Query 013624
Match_columns 439
No_of_seqs 76 out of 78
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 05:44:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013624.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013624hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12483 GIDE: E3 Ubiquitin li 97.9 0.00012 2.5E-09 65.2 10.5 117 278-405 2-121 (160)
2 cd06094 RP_Saci_like RP_Saci_l 80.0 1.5 3.3E-05 37.6 2.6 24 311-334 1-24 (89)
3 PRK14762 membrane protein; Pro 62.8 6.7 0.00014 27.4 2.1 17 215-231 2-18 (27)
4 PF03100 CcmE: CcmE; InterPro 60.7 7.4 0.00016 34.5 2.6 17 244-260 48-64 (131)
5 TIGR01789 lycopene_cycl lycope 47.3 77 0.0017 32.1 7.7 63 308-379 167-236 (370)
6 PRK13254 cytochrome c-type bio 44.1 16 0.00036 33.7 2.2 17 244-260 49-65 (148)
7 cd04486 YhcR_OBF_like YhcR_OBF 38.1 43 0.00094 27.4 3.5 25 232-256 34-58 (78)
8 PF10907 DUF2749: Protein of u 38.0 32 0.00069 28.6 2.7 14 237-250 50-63 (66)
9 KOG0887 60S ribosomal protein 35.7 29 0.00063 31.3 2.3 46 245-302 30-75 (111)
10 PRK13165 cytochrome c-type bio 35.1 27 0.00058 33.0 2.1 18 243-260 54-71 (160)
11 PF13567 DUF4131: Domain of un 35.0 2.6E+02 0.0057 23.2 8.8 22 347-368 147-168 (176)
12 KOG1016 Predicted DNA helicase 33.7 21 0.00045 41.8 1.4 17 7-23 1199-1215(1387)
13 PF10281 Ish1: Putative stress 31.6 37 0.0008 24.3 1.9 17 352-368 6-22 (38)
14 PRK07718 fliL flagellar basal 31.5 39 0.00085 30.4 2.5 22 215-236 4-26 (142)
15 cd04486 YhcR_OBF_like YhcR_OBF 30.0 69 0.0015 26.2 3.5 28 376-403 43-70 (78)
16 PF11432 DUF3197: Protein of u 28.5 68 0.0015 29.1 3.4 59 311-383 19-86 (113)
17 PF10572 UPF0556: Uncharacteri 27.8 1.5E+02 0.0033 28.3 5.7 45 268-317 45-94 (158)
18 PF13869 NUDIX_2: Nucleotide h 27.7 8.5 0.00018 37.1 -2.5 35 361-395 21-55 (188)
19 PF05834 Lycopene_cycl: Lycope 26.6 2.5E+02 0.0053 28.4 7.4 44 336-380 198-243 (374)
20 PRK13150 cytochrome c-type bio 25.3 49 0.0011 31.3 2.1 18 243-260 54-71 (159)
21 KOG0558 Dihydrolipoamide trans 24.0 26 0.00056 37.5 0.0 18 369-386 77-94 (474)
22 PF02037 SAP: SAP domain; Int 22.9 68 0.0015 22.7 2.0 17 353-369 7-23 (35)
23 PF12273 RCR: Chitin synthesis 22.9 30 0.00065 30.4 0.2 22 215-236 1-22 (130)
24 PF11151 DUF2929: Protein of u 22.7 50 0.0011 26.1 1.4 19 216-234 6-24 (57)
25 COG5336 Uncharacterized protei 22.3 31 0.00068 31.3 0.2 18 219-236 75-92 (116)
26 PRK06437 hypothetical protein; 22.2 86 0.0019 24.9 2.6 37 353-390 21-64 (67)
27 PF03144 GTP_EFTU_D2: Elongati 21.8 76 0.0016 24.2 2.2 19 370-388 5-23 (74)
28 cd04488 RecG_wedge_OBF RecG_we 21.7 1.4E+02 0.003 21.9 3.5 27 377-403 45-71 (75)
29 KOG2362 Uncharacterized Fe-S p 21.4 60 0.0013 34.0 2.0 17 373-389 316-332 (336)
30 PF06295 DUF1043: Protein of u 20.7 36 0.00077 30.3 0.2 16 221-236 2-17 (128)
31 PF08078 PsaX: PsaX family; I 20.6 45 0.00097 25.0 0.7 25 204-235 9-33 (37)
32 COG4303 EutB Ethanolamine ammo 20.3 71 0.0015 34.1 2.3 28 348-376 420-447 (453)
33 cd04478 RPA2_DBD_D RPA2_DBD_D: 20.3 85 0.0018 25.3 2.3 19 239-257 44-62 (95)
No 1
>PF12483 GIDE: E3 Ubiquitin ligase; InterPro: IPR022170 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis. ; GO: 0016881 acid-amino acid ligase activity
Probab=97.89 E-value=0.00012 Score=65.24 Aligned_cols=117 Identities=21% Similarity=0.264 Sum_probs=75.3
Q ss_pred eeeeeecCCCCCCCCCCccccccceeeeeeeecEEEEecCCceeEEE-EeCCCCeeeeeeecceEEecCCCCCCCCHHHH
Q 013624 278 SLYEYRAWGSKPANPKHRHFTWGLRSLERHVVDFYISDFQSGLRALV-KTGSGARVTPFVDDSVVIDIKPENKDLSPEFI 356 (439)
Q Consensus 278 ~LyE~rgw~~k~an~kh~~f~W~lr~~Er~~~DFYIsD~~SG~RALV-KaG~GakVtp~V~e~~vv~~~~~~kdlS~~f~ 356 (439)
+.++++.|. + .. ...-.|++.+..+..+.||+.| ..-|.+| ....++.+.--.+-+...... ......+.
