Query 034297
Match_columns 99
No_of_seqs 84 out of 86
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 11:56:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034297.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034297hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12165 DUF3594: Domain of un 100.0 2.2E-40 4.7E-45 243.9 5.0 62 1-62 76-137 (137)
2 KOG1632 Uncharacterized PHD Zn 99.0 3.4E-11 7.3E-16 96.8 0.2 58 1-58 117-179 (345)
3 PF11882 DUF3402: Domain of un 66.9 2.2 4.7E-05 35.7 0.4 60 35-99 262-340 (409)
4 PTZ00211 ribonucleoside-diphos 56.9 15 0.00033 29.1 3.5 38 9-51 110-147 (330)
5 PRK13307 bifunctional formalde 52.4 15 0.00032 30.8 2.9 39 36-80 134-172 (391)
6 PF11351 DUF3154: Protein of u 51.0 9.2 0.0002 26.9 1.3 14 16-29 100-115 (123)
7 PF07136 DUF1385: Protein of u 46.8 13 0.00029 29.6 1.7 47 39-86 97-146 (236)
8 smart00464 LON Found in ATP-de 46.1 19 0.00042 22.8 2.1 24 20-43 57-80 (92)
9 COG0721 GatC Asp-tRNAAsn/Glu-t 45.7 22 0.00047 24.4 2.4 55 26-81 14-68 (96)
10 PF14367 DUF4411: Domain of un 44.8 39 0.00085 24.2 3.8 55 12-91 103-157 (162)
11 PLN02492 ribonucleoside-diphos 39.6 41 0.00089 26.6 3.5 38 10-52 100-137 (324)
12 COG1993 PII-like signaling pro 39.5 7.1 0.00015 28.4 -0.7 20 36-55 57-76 (109)
13 PRK03598 putative efflux pump 35.6 12 0.00026 28.6 -0.0 27 1-27 1-27 (331)
14 PF12550 GCR1_C: Transcription 35.2 6.2 0.00013 25.6 -1.4 49 40-97 2-57 (81)
15 PF13950 Epimerase_Csub: UDP-g 32.7 11 0.00024 23.6 -0.5 13 81-93 47-59 (62)
16 PF13111 DUF3962: Protein of u 32.6 36 0.00077 27.5 2.2 33 4-45 24-56 (216)
17 PF13023 HD_3: HD domain; PDB: 32.3 68 0.0015 23.0 3.4 40 10-55 23-65 (165)
18 COG2074 2-phosphoglycerate kin 31.3 40 0.00086 28.4 2.3 49 20-68 104-159 (299)
19 KOG1567 Ribonucleotide reducta 29.8 57 0.0012 27.9 3.0 35 11-50 125-159 (344)
20 cd01182 INT_REC_C DNA breaking 29.1 59 0.0013 19.8 2.3 17 13-29 15-31 (162)
21 cd05112 PTKc_Itk Catalytic dom 28.4 71 0.0015 21.8 2.8 33 12-44 180-215 (256)
22 PF03241 HpaB: 4-hydroxyphenyl 28.1 40 0.00086 25.3 1.7 32 24-55 137-176 (205)
23 cd05036 PTKc_ALK_LTK Catalytic 27.8 72 0.0016 22.4 2.8 33 12-44 200-235 (277)
24 cd05060 PTKc_Syk_like Catalyti 26.0 91 0.002 21.5 3.0 34 12-45 177-213 (257)
25 cd04436 DEP_fRgd2 DEP (Disheve 25.7 95 0.0021 21.5 3.0 42 36-94 3-44 (84)
26 TIGR01286 nifK nitrogenase mol 25.2 74 0.0016 27.3 2.9 33 14-46 324-357 (515)
27 PF14071 YlbD_coat: Putative c 24.8 56 0.0012 24.1 1.9 40 32-71 78-121 (124)
28 PF05119 Terminase_4: Phage te 24.1 48 0.001 21.0 1.3 16 25-40 76-91 (100)
29 TIGR00444 mazG MazG family pro 23.0 1.2E+02 0.0026 24.0 3.5 36 18-53 54-94 (248)
30 PRK13965 ribonucleotide-diphos 22.1 1.1E+02 0.0023 24.7 3.1 38 9-52 113-150 (335)
31 PF11385 DUF3189: Protein of u 20.7 81 0.0017 23.2 2.0 45 12-56 100-145 (148)
32 PF08040 NADH_oxidored: MNLL s 20.4 90 0.0019 20.7 2.0 32 8-41 3-37 (59)
No 1
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=100.00 E-value=2.2e-40 Score=243.87 Aligned_cols=62 Identities=82% Similarity=1.342 Sum_probs=60.8
Q ss_pred CcccchhhHhhhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchhhhhhcCCcCCCC
Q 034297 1 MQEKDWLSLVAVHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIFEVVTGNAKQPKD 62 (99)
Q Consensus 1 M~RkDWLSLVAVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~EvVtg~~~k~~~ 62 (99)
|+|+||||||||||||||||||||||||||||+++|+|||+|||+||||||+|+|+++||.|
T Consensus 76 M~r~dWLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~~~~q~k 137 (137)
T PF12165_consen 76 MQRKDWLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGRAKKQSK 137 (137)
T ss_pred ccHHHHHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhccccccCC
Confidence 89999999999999999999999999999999999999999999999999999999999876
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=99.04 E-value=3.4e-11 Score=96.76 Aligned_cols=58 Identities=48% Similarity=0.591 Sum_probs=55.5
