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~l 103 (118)
.+++=++|+..|+.|+|+++| |.--..+|.-++
T Consensus 268 veDmNe~ERqfLelLqfNinv--p~svYAKyYfdl 300 (343)
T KOG1675|consen 268 VDDMNALERQFLELLQFNINV--PSSEYAKYYFDL 300 (343)
T ss_pred HhhHHHHHHHHHHHHhhccCc--cHHHHHHHHHHH
Confidence 578999999999999998876 444444454444
No 25
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=25.37 E-value=64 Score=25.08 Aligned_cols=31 Identities=16% Similarity=0.198 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHH
Q 038406 25 WKLYCSFLQELGTKLKLPQVIVACAMMLCHQ 55 (118)
Q Consensus 25 r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hR 55 (118)
++.+-.-+.+++.+|+|||.++++-+--+-+
T Consensus 33 ~~k~plNvneiAe~lgLpqst~s~~ik~Le~ 63 (308)
T COG4189 33 HRKGPLNVNEIAEALGLPQSTMSANIKVLEK 63 (308)
T ss_pred HHhCCCCHHHHHHHhCCchhhhhhhHHHHHh
Confidence 3444455677889999999999887766543
No 26
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=25.34 E-value=39 Score=21.67 Aligned_cols=41 Identities=0% Similarity=-0.065 Sum_probs=26.6
Q ss_pred hCCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHH
Q 038406 8 FSPSKKDGISFKKDSELWKLYCSFLQELGTKLKLPQVIVAC 48 (118)
Q Consensus 8 ~tPS~~~gi~~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aT 48 (118)
-||+-++.+++..+.......-.-..+++..++++..|+..
T Consensus 29 ~t~~e~~~Ls~R~~I~~ll~~G~S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 29 ATINEIQSLAQRLQVAKMLKQGKTYSDIEAETGASTATISR 69 (88)
T ss_pred CCHHHHHhhhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHH
Confidence 46776666666644333333334678888999999988754
No 27
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=22.83 E-value=1.8e+02 Score=23.63 Aligned_cols=79 Identities=11% Similarity=0.077 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhhcchH----------------HHH-----------------HHHH
Q 038406 24 LWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFYMHQLHD----------------VYY-----------------KQKE 70 (118)
Q Consensus 24 ~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy~~~S~~----------------~~~-----------------~~~~ 70 (118)
.|.-.+.+..+++...++...+..-+..+.+||...+... .|+ -.+.
T Consensus 136 mrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~ 215 (359)
T KOG0654|consen 136 MRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYW 215 (359)
T ss_pred hhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHH
Confidence 4556667777777666666777777777888886544333 111 2468
Q ss_pred HHHHHHHHHHHHcCcceeecCChHHHHHHHHH
Q 038406 71 LILTAERLLPATIAFDFDIQLPYEPLVAAFTR 102 (118)
Q Consensus 71 ~Il~~E~~iL~~L~Fdl~v~hP~~~l~~~~~~ 102 (118)
++..+|..+|..+.|++.+.-...++..+...