T Consensus 2 e~~~~~~~~-~-~~--~~~~~~~~v~~~~~~vPF~L~D--~tg~v~V~~~p~~a~l~l~~v~~~f~p~~---~~~~~~~~ 72 (160)
T PF12483_consen 2 EVVEKRESN-K-SR--RWSSSWRTVSSGTSEVPFYLED--GTGRVRVVDDPEGAELDLETVYDRFEPSP---SSPPDGLF 72 (160)
T ss_pred eEEEEEEcc-c-CC--cccccEEEEEcceeEcCEEEEC--CceEEEEecCcccCccceeeEEEEeEECC---CCccceee
Confidence 356677665 3 21 1223499999999999999999 3455555 566666554323333322211 23444444
Q ss_pred HHhhhcC-CCCCCceeEEeeeeeeeCCEEEEEEEEE-ecCceeeEeCCCCc
Q 013624 357 RWLGQKS-LSSDDRLMRLKEGYIKEGSTVSVMGIVQ-RNDNVLMIVPPPEP 405 (439)
Q Consensus 357 ~WL~erN-LSsd~r~mRlkEGyIkEGstvSVmGvvk-r~~~~~mi~~p~e~ 405 (439)
.|+..+- +. .+=.||+|-.|.+|++|.|+|.+. ..|..++|-+|.+.
T Consensus 73 ~~~~~~~~~~--~~G~r~~E~~L~~G~~ltvvGe~~~~~~g~~~i~~p~~g 121 (160)
T PF12483_consen 73 GFFSGERELE--PKGYRYTEEILPVGTPLTVVGELVRDGDGNLVIQPPKDG 121 (160)
T ss_pred eeeccceecc--ccccEEEEEEcCCCCEEEEEEEEEEcCCCcEEEeCCCCC
Confidence 4443322 11 334799999999999999999994 55668999998886
No 2
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=79.95 E-value=1.5 Score=37.65 Aligned_cols=24 Identities=46% Similarity=0.661 Sum_probs=20.6
Q ss_pred EEEEecCCceeEEEEeCCCCeeee
Q 013624 311 FYISDFQSGLRALVKTGSGARVTP 334 (439)
Q Consensus 311 FYIsD~~SG~RALVKaG~GakVtp 334 (439)
|||.|++||+|+||-||..-.|-|
T Consensus 1 l~v~D~~s~~~fLVDTGA~vSviP 24 (89)
T cd06094 1 LHVRDRTSGLRFLVDTGAAVSVLP 24 (89)
T ss_pred CeeEECCCCcEEEEeCCCceEeec
Confidence 799999999999999988755554
No 3
>PRK14762 membrane protein; Provisional
Probab=62.78 E-value=6.7 Score=27.36 Aligned_cols=17 Identities=41% Similarity=1.107 Sum_probs=15.2
Q ss_pred hhhHHHHHHHHHHHHhh
Q 013624 215 KPVLWLVILIFVMGFIA 231 (439)
Q Consensus 215 k~~~w~~~~l~~~g~~~ 231 (439)
|.++|++..+|.+|+++
T Consensus 2 ki~lw~i~iifligllv 18 (27)
T PRK14762 2 KIILWAVLIIFLIGLLV 18 (27)
T ss_pred eeHHHHHHHHHHHHHHH
Confidence 67899999999999975
No 4
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=60.71 E-value=7.4 Score=34.52 Aligned_cols=17 Identities=47% Similarity=0.688 Sum_probs=14.3
Q ss_pred ccCcEEEEEEEEEeccc
Q 013624 244 KSGQFVKVTGVVTCGNV 260 (439)
Q Consensus 244 ~dGq~VKItG~VtcG~~ 260 (439)
+.|+.|+|.|.|.-|++
T Consensus 48 ~~~~~vrv~G~V~~gSv 64 (131)
T PF03100_consen 48 KVGRKVRVGGLVVEGSV 64 (131)
T ss_dssp -TTSEEEEEEEEECTTE
T ss_pred cCCceEEEeeEEccCCE
Confidence 36999999999998874
No 5
>TIGR01789 lycopene_cycl lycopene cyclase. This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium.