Q ss_pred CcccchhhHhhhhhhhHHHHHHHHhhhhc-----CCChhHHHHHHHHhhcCcchhhhhhcCCc
Q 034297 1 MQEKDWLSLVAVHSDSWLLAVAFYFGARF-----GFGKNERKKLFQMINDLPTIFEVVTGNAK 58 (99)
Q Consensus 1 M~RkDWLSLVAVHSDsWLlsVAFyfGArl-----gfd~~eRkrLF~mINdLPTV~EvVtg~~~ 58 (99)
|+.+|||+++++|+|+|+.+++||||+++ ++.+.+|+|++.++|+.|||+|+++|.+.
T Consensus 117 ~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~ 179 (345)
T KOG1632|consen 117 MSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTAT 179 (345)
T ss_pred hhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhccccccc
Confidence 67899999999999999999999999998 89999999999999999999999999764
No 3
>PF11882 DUF3402: Domain of unknown function (DUF3402); InterPro: IPR021819 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with PF07923 from PFAM.
Probab=66.95 E-value=2.2 Score=35.67 Aligned_cols=60 Identities=28% Similarity=0.597 Sum_probs=37.9
Q ss_pred HHHHHHHHhhcCcchhhhhhcCCcCCCCCCCCCCCccch-------------------hhhccCCCCCcchHHHHhhhhh
Q 034297 35 ERKKLFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSR-------------------ILRNFSGRCGSSWRWLQRNLKL 95 (99)
Q Consensus 35 eRkrLF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~ 95 (99)
..+-+|+.||-|=...- +|+ .|...--..+++.++. |+|+--|-||-.|| |.|.++
T Consensus 262 s~Rn~fs~in~LrIlqK-itK--~k~~R~~~Lv~~Kss~iLKk~l~v~~~~l~ly~LKl~K~qvPy~GRKWr--~~NM~v 336 (409)
T PF11882_consen 262 SWRNFFSLINLLRILQK-ITK--NKPHRIKMLVQYKSSNILKKILKVPNPMLQLYILKLLKSQVPYCGRKWR--QSNMRV 336 (409)
T ss_pred chhHHHHHHHHHHHHHH-HHc--CcHHHHHHHHccCcHHHHHHHHcCCChHHHHHHHHHHHHhcccccchhh--hhhHHH
Confidence 35567999996655555 555 2222112344444443 44555699999887 899999
Q ss_pred hhcC
Q 034297 96 ITKI 99 (99)
Q Consensus 96 ~~~~ 99 (99)
||.|
T Consensus 337 IS~I 340 (409)
T PF11882_consen 337 ISAI 340 (409)
T ss_pred HHHH
Confidence 9975
No 4
>PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional
Probab=56.91 E-value=15 Score=29.12 Aligned_cols=38 Identities=24% Similarity=0.535 Sum_probs=29.1
Q ss_pred HhhhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchhh
Q 034297 9 LVAVHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIFE 51 (99)
Q Consensus 9 LVAVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~E 51 (99)
.=++|+++--.-+.- ++-|..+|.++|..+.+.|.|-+
T Consensus 110 ~E~iHs~sYs~il~t-----l~~~~~~~~~~f~~~~~~p~i~~ 147 (330)
T PTZ00211 110 MENIHSETYSLLIDT-----YITDEEEKDRLFHAIETIPAIKK 147 (330)
T ss_pred HHHHHHHHHHHHHHH-----cCCCHHHHHHHHHHHHhCHHHHH
Confidence 347999988655443 44588999999999999998654
No 5
>PRK13307 bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase; Provisional
Probab=52.42 E-value=15 Score=30.82 Aligned_cols=39 Identities=15% Similarity=0.325 Sum_probs=32.0
Q ss_pred HHHHHHHhhcCcchhhhhhcCCcCCCCCCCCCCCccchhhhccCC
Q 034297 36 RKKLFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSRILRNFSG 80 (99)
Q Consensus 36 RkrLF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~~~~~~~~ 80 (99)
|..|-.-++..|++=|++.. +....|||.+.++.|+..|
T Consensus 134 ~~ai~~a~~~~p~~~~~~~~------~~~~~h~~~~~~~~~~~~~ 172 (391)
T PRK13307 134 KLAIKRALEGFPDVDKVLYE------KDRALHPIMGFKVTRLWDP 172 (391)
T ss_pred HHHHHHHHhCCCCHHHHHhh------hhcccCCccccchhhhccc
Confidence 45677789999999999876 3445899999999998765
No 6
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=51.03 E-value=9.2 Score=26.90 Aligned_cols=14 Identities=64% Similarity=1.001 Sum_probs=11.8
Q ss_pred hHHH--HHHHHhhhhc
Q 034297 16 SWLL--AVAFYFGARF 29 (99)
Q Consensus 16 sWLl--sVAFyfGArl 29 (99)
-||| .|.||+|+|-
T Consensus 100 w~Llg~~vlgy~~~Rs 115 (123)
T PF11351_consen 100 WWLLGAGVLGYFGARS 115 (123)
T ss_pred HHHHHHHHhhhHHHhh
Confidence 4777 8999999994
No 7
>PF07136 DUF1385: Protein of unknown function (DUF1385); InterPro: IPR010787 This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.