T Consensus 216 qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~ 247 (359)
T KOG0654|consen 216 QVLRMEIDILNALTFELVRPTSKTFLRRFLRV 247 (359)
T ss_pred HHHHHHHHHHHHhHHHHhCchHHHHHHHHHHh
Confidence 89999999999999999988777777666443
No 28
>KOG3918 consensus Predicted membrane protein [Function unknown]
Probab=22.65 E-value=63 Score=21.97 Aligned_cols=44 Identities=14% Similarity=0.302 Sum_probs=27.2
Q ss_pred HHHHhhhcchHHHHHHHHHHHHHHHHHHHHcCccee-ecCChHHH
Q 038406 53 CHQFYMHQLHDVYYKQKELILTAERLLPATIAFDFD-IQLPYEPL 96 (118)
Q Consensus 53 ~hRFy~~~S~~~~~~~~~~Il~~E~~iL~~L~Fdl~-v~hP~~~l 96 (118)
=||||++-.-++++.+.-+|+.---+-|-.+.|... +-.|++.+
T Consensus 26 qHR~YlRLTEqe~~sLP~DivlQTvisli~~iYgi~~iag~Fk~i 70 (129)
T KOG3918|consen 26 QHRFYLRLTEQEFISLPSDIVLQTVISLIALIYGISFIAGPFKFI 70 (129)
T ss_pred HHHHHHhhhhcccccCcHHHHHHHHHHHHHHHHhHHHHcchHHhh
Confidence 399999877667777666665555555555555543 44555444
No 29
>PTZ00142 6-phosphogluconate dehydrogenase; Provisional
Probab=22.45 E-value=2.2e+02 Score=23.73 Aligned_cols=39 Identities=8% Similarity=0.092 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHh
Q 038406 19 KKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQFY 57 (118)
Q Consensus 19 ~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy 57 (118)
..+..-...+.+.+...+...++|..++++|..||--+-
T Consensus 397 ~~~i~~~~~~~R~vV~~a~~~gip~P~~s~aL~y~~s~~ 435 (470)
T PTZ00142 397 NDELKNKQPSWRKVVSMATKNGIPTPAFSASLAYYQMYR 435 (470)
T ss_pred HHHHHHhhHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhh
Confidence 455566677888999999999999999999999776543
No 30
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.72 E-value=1.6e+02 Score=22.98 Aligned_cols=30 Identities=10% Similarity=0.156 Sum_probs=24.1
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHh
Q 038406 28 YCSFLQELGTKLKLPQVIVACAMMLCHQFY 57 (118)
Q Consensus 28 ~~~~I~~~g~~L~lp~~~~aTA~~~~hRFy 57 (118)
...+|.+++..|++|..+.-+|..++.+..
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~ 248 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAK 248 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 358888888999999888888888887654
No 31
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=21.44 E-value=1.8e+02 Score=23.13 Aligned_cols=30 Identities=17% Similarity=0.254 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhhcCCCHHHHHHHHHHHHHH
Q 038406 27 LYCSFLQELGTKLKLPQVIVACAMMLCHQF 56 (118)
Q Consensus 27 ~~~~~I~~~g~~L~lp~~~~aTA~~~~hRF 56 (118)
....||.+.|..|+||..+...|.-.-.+.
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka 231 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKA 231 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 367888888888999888877777666553
No 32
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=21.38 E-value=1.3e+02 Score=16.37 Aligned_cols=19 Identities=11% Similarity=0.207 Sum_probs=15.3
Q ss_pred HHHHHhhcCCCHHHHHHHH
Q 038406 32 LQELGTKLKLPQVIVACAM 50 (118)
Q Consensus 32 I~~~g~~L~lp~~~~aTA~ 50 (118)
+.+++..|++++.++..++
T Consensus 20 ~~eAa~~lg~~~~~I~~~~ 38 (53)
T smart00497 20 IREAAKYLGISHSSISKYL 38 (53)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 6788899999988877654
No 33
>KOG2653 consensus 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
Probab=20.65 E-value=2.4e+02 Score=23.45 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHH
Q 038406 18 FKKDSELWKLYCSFLQELGTKLKLPQVIVACAMMLCHQF 56 (118)
Q Consensus 18 ~~~E~~~r~~~~~~I~~~g~~L~lp~~~~aTA~~~~hRF 56 (118)
+..+...++.+..-....+...+.|..++.||..||--|
T Consensus 399 F~~~v~~~q~~wr~vV~~a~~~gIptP~~st~Lafydgy 437 (487)
T KOG2653|consen 399 FAKAVEEAQDSWRRVVALAVEAGIPTPAFSTALAFYDGY 437 (487)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhhh
Confidence 455666677888888888999999999999999998744
Done!