Probab=47.26 E-value=77 Score=32.12 Aligned_cols=63 Identities=16% Similarity=0.312 Sum_probs=36.4
Q ss_pred eecEEEEecCCceeEEEEeCCCCeeeee-----eecceEEecCC--CCCCCCHHHHHHhhhcCCCCCCceeEEeeeeee
Q 013624 308 VVDFYISDFQSGLRALVKTGSGARVTPF-----VDDSVVIDIKP--ENKDLSPEFIRWLGQKSLSSDDRLMRLKEGYIK 379 (439)
Q Consensus 308 ~~DFYIsD~~SG~RALVKaG~GakVtp~-----V~e~~vv~~~~--~~kdlS~~f~~WL~erNLSsd~r~mRlkEGyIk 379 (439)
.-||.+.+ ..|.|++- |.|+ ++|++.++-.+ ...++...|.+|++++++.... +++.|.|.|-
T Consensus 167 lMD~~~~q-~~g~~F~Y-------~lP~~~~~~lvE~T~~s~~~~l~~~~l~~~l~~~~~~~g~~~~~-i~~~e~g~iP 236 (370)
T TIGR01789 167 IMDATVDQ-LAGYRFVY-------VLPLGSHDLLIEDTYYADDPLLDRNALSQRIDQYARANGWQNGT-PVRHEQGVLP 236 (370)
T ss_pred EEeeeccC-CCCceEEE-------ECcCCCCeEEEEEEeccCCCCCCHHHHHHHHHHHHHHhCCCceE-EEEeeeeEEe
Confidence 34566643 34566655 4554 24555544321 1234556788999888766555 7777777664
No 6
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=44.07 E-value=16 Score=33.65 Aligned_cols=17 Identities=29% Similarity=0.563 Sum_probs=14.4
Q ss_pred ccCcEEEEEEEEEeccc
Q 013624 244 KSGQFVKVTGVVTCGNV 260 (439)
Q Consensus 244 ~dGq~VKItG~VtcG~~ 260 (439)
..|+.|+|.|.|.-|++
T Consensus 49 ~~g~~vrvgG~V~~gSi 65 (148)
T PRK13254 49 PAGRRFRLGGLVEKGSV 65 (148)
T ss_pred cCCCeEEEeEEEecCcE
Confidence 45999999999998854
No 7
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=38.10 E-value=43 Score=27.39 Aligned_cols=25 Identities=36% Similarity=0.525 Sum_probs=17.8
Q ss_pred eeeEeeecccccccCcEEEEEEEEE
Q 013624 232 GGFILDTDLRTAKSGQFVKVTGVVT 256 (439)
Q Consensus 232 g~fild~~Lr~a~dGq~VKItG~Vt 256 (439)
|.|+.......++.|+.|.|+|+|+
T Consensus 34 gifV~~~~~~~~~~Gd~V~vtG~v~ 58 (78)
T cd04486 34 GIFVYTGSGADVAVGDLVRVTGTVT 58 (78)
T ss_pred eEEEecCCCCCCCCCCEEEEEEEEE
Confidence 3444422256778999999999976
No 8
>PF10907 DUF2749: Protein of unknown function (DUF2749); InterPro: IPR024475 This bacterial family of proteins represent the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon [].