Probab=46.82 E-value=13 Score=29.60 Aligned_cols=47 Identities=17% Similarity=0.376 Sum_probs=23.1
Q ss_pred HHHHhhcCcchhhhhhcCCcCCCCC-CCCCCCccchhhhc--cCCCCCcch
Q 034297 39 LFQMINDLPTIFEVVTGNAKQPKDP-YLLNPFSGSRILRN--FSGRCGSSW 86 (99)
Q Consensus 39 LF~mINdLPTV~EvVtg~~~k~~~~-~~~~~~~~~~~~~~--~~~~~~~~~ 86 (99)
+.+.+.|+--||+- -|...|--.. .+..|-....+-+. +.||||+|.
T Consensus 97 ~is~~~dI~Rvf~Y-HGAEHK~I~~yE~g~~Ltvenvrk~sr~HpRCGTsF 146 (236)
T PF07136_consen 97 LISRMKDIKRVFQY-HGAEHKVINCYEAGEELTVENVRKYSRLHPRCGTSF 146 (236)
T ss_pred HHHhhHHHHHHHHH-cchhhhhHHhhcCCCCCCHHHHHhcCCcCCCcchhH
Confidence 34445555555543 2333333111 12234445555544 789999985
No 8
>smart00464 LON Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.
Probab=46.14 E-value=19 Score=22.81 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=21.1
Q ss_pred HHHHHhhhhcCCChhHHHHHHHHh
Q 034297 20 AVAFYFGARFGFGKNERKKLFQMI 43 (99)
Q Consensus 20 sVAFyfGArlgfd~~eRkrLF~mI 43 (99)
-+|+..++++++|..++++|..|-
T Consensus 57 ~~~~~~a~~~~~~~~~~q~lL~~~ 80 (92)
T smart00464 57 PLSDTIAALMPLELHEKQELLELE 80 (92)
T ss_pred hhhHHHhhcccccHHHHHHHHhcc
Confidence 478889999999999999999774
No 9
>COG0721 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]
Probab=45.71 E-value=22 Score=24.35 Aligned_cols=55 Identities=18% Similarity=0.175 Sum_probs=42.2
Q ss_pred hhhcCCChhHHHHHHHHhhcCcchhhhhhcCCcCCCCCCCCCCCccchhhhccCCC
Q 034297 26 GARFGFGKNERKKLFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSRILRNFSGR 81 (99)
Q Consensus 26 GArlgfd~~eRkrLF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~~~~~~~~~ 81 (99)
-|||.|..++...+..-+|+...-+|-+.......- ++..+|...+..+|-=.+.
T Consensus 14 LarL~lseee~e~~~~~l~~Il~~veql~evD~~~v-ep~~~~~~~~~~lReD~~~ 68 (96)
T COG0721 14 LARLELSEEELEKFATQLEDILGYVEQLNEVDTEGV-EPTTHPLEVSNVLREDEVT 68 (96)
T ss_pred HhhcccCHHHHHHHHHHHHHHHHHHHHHHhccccCC-CcccccccccccccCCCCC
Confidence 378889999999999988888888888876554333 6778898888777764443
No 10
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=44.79 E-value=39 Score=24.19 Aligned_cols=55 Identities=25% Similarity=0.420 Sum_probs=35.4
Q ss_pred hhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchhhhhhcCCcCCCCCCCCCCCccchhhhccCCCCCcchHHHHh
Q 034297 12 VHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSRILRNFSGRCGSSWRWLQR 91 (99)
Q Consensus 12 VHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (99)
--.|.||+|.|--+|+ .|||.....+.+++ .+++- -.|-..|.=+|-+-..-|++
T Consensus 103 ~~ADp~LIA~A~~~~~-----------------------~VVT~E~~~~~~~~-~~~KI-PdvC~~~gV~ci~~~~~lr~ 157 (162)
T PF14367_consen 103 SVADPWLIAYAKAYGA-----------------------TVVTHEVSNPNKKK-KKIKI-PDVCEHFGVPCINLFEFLRE 157 (162)
T ss_pred ccCCHHHHHHHHhcCC-----------------------EEEccCCCCCCCCc-cCCCC-ChhHHhCCCcCCCHHHHHHH
Confidence 5689999999988776 45777433222221 12322 45566788889888877754
No 11
>PLN02492 ribonucleoside-diphosphate reductase
Probab=39.62 E-value=41 Score=26.56 Aligned_cols=38 Identities=21% Similarity=0.419 Sum_probs=28.3
Q ss_pred hhhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchhhh
Q 034297 10 VAVHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIFEV 52 (99)
Q Consensus 10 VAVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~Ev 52 (99)
=+||+++--.-+-. ++-|..+|.++|..+.++|+|-+-
T Consensus 100 E~iH~~sYs~i~~t-----l~~d~~~~~~~f~~~~~~p~l~~K 137 (324)
T PLN02492 100 ENIHSEMYSLLLDT-----YIKDPKEKDRLFNAIETIPCVAKK 137 (324)
T ss_pred HHHHHHHHHHHHHH-----hCCCHHHHHHHHHHHHhCHHHHHH
Confidence 37899987543333 334788999999999999987654
No 12
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=39.49 E-value=7.1 Score=28.39 Aligned_cols=20 Identities=40% Similarity=0.737 Sum_probs=17.7
Q ss_pred HHHHHHHhhcCcchhhhhhc
Q 034297 36 RKKLFQMINDLPTIFEVVTG 55 (99)
Q Consensus 36 RkrLF~mINdLPTV~EvVtg 55 (99)
.-++|.+-+|||.|.|+|-.
T Consensus 57 ~~~if~Ls~~LPVviEvVD~ 76 (109)
T COG1993 57 GSKIFRLSTDLPVVVEVVDE 76 (109)
T ss_pred ccchhhccCCCCEEEEEeCC
Confidence 46799999999999999965
No 13
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=35.56 E-value=12 Score=28.59 Aligned_cols=27 Identities=15% Similarity=0.196 Sum_probs=17.6
Q ss_pred CcccchhhHhhhhhhhHHHHHHHHhhh
Q 034297 1 MQEKDWLSLVAVHSDSWLLAVAFYFGA 27 (99)
Q Consensus 1 M~RkDWLSLVAVHSDsWLlsVAFyfGA 27 (99)
|.+++|++|.|+-.=.=+..+.+.||.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (331)
T PRK03598 1 MKKKVVIGLAVVVLAAAVAGGWWWYQS 27 (331)
T ss_pred CCceEEEEhHHHHHHHHHHHheeEeee
Confidence 889999999988664433333344443
No 14
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=35.21 E-value=6.2 Score=25.56 Aligned_cols=49 Identities=24% Similarity=0.450 Sum_probs=29.5
Q ss_pred HHHhhcCcchhhhhhcCCcCCCCCCCCCCCccchhhhccCCCCCcchH-------HHHhhhhhhh
Q 034297 40 FQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSRILRNFSGRCGSSWR-------WLQRNLKLIT 97 (99)
Q Consensus 40 F~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~ 97 (99)
|.|..++-||.|+...=. .+ .+.+| | +++..-+.|++|| +.+|-..+|.