Probab=37.98 E-value=32 Score=28.63 Aligned_cols=14 Identities=50% Similarity=0.731 Sum_probs=11.5
Q ss_pred eecccccccCcEEE
Q 013624 237 DTDLRTAKSGQFVK 250 (439)
Q Consensus 237 d~~Lr~a~dGq~VK 250 (439)
|.+|+..++||..|
T Consensus 50 ~~~l~~i~~gqem~ 63 (66)
T PF10907_consen 50 DKDLRDIRGGQEMK 63 (66)
T ss_pred CCCCCCCCCCcccC
Confidence 77899999999654
No 9
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=35.68 E-value=29 Score=31.28 Aligned_cols=46 Identities=28% Similarity=0.437 Sum_probs=34.0
Q ss_pred cCcEEEEEEEEEeccccccCCcCCCCceEEEeeeeeeeecCCCCCCCCCCccccccce
Q 013624 245 SGQFVKVTGVVTCGNVPLESSFRRVPRCVYTSTSLYEYRAWGSKPANPKHRHFTWGLR 302 (439)
Q Consensus 245 dGq~VKItG~VtcG~~PL~ss~~k~~rCVYtst~LyE~rgw~~k~an~kh~~f~W~lr 302 (439)
+-.+|||.|+ ...=|+.|-.-.||+|.+-.=.+- ++++.+..|+..
T Consensus 30 ~t~llkIEGv----~skeEa~fYlGkR~~yvYKa~~~~--------~~~k~RvIWGkV 75 (111)
T KOG0887|consen 30 NTSLLKIEGV----YSKEEASFYLGKRCVYVYKAKPEV--------RGSKTRVIWGKV 75 (111)
T ss_pred CcEEEEEecc----cchhhhheeecCcEEEEEecCCCC--------CCceEEEEEEEE
Confidence 3348999997 456788898889999976544333 367788889874
No 10
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=35.08 E-value=27 Score=32.98 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=15.5
Q ss_pred cccCcEEEEEEEEEeccc
Q 013624 243 AKSGQFVKVTGVVTCGNV 260 (439)
Q Consensus 243 a~dGq~VKItG~VtcG~~ 260 (439)
+..|+.+.|-|.|.-|++
T Consensus 54 ~~~g~~iRvgG~V~~GSi 71 (160)
T PRK13165 54 PEVGQRLRVGGMVMPGSV 71 (160)
T ss_pred cCCCCEEEEeeEEeCCcE
Confidence 357999999999998876
No 11
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=35.03 E-value=2.6e+02 Score=23.17 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=17.0
Q ss_pred CCCCCCHHHHHHhhhcCCCCCC
Q 013624 347 ENKDLSPEFIRWLGQKSLSSDD 368 (439)
Q Consensus 347 ~~kdlS~~f~~WL~erNLSsd~ 368 (439)
..|.=.-++++||..+|+....
T Consensus 147 ~~Npg~FD~~~yl~~~gI~~~~ 168 (176)
T PF13567_consen 147 PTNPGGFDYQRYLRSKGIYAQG 168 (176)
T ss_pred CCCCCCcCHHHHHHHCCCEEEE
Confidence 4455666799999999998765
No 12
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=33.66 E-value=21 Score=41.76 Aligned_cols=17 Identities=47% Similarity=0.792 Sum_probs=15.0
Q ss_pred ccccCCceeeeCCCCCC
Q 013624 7 SHQLSNGLFVSGRPEQP 23 (439)
Q Consensus 7 sHqLsnGLyVSGrpeq~ 23 (439)
-|||.|||||+|+|-|.
T Consensus 1199 qH~Lps~l~v~~qp~qs 1215 (1387)
T KOG1016|consen 1199 QHQLPSGLYVKLQPGQS 1215 (1387)
T ss_pred ccccCccceEecCCccc
Confidence 59999999999999843
No 13
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=31.57 E-value=37 Score=24.25 Aligned_cols=17 Identities=12% Similarity=0.464 Sum_probs=14.8
Q ss_pred CHHHHHHhhhcCCCCCC
Q 013624 352 SPEFIRWLGQKSLSSDD 368 (439)
Q Consensus 352 S~~f~~WL~erNLSsd~ 368 (439)
..+|+.||.++|+....
T Consensus 6 ~~~L~~wL~~~gi~~~~ 22 (38)
T PF10281_consen 6 DSDLKSWLKSHGIPVPK 22 (38)
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 47899999999998775
No 14
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=31.55 E-value=39 Score=30.42 Aligned_cols=22 Identities=23% Similarity=0.581 Sum_probs=14.4
Q ss_pred hhhHHHHHHHHHHHHhh-eeeEe
Q 013624 215 KPVLWLVILIFVMGFIA-GGFIL 236 (439)
Q Consensus 215 k~~~w~~~~l~~~g~~~-g~fil 236 (439)
|.++|++++|++++++. |+|+|
T Consensus 4 kl~~i~~i~l~~l~~~g~~~~~~ 26 (142)
T PRK07718 4 KLIKIMLIILIVIALIGTAALVL 26 (142)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhh
Confidence 67888887777666555 44444
No 15
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=29.97 E-value=69 Score=26.23 Aligned_cols=28 Identities=18% Similarity=0.210 Sum_probs=24.3
Q ss_pred eeeeeCCEEEEEEEEEecCceeeEeCCC
Q 013624 376 GYIKEGSTVSVMGIVQRNDNVLMIVPPP 403 (439)
Q Consensus 376 GyIkEGstvSVmGvvkr~~~~~mi~~p~ 403 (439)
.-+++||+|.|-|.++...+..=|.++.
T Consensus 43 ~~~~~Gd~V~vtG~v~ey~g~tql~~~~ 70 (78)
T cd04486 43 ADVAVGDLVRVTGTVTEYYGLTQLTAVS 70 (78)
T ss_pred CCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence 3568899999999999999988888776
No 16
>PF11432 DUF3197: Protein of unknown function (DUF3197); InterPro: IPR024443 This domain, whose function is unknown, is found in bacterial proteins.; PDB: 1WN9_A 1WNA_A.
Probab=28.52 E-value=68 Score=29.09 Aligned_cols=59 Identities=22% Similarity=0.506 Sum_probs=34.2
Q ss_pred EEEEecCC-----ceeEEEEeCCCCeeeeeeecceEEecCCCC----CCCCHHHHHHhhhcCCCCCCceeEEeeeeeeeC
Q 013624 311 FYISDFQS-----GLRALVKTGSGARVTPFVDDSVVIDIKPEN----KDLSPEFIRWLGQKSLSSDDRLMRLKEGYIKEG 381 (439)
Q Consensus 311 FYIsD~~S-----G~RALVKaG~GakVtp~V~e~~vv~~~~~~----kdlS~~f~~WL~erNLSsd~r~mRlkEGyIkEG 381 (439)
.||||.|. +..++|..|. ++.+.+|. .++-. ..+=.||.+||.+++. |++|-.+-.|
T Consensus 19 ~liTDwQd~R~~ARYa~ll~~gk----~~llt~dA---FGPafG~~G~~ALaELv~wl~~~G~-------~f~EaVl~p~ 84 (113)
T PF11432_consen 19 YLITDWQDQRPQARYALLLRGGK----EPLLTPDA---FGPAFGPEGERALAELVRWLQERGA-------RFYEAVLSPS 84 (113)
T ss_dssp EEEEE--SSCCC--EEEEEE-SS-----EEEEEEE---ESTTS-TTHHHHHHHHHHHHHHTT--------EEEEEEE-GG
T ss_pred EEEeccccchhhhhhhhheecCC----cccccccc---cCcccCccHHHHHHHHHHHHHHcCC-------chhheecCHH
Confidence 68999885 3456665554 45555555 23332 2445689999999984 6778776665
Q ss_pred CE
Q 013624 382 ST 383 (439)
Q Consensus 382 st 383 (439)
|-
T Consensus 85 e~ 86 (113)
T PF11432_consen 85 EF 86 (113)
T ss_dssp GH
T ss_pred HH
Confidence 53
No 17
>PF10572 UPF0556: Uncharacterised protein family UPF0556; InterPro: IPR018887 This family of proteins has no known function.
Probab=27.84 E-value=1.5e+02 Score=28.33 Aligned_cols=45 Identities=16% Similarity=0.423 Sum_probs=27.9
Q ss_pred CCCceEEEeeeeeee-ecC----CCCCCCCCCccccccceeeeeeeecEEEEecC
Q 013624 268 RVPRCVYTSTSLYEY-RAW----GSKPANPKHRHFTWGLRSLERHVVDFYISDFQ 317 (439)
Q Consensus 268 k~~rCVYtst~LyE~-rgw----~~k~an~kh~~f~W~lr~~Er~~~DFYIsD~~ 317 (439)
+- +|.|||...=-- --| +....|..+.|+.||.- --..-|.+||+
T Consensus 45 ~~-~C~FTYAaqGGTNEqW~msi~~s~d~~~~sC~I~RPq----gkSYL~F~qFk 94 (158)
T PF10572_consen 45 KY-KCTFTYAAQGGTNEQWQMSIGLSDDNGHYSCIIWRPQ----GKSYLFFTQFK 94 (158)
T ss_pred ce-EEEEEEEecCCccceEEEEeeecCCCCceEEEEECCC----CCcEEEEEEEE
Confidence 44 999999865111 124 44567788889999973 23445555554
No 18
>PF13869 NUDIX_2: Nucleotide hydrolase; PDB: 3MDG_B 2J8Q_B 3Q2S_A 3P5T_D 3BAP_A 2CL3_A 3P6Y_A 3Q2T_B 3BHO_A 3N9U_A ....