T Consensus 2 ~~m~~~~~TV~dlw~Ew~--~g--~~g~p-s----I~~le~~yG~~WR~~~~~~~~y~rRK~Ii~ 57 (81)
T PF12550_consen 2 FKMSRSIKTVYDLWREWF--TG--LNGQP-S----IRSLEKKYGSKWRRDSKERRTYSRRKVIID 57 (81)
T ss_pred eecCCCCCcHHHHHHHHh--cC--CCCCC-C----HHHHHHHhChhhccCcccchhHHHHHHHHH
Confidence 467788889998886511 11 12233 3 3444556688898 7777665554
No 15
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=32.65 E-value=11 Score=23.61 Aligned_cols=13 Identities=23% Similarity=0.785 Sum_probs=10.8
Q ss_pred CCCcchHHHHhhh
Q 034297 81 RCGSSWRWLQRNL 93 (99)
Q Consensus 81 ~~~~~~~~~~~~~ 93 (99)
-|.+.|+|.|.|-
T Consensus 47 ~i~~~w~W~~~np 59 (62)
T PF13950_consen 47 MIRDAWNWQKKNP 59 (62)
T ss_dssp HHHHHHHHHHHST
T ss_pred HHHHHHHHHHHCc
Confidence 3778999999884
No 16
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=32.64 E-value=36 Score=27.49 Aligned_cols=33 Identities=30% Similarity=0.736 Sum_probs=25.8
Q ss_pred cchhhHhhhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhc
Q 034297 4 KDWLSLVAVHSDSWLLAVAFYFGARFGFGKNERKKLFQMIND 45 (99)
Q Consensus 4 kDWLSLVAVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINd 45 (99)
.||+.||-.|-|-|++-+-+ +.-++||+.|.-|
T Consensus 24 ~~W~~ll~~~~~~~~l~~Kl---------~~l~erL~~mFsd 56 (216)
T PF13111_consen 24 IEWLDLLEIHYKTFLLTSKL---------KRLNERLYDMFSD 56 (216)
T ss_pred HHHHHHHHHhccccccHHHH---------HHHHHHHHHHHHH
Confidence 58999999999999987754 2336788877654
No 17
>PF13023 HD_3: HD domain; PDB: 1XX7_D 2GZ4_B 4DMB_B.
Probab=32.33 E-value=68 Score=23.02 Aligned_cols=40 Identities=33% Similarity=0.627 Sum_probs=23.0
Q ss_pred hhhhhhhHHHHHH-HHhhhhcC--CChhHHHHHHHHhhcCcchhhhhhc
Q 034297 10 VAVHSDSWLLAVA-FYFGARFG--FGKNERKKLFQMINDLPTIFEVVTG 55 (99)
Q Consensus 10 VAVHSDsWLlsVA-FyfGArlg--fd~~eRkrLF~mINdLPTV~EvVtg 55 (99)
||=|| |.+++- +.++..+| +|.+ |.....++-|+| |+++|
T Consensus 23 VAeHS--~~vA~~a~~la~~~~~~~d~~-k~~~~aL~HDl~---E~~~G 65 (165)
T PF13023_consen 23 VAEHS--WRVALIALLLAEEAGPDLDIE-KVVKMALFHDLP---EAITG 65 (165)
T ss_dssp HHHHH--HHHHHHHHHHHHHHH-HC-HH-HHHHHHHHTTTT---HHHH-
T ss_pred HHHHH--HHHHHHHHHHhHHhcccCCHH-HHHHHHhhccch---hhhcC
Confidence 55664 777654 44444454 5665 444455888887 67777
No 18
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=31.29 E-value=40 Score=28.35 Aligned_cols=49 Identities=29% Similarity=0.335 Sum_probs=38.7
Q ss_pred HHHHHhhhhcCCCh-----hHHHHHHHHhh--cCcchhhhhhcCCcCCCCCCCCCC
Q 034297 20 AVAFYFGARFGFGK-----NERKKLFQMIN--DLPTIFEVVTGNAKQPKDPYLLNP 68 (99)
Q Consensus 20 sVAFyfGArlgfd~-----~eRkrLF~mIN--dLPTV~EvVtg~~~k~~~~~~~~~ 68 (99)
++|++.|-|||.+. -=|.-|-.+|- .+||+++.+-..-+--..++..||
T Consensus 104 tIA~ElA~rLgI~~visTD~IREvlR~ii~~~l~PtLh~Ssy~Awkalr~~~~~~p 159 (299)
T COG2074 104 TIAGELARRLGIRSVISTDSIREVLRKIISPELLPTLHTSSYDAWKALRDPTDENP 159 (299)
T ss_pred HHHHHHHHHcCCceeecchHHHHHHHHhCCHHhcchhhHhHHHHHHHhcCCCCCcc
Confidence 68999999999653 45788888888 999999998876665556666676
No 19
>KOG1567 consensus Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]
Probab=29.83 E-value=57 Score=27.93 Aligned_cols=35 Identities=29% Similarity=0.553 Sum_probs=27.7
Q ss_pred hhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchh
Q 034297 11 AVHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIF 50 (99)
Q Consensus 11 AVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~ 50 (99)
-+||...-+-+--|.- |+.||..||+-|..+|.|=
T Consensus 125 NIHSEmYSlLidtyIr-----D~ker~~LFnAI~t~p~vk 159 (344)
T KOG1567|consen 125 NIHSEMYSLLIDTYIR-----DPKEREFLFNAIETIPEVK 159 (344)
T ss_pred HHHHHHHHHHHHHHhc-----ChhhhhHHHHHHHhhHHHH
Confidence 4788877666655542 9999999999999999873
No 20
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include 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. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=29.08 E-value=59 Score=19.83 Aligned_cols=17 Identities=29% Similarity=0.464 Sum_probs=14.6
Q ss_pred hhhhHHHHHHHHhhhhc
Q 034297 13 HSDSWLLAVAFYFGARF 29 (99)
Q Consensus 13 HSDsWLlsVAFyfGArl 29 (99)
..+.|.+.++++.|.|.