Probab=27.72 E-value=8.5 Score=37.14 Aligned_cols=35 Identities=43% Similarity=0.561 Sum_probs=28.1
Q ss_pred hcCCCCCCceeEEeeeeeeeCCEEEEEEEEEecCc
Q 013624 361 QKSLSSDDRLMRLKEGYIKEGSTVSVMGIVQRNDN 395 (439)
Q Consensus 361 erNLSsd~r~mRlkEGyIkEGstvSVmGvvkr~~~ 395 (439)
|+..+..+|.+|++|-|-++|++-||-||+==|..
T Consensus 21 ekd~s~~~rl~rl~~~y~~~GmRrsVe~Vllvh~h 55 (188)
T PF13869_consen 21 EKDPSVAARLQRLKENYEKEGMRRSVEGVLLVHEH 55 (188)
T ss_dssp -SSSSHHHHHHHHHHHHHHHSSEEEEEEEEEEEET
T ss_pred ccccCHHHHHHHHHHHHHHhCCceEEEEEEEEecC
Confidence 34466667999999999999999999998755444
No 19
>PF05834 Lycopene_cycl: Lycopene cyclase protein; InterPro: IPR008671 This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare [].; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0016117 carotenoid biosynthetic process
Probab=26.56 E-value=2.5e+02 Score=28.39 Aligned_cols=44 Identities=14% Similarity=0.349 Sum_probs=32.9
Q ss_pred eecceEEecCC--CCCCCCHHHHHHhhhcCCCCCCceeEEeeeeeee
Q 013624 336 VDDSVVIDIKP--ENKDLSPEFIRWLGQKSLSSDDRLMRLKEGYIKE 380 (439)
Q Consensus 336 V~e~~vv~~~~--~~kdlS~~f~~WL~erNLSsd~r~mRlkEGyIkE 380 (439)
++|.+.++..+ ...++...+.+||+++|+.... ++|-|.|+|--
T Consensus 198 lvE~T~fs~~~~~~~~~~~~~l~~~l~~~g~~~~~-i~~~E~G~IPm 243 (374)
T PF05834_consen 198 LVEETSFSPRPALPEEELKARLRRYLERLGIDDYE-ILEEERGVIPM 243 (374)
T ss_pred EEEEEEEcCCCCCCHHHHHHHHHHHHHHcCCCcee-EEEeecceeec
Confidence 56667666554 2246778899999998888654 88999998876
No 20
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=25.33 E-value=49 Score=31.26 Aligned_cols=18 Identities=39% Similarity=0.567 Sum_probs=15.8
Q ss_pred cccCcEEEEEEEEEeccc
Q 013624 243 AKSGQFVKVTGVVTCGNV 260 (439)
Q Consensus 243 a~dGq~VKItG~VtcG~~ 260 (439)
...|+.+.|-|.|.-|++
T Consensus 54 ~~~g~~iRvgG~V~~GSv 71 (159)
T PRK13150 54 PAVGQRLRVGGMVMPGSV 71 (159)
T ss_pred cCCCCEEEEeeEEeCCcE
Confidence 457999999999998876
No 21
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=24.00 E-value=26 Score=37.47 Aligned_cols=18 Identities=39% Similarity=0.543 Sum_probs=15.7
Q ss_pred ceeEEeeeeeeeCCEEEE
Q 013624 369 RLMRLKEGYIKEGSTVSV 386 (439)
Q Consensus 369 r~mRlkEGyIkEGstvSV 386 (439)
|-..+||.|+||||||+=
T Consensus 77 ~Ev~vkeWfVKEGDtVeq 94 (474)
T KOG0558|consen 77 AEVTVKEWFVKEGDTVEQ 94 (474)
T ss_pred eeeeeeeehhhcCCcHHH
Confidence 567899999999999863
No 22
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=22.93 E-value=68 Score=22.67 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=14.4
Q ss_pred HHHHHHhhhcCCCCCCc
Q 013624 353 PEFIRWLGQKSLSSDDR 369 (439)
Q Consensus 353 ~~f~~WL~erNLSsd~r 369 (439)
.+|+.+|+++||+..+.
T Consensus 7 ~eLk~~l~~~gL~~~G~ 23 (35)
T PF02037_consen 7 AELKEELKERGLSTSGK 23 (35)
T ss_dssp HHHHHHHHHTTS-STSS
T ss_pred HHHHHHHHHCCCCCCCC
Confidence 68999999999999983
No 23
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=22.86 E-value=30 Score=30.39 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=13.8
Q ss_pred hhhHHHHHHHHHHHHhheeeEe
Q 013624 215 KPVLWLVILIFVMGFIAGGFIL 236 (439)
Q Consensus 215 k~~~w~~~~l~~~g~~~g~fil 236 (439)
|.+||++++++++-|+++.++.
T Consensus 1 RW~l~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYCH 22 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHHH
Confidence 4567777766666666655554
No 24
>PF11151 DUF2929: Protein of unknown function (DUF2929); InterPro: IPR021324 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=22.74 E-value=50 Score=26.09 Aligned_cols=19 Identities=32% Similarity=0.667 Sum_probs=16.8
Q ss_pred hhHHHHHHHHHHHHhheee
Q 013624 216 PVLWLVILIFVMGFIAGGF 234 (439)
Q Consensus 216 ~~~w~~~~l~~~g~~~g~f 234 (439)
.++|++++..++||+++++
T Consensus 6 t~fWs~il~~vvgyI~ssL 24 (57)
T PF11151_consen 6 TFFWSFILGEVVGYIGSSL 24 (57)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 5789999999999998865
No 25
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.32 E-value=31 Score=31.31 Aligned_cols=18 Identities=33% Similarity=0.755 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhheeeEe
Q 013624 219 WLVILIFVMGFIAGGFIL 236 (439)
Q Consensus 219 w~~~~l~~~g~~~g~fil 236 (439)
|-+|+++.+||+||.|++
T Consensus 75 wglIv~lllGf~AG~lnv 92 (116)
T COG5336 75 WGLIVFLLLGFGAGVLNV 92 (116)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999987
No 26
>PRK06437 hypothetical protein; Provisional
Probab=22.19 E-value=86 Score=24.91 Aligned_cols=37 Identities=8% Similarity=0.170 Sum_probs=27.7
Q ss_pred HHHHHHhhhcCCCCCC-------ceeEEeeeeeeeCCEEEEEEEE
Q 013624 353 PEFIRWLGQKSLSSDD-------RLMRLKEGYIKEGSTVSVMGIV 390 (439)
Q Consensus 353 ~~f~~WL~erNLSsd~-------r~mRlkEGyIkEGstvSVmGvv 390 (439)
.++..+|++.|+..+. +++. .|=.|++||+|.++=.+
T Consensus 21 ~tv~dLL~~Lgi~~~~vaV~vNg~iv~-~~~~L~dgD~Veiv~~V 64 (67)
T PRK06437 21 LTVNDIIKDLGLDEEEYVVIVNGSPVL-EDHNVKKEDDVLILEVF 64 (67)
T ss_pred CcHHHHHHHcCCCCccEEEEECCEECC-CceEcCCCCEEEEEecc
Confidence 3588899999998654 4444 67789999999887544
No 27
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=21.83 E-value=76 Score=24.23 Aligned_cols=19 Identities=32% Similarity=0.469 Sum_probs=17.4
Q ss_pred eeEEeeeeeeeCCEEEEEE
Q 013624 370 LMRLKEGYIKEGSTVSVMG 388 (439)
Q Consensus 370 ~mRlkEGyIkEGstvSVmG 388 (439)
..|+..|-|+.||+|.+++
T Consensus 5 ~grV~sG~l~~gd~v~~~~ 23 (74)
T PF03144_consen 5 TGRVYSGTLKKGDKVRVLP 23 (74)
T ss_dssp EEEEEESEEETTEEEEEES
T ss_pred EEEEEEeEEcCCCEEEECc
Confidence 4699999999999999987
No 28
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=21.70 E-value=1.4e+02 Score=21.89 Aligned_cols=27 Identities=37% Similarity=0.461 Sum_probs=21.5
Q ss_pred eeeeCCEEEEEEEEEecCceeeEeCCC
Q 013624 377 YIKEGSTVSVMGIVQRNDNVLMIVPPP 403 (439)
Q Consensus 377 yIkEGstvSVmGvvkr~~~~~mi~~p~ 403 (439)
.+++|+++.|.|.+++..+..-|..|.