T Consensus 15 ~~~~~~~~l~~~~G~R~ 31 (162)
T cd01182 15 PRDRALILLLLYTGLRV 31 (162)
T ss_pred HHHHHHHHHHHHhCCCH
Confidence 45788999999999998
No 21
>cd05112 PTKc_Itk Catalytic domain of the Protein Tyrosine Kinase, Interleukin-2-inducible T-cell Kinase. Protein Tyrosine Kinase (PTK) family; Interleukin-2 (IL-2)-inducible T-cell kinase (Itk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Itk (also known as Tsk or Emt) is a member of the Tec subfamily of proteins, which are cytoplasmic (or nonreceptor) tyr kinases with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members (except Rlk) also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activ
Probab=28.44 E-value=71 Score=21.83 Aligned_cols=33 Identities=18% Similarity=0.387 Sum_probs=22.6
Q ss_pred hhhhhHHHHHHHHhh---hhcCCChhHHHHHHHHhh
Q 034297 12 VHSDSWLLAVAFYFG---ARFGFGKNERKKLFQMIN 44 (99)
Q Consensus 12 VHSDsWLlsVAFyfG---Arlgfd~~eRkrLF~mIN 44 (99)
-.+|.|-+++.+|.- .+.-|+......+...++
T Consensus 180 ~~~Dv~slG~~l~el~~~g~~p~~~~~~~~~~~~~~ 215 (256)
T cd05112 180 SKSDVWSFGVLMWEVFSEGKTPYENRSNSEVVETIN 215 (256)
T ss_pred hHHHHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHHh
Confidence 359999999999862 445566666666665553
No 22
>PF03241 HpaB: 4-hydroxyphenylacetate 3-hydroxylase C terminal; InterPro: IPR024719 This C-terminal domain is found in HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This domain is also found in pyoverdin chromophore biosynthetic protein PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=28.12 E-value=40 Score=25.31 Aligned_cols=32 Identities=28% Similarity=0.522 Sum_probs=21.1
Q ss_pred HhhhhcCCChhHHHHHHHHhhcC--------cchhhhhhc
Q 034297 24 YFGARFGFGKNERKKLFQMINDL--------PTIFEVVTG 55 (99)
Q Consensus 24 yfGArlgfd~~eRkrLF~mINdL--------PTV~EvVtg 55 (99)
|+.+.=+++++||.|||.++=|+ -++||..-+
T Consensus 137 Yl~g~~~~~aeeR~rl~rLawDl~~s~fg~r~~~ye~~~~ 176 (205)
T PF03241_consen 137 YLQGANGVSAEERVRLFRLAWDLTGSEFGGRQELYERFYA 176 (205)
T ss_dssp HT-BTTTC-HHHHHHHHHHHHHHHTSHHHHHHHHHHHHTT
T ss_pred HhcccCCCCHHHHHHHHHHHHHHhcCcchhhhHhhhhhcC
Confidence 44444245999999999999887 355665544
No 23
>cd05036 PTKc_ALK_LTK Catalytic domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family; Anaplastic Lymphoma Kinase (ALK) and Leukocyte Tyrosine (tyr) Kinase (LTK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor tyr kinases (RTKs) whose ligands are not yet well-defined. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. ALK appears to play an important role in mammalian neural development as well
Probab=27.78 E-value=72 Score=22.41 Aligned_cols=33 Identities=9% Similarity=0.345 Sum_probs=22.4
Q ss_pred hhhhhHHHHHHHHh---hhhcCCChhHHHHHHHHhh
Q 034297 12 VHSDSWLLAVAFYF---GARFGFGKNERKKLFQMIN 44 (99)
Q Consensus 12 VHSDsWLlsVAFyf---GArlgfd~~eRkrLF~mIN 44 (99)
-.||.|-++|.+|. +.++-|+......+..++.