T Consensus 45 ~~~~G~~~~v~Gkv~~~~~~~qi~~P~ 71 (75)
T cd04488 45 QLPPGTRVRVSGKVKRFRGGLQIVHPE 71 (75)
T ss_pred cCCCCCEEEEEEEEeecCCeeEEeCCc
Confidence 478899999999999987766565553
No 29
>KOG2362 consensus Uncharacterized Fe-S protein [General function prediction only]
Probab=21.43 E-value=60 Score=34.03 Aligned_cols=17 Identities=47% Similarity=0.538 Sum_probs=14.9
Q ss_pred EeeeeeeeCCEEEEEEE
Q 013624 373 LKEGYIKEGSTVSVMGI 389 (439)
Q Consensus 373 lkEGyIkEGstvSVmGv 389 (439)
++||||+.||+|.|+.-
T Consensus 316 ~~~g~I~vGd~Vyv~~k 332 (336)
T KOG2362|consen 316 VNEGTIKVGDTVYVLYK 332 (336)
T ss_pred cccceEEeCCEEEEEec
Confidence 56899999999999864
No 30
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.74 E-value=36 Score=30.35 Aligned_cols=16 Identities=38% Similarity=0.505 Sum_probs=12.5
Q ss_pred HHHHHHHHHhheeeEe
Q 013624 221 VILIFVMGFIAGGFIL 236 (439)
Q Consensus 221 ~~~l~~~g~~~g~fil 236 (439)
+++.|++|+|+|.|+.
T Consensus 2 ~~i~lvvG~iiG~~~~ 17 (128)
T PF06295_consen 2 AIIGLVVGLIIGFLIG 17 (128)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4567888888888876
No 31
>PF08078 PsaX: PsaX family; InterPro: IPR012986 This family consists of the PsaX family of photosystem I (PSI) protein subunits. PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus [].; PDB: 3PCQ_X 1JB0_X.
Probab=20.58 E-value=45 Score=24.95 Aligned_cols=25 Identities=24% Similarity=0.777 Sum_probs=15.1
Q ss_pred CcceeeecCCchhhHHHHHHHHHHHHhheeeE
Q 013624 204 EDDYSFRKNFPKPVLWLVILIFVMGFIAGGFI 235 (439)
Q Consensus 204 ~~~~s~~~~~Pk~~~w~~~~l~~~g~~~g~fi 235 (439)
.-.|-|| ..|++ +|+++-|++.+|.
T Consensus 9 kp~Y~fr------t~Wa~-llLaINflVAayY 33 (37)
T PF08078_consen 9 KPPYTFR------TGWAL-LLLAINFLVAAYY 33 (37)
T ss_dssp -----HH------HHHHH-HHHHHHHHHHHHH
T ss_pred CCCeehh------HHHHH-HHHHHHHHHHHHH
Confidence 3446666 67998 7778888887753
No 32
>COG4303 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]
Probab=20.33 E-value=71 Score=34.10 Aligned_cols=28 Identities=32% Similarity=0.625 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHhhhcCCCCCCceeEEeee
Q 013624 348 NKDLSPEFIRWLGQKSLSSDDRLMRLKEG 376 (439)
Q Consensus 348 ~kdlS~~f~~WL~erNLSsd~r~mRlkEG 376 (439)
.....+||++||.+.++..++|+ +...|
T Consensus 420 glrP~~EFe~wl~~mGi~~~Grl-t~~ag 447 (453)
T COG4303 420 GLRPIPEFERWLERMGIMANGRL-TKRAG 447 (453)
T ss_pred CCCCchHHHHHHHHhCcccCCce-eccCC
Confidence 45688999999999999998874 44443
No 33
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=20.32 E-value=85 Score=25.28 Aligned_cols=19 Identities=21% Similarity=0.545 Sum_probs=16.4
Q ss_pred cccccccCcEEEEEEEEEe
Q 013624 239 DLRTAKSGQFVKVTGVVTC 257 (439)
Q Consensus 239 ~Lr~a~dGq~VKItG~Vtc 257 (439)
+...++.|+||||.|.|..
T Consensus 44 ~~~~~~~g~~v~v~G~v~~ 62 (95)
T cd04478 44 EVEPIEEGTYVRVFGNLKS 62 (95)
T ss_pred cccccccCCEEEEEEEEcc
Confidence 5778999999999999764
Done!