T Consensus 200 ~~~DiwslG~il~el~~~g~~pf~~~~~~~~~~~~~ 235 (277)
T cd05036 200 SKTDVWSFGVLLWEIFSLGYMPYPGRTNQEVMEFVT 235 (277)
T ss_pred chhHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHH
Confidence 46999999999885 3555466655555555554
No 24
>cd05060 PTKc_Syk_like Catalytic domain of Spleen Tyrosine Kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Spleen Tyrosine Kinase (Syk) subfamily; catalytic (c) domain. The Syk subfamily is composed of Syk, ZAP-70, Shark, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk subfamily kinases are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. They are involved in the signaling downstream of activated receptors (including B-cell, T-cell, and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, mi
Probab=25.96 E-value=91 Score=21.48 Aligned_cols=34 Identities=18% Similarity=0.395 Sum_probs=22.1
Q ss_pred hhhhhHHHHHHHHhhhh---cCCChhHHHHHHHHhhc
Q 034297 12 VHSDSWLLAVAFYFGAR---FGFGKNERKKLFQMIND 45 (99)
Q Consensus 12 VHSDsWLlsVAFyfGAr---lgfd~~eRkrLF~mINd 45 (99)
..+|.|-+++.+|.-.- .-|+..+...+...|+.
T Consensus 177 ~~~Di~slG~~l~~~~~~g~~p~~~~~~~~~~~~~~~ 213 (257)
T cd05060 177 SKSDVWSYGVTLWEAFSYGAKPYGEMKGAEVIAMLES 213 (257)
T ss_pred ccchHHHHHHHHHHHHcCCCCCcccCCHHHHHHHHHc
Confidence 36999999999986543 33555555555555543
No 25
>cd04436 DEP_fRgd2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGAP (GTPase-activator protein) Rgd2-like proteins. Rgd2-like proteins share a common domain architecture, containing, beside the RhoGAP domain, a DEP and a FCH (Fes/CIP4 homology) domain. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5.
Probab=25.73 E-value=95 Score=21.48 Aligned_cols=42 Identities=33% Similarity=0.522 Sum_probs=26.6
Q ss_pred HHHHHHHhhcCcchhhhhhcCCcCCCCCCCCCCCccchhhhccCCCCCcchHHHHhhhh
Q 034297 36 RKKLFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSGSRILRNFSGRCGSSWRWLQRNLK 94 (99)
Q Consensus 36 RkrLF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (99)
|+-|-.|++++|.. ..|-+-.-.-.|-++++.|- .|||+|+.
T Consensus 3 k~lL~~ml~~ip~~------~~kvPilGty~nt~sG~~Iv-----------~~L~~n~~ 44 (84)
T cd04436 3 KELLAAMLKEIPLA------DYKVPILGTYQNTSSGSEIV-----------SWLQENMP 44 (84)
T ss_pred HHHHHHHHHhCCCc------cceecccccccCcccHHHHH-----------HHHHHcCC
Confidence 45677889998863 23333223345777887775 58888763
No 26
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length.
Probab=25.21 E-value=74 Score=27.28 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=24.9
Q ss_pred hhhHHHHHHHHhhhhcC-CChhHHHHHHHHhhcC
Q 034297 14 SDSWLLAVAFYFGARFG-FGKNERKKLFQMINDL 46 (99)
Q Consensus 14 SDsWLlsVAFyfGArlg-fd~~eRkrLF~mINdL 46 (99)
+|.||+.|+=++|.-.- .=+.+|.||.+.|.|.
T Consensus 324 Td~fL~~la~~~g~~ip~~i~~eR~rl~dam~d~ 357 (515)
T TIGR01286 324 TDEFLMKVSEISGQPIPAELTKERGRLVDAMTDS 357 (515)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Confidence 79999999999985310 0146888999998874
No 27
>PF14071 YlbD_coat: Putative coat protein
Probab=24.81 E-value=56 Score=24.05 Aligned_cols=40 Identities=23% Similarity=0.317 Sum_probs=26.1
Q ss_pred ChhHHHH----HHHHhhcCcchhhhhhcCCcCCCCCCCCCCCcc
Q 034297 32 GKNERKK----LFQMINDLPTIFEVVTGNAKQPKDPYLLNPFSG 71 (99)
Q Consensus 32 d~~eRkr----LF~mINdLPTV~EvVtg~~~k~~~~~~~~~~~~ 71 (99)
|.++=.. +-..|..+.+|..-..|...++...+..||||-
T Consensus 78 D~nq~q~hl~~~sqai~~vQ~~l~qFq~~~~~~~~~~~~~PFsF 121 (124)
T PF14071_consen 78 DVNQMQKHLNNVSQAIGSVQQVLSQFQGNGQKQSQRSPEHPFSF 121 (124)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCcc
Confidence 6665432 445566666666666676666666677899984
No 28
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=24.06 E-value=48 Score=20.97 Aligned_cols=16 Identities=25% Similarity=0.459 Sum_probs=13.5
Q ss_pred hhhhcCCChhHHHHHH
Q 034297 25 FGARFGFGKNERKKLF 40 (99)
Q Consensus 25 fGArlgfd~~eRkrLF 40 (99)
++..|||++..|.+|-
T Consensus 76 l~~~lGLtP~sR~kl~ 91 (100)
T PF05119_consen 76 LASELGLTPASRAKLA 91 (100)
T ss_pred HHHHcCCCHHHHhhcc
Confidence 5678999999999874
No 29
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=23.03 E-value=1.2e+02 Score=23.97 Aligned_cols=36 Identities=28% Similarity=0.459 Sum_probs=26.6
Q ss_pred HHHHHHHh--hhhcC-CChhH--HHHHHHHhhcCcchhhhh
Q 034297 18 LLAVAFYF--GARFG-FGKNE--RKKLFQMINDLPTIFEVV 53 (99)
Q Consensus 18 LlsVAFyf--GArlg-fd~~e--RkrLF~mINdLPTV~EvV 53 (99)
|+.|.|+- |...| ||.++ +...-.||..+|-||.-+
T Consensus 54 L~qvv~~a~iar~~g~f~~edvl~~~~~K~irRhphVf~~~ 94 (248)
T TIGR00444 54 LLQVVFYAQMAQEEGYFDFDDVCAGISEKLVRRHPHVFADV 94 (248)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchhhhhcc
Confidence 67777774 55666 77765 566667999999999765
No 30
>PRK13965 ribonucleotide-diphosphate reductase subunit beta; Provisional
Probab=22.12 E-value=1.1e+02 Score=24.68 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=27.0
Q ss_pred HhhhhhhhHHHHHHHHhhhhcCCChhHHHHHHHHhhcCcchhhh
Q 034297 9 LVAVHSDSWLLAVAFYFGARFGFGKNERKKLFQMINDLPTIFEV 52 (99)
Q Consensus 9 LVAVHSDsWLlsVAFyfGArlgfd~~eRkrLF~mINdLPTV~Ev 52 (99)
.=+||++|--.-+.-+ + +.+++.++|..+.+.|.+-+-
T Consensus 113 ~E~IHs~sYs~il~tl-----~-~~~~~~~~f~~~~~~p~l~~K 150 (335)
T PRK13965 113 MVAIHARSYGTIFSTL-----C-SSEQIEEAHEWVVSTESLQRR 150 (335)
T ss_pred HHHHHHHHHHHHHHHh-----C-CCHHHHHHHHHHhcCHHHHHH
Confidence 3478999876555443 2 344778999999999998653
No 31
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=20.74 E-value=81 Score=23.16 Aligned_cols=45 Identities=20% Similarity=0.313 Sum_probs=35.7
Q ss_pred hhhhhHHHHHHHHhhhhcCCChhHHHHH-HHHhhcCcchhhhhhcC
Q 034297 12 VHSDSWLLAVAFYFGARFGFGKNERKKL-FQMINDLPTIFEVVTGN 56 (99)
Q Consensus 12 VHSDsWLlsVAFyfGArlgfd~~eRkrL-F~mINdLPTV~EvVtg~ 56 (99)
....-|+|.+..|+.-|+|+..=.|--+ -......|.+.|.|...
T Consensus 100 ~~~vn~~m~iGg~lsrrl~l~~iGrpl~~~g~~k~y~~i~~lV~~v 145 (148)
T PF11385_consen 100 SPYVNLLMKIGGFLSRRLGLVKIGRPLVVWGIQKAYPNIVELVEEV 145 (148)
T ss_pred cccchHHHHHHHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456799999999999999999998554 44556778888888763
No 32
>PF08040 NADH_oxidored: MNLL subunit; InterPro: IPR012575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the MNLL subunits of NADH:ubiquinone oxidoreductase complex []. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear [].; GO: 0003954 NADH dehydrogenase activity, 0005739 mitochondrion
Probab=20.42 E-value=90 Score=20.74 Aligned_cols=32 Identities=22% Similarity=0.591 Sum_probs=23.6
Q ss_pred hHhhhhhhhHHHH---HHHHhhhhcCCChhHHHHHHH
Q 034297 8 SLVAVHSDSWLLA---VAFYFGARFGFGKNERKKLFQ 41 (99)
Q Consensus 8 SLVAVHSDsWLls---VAFyfGArlgfd~~eRkrLF~ 41 (99)
.+++++-|-|+-. +.|.+|..| |+.+-.||-.
T Consensus 3 n~~~~vr~~~~~~~vPlgf~iG~yL--Dr~~~erlT~ 37 (59)
T PF08040_consen 3 NLIQIVRDHWVWILVPLGFVIGCYL--DRKETERLTA 37 (59)
T ss_pred cHHHHHHHHHHHHHHhhHhhheeee--cccchHHHHh
Confidence 3567788888644 578888888 9888777653
Done!