Query 014250
Match_columns 428
No_of_seqs 156 out of 506
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:18:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014250.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014250hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00463 SMR Small MutS-rela 99.6 1.1E-15 2.5E-20 123.0 7.9 77 304-423 1-79 (80)
2 PF01713 Smr: Smr domain; Int 99.6 1.9E-15 4.2E-20 122.5 6.1 72 307-424 1-83 (83)
3 PF08590 DUF1771: Domain of un 99.5 6.1E-15 1.3E-19 116.4 1.3 66 235-300 1-66 (66)
4 KOG2401 Predicted MutS-related 98.6 1.3E-08 2.8E-13 106.3 3.3 120 1-120 14-141 (448)
5 COG2840 Uncharacterized protei 98.6 2.2E-07 4.7E-12 87.7 8.2 80 303-427 95-182 (184)
6 PRK04946 hypothetical protein; 98.2 4E-06 8.7E-11 78.9 7.6 75 303-426 94-175 (181)
7 PRK00409 recombination and DNA 97.6 9.8E-05 2.1E-09 82.7 7.1 71 305-424 705-782 (782)
8 TIGR01069 mutS2 MutS2 family p 97.4 0.00027 5.8E-09 79.2 7.1 70 305-423 694-770 (771)
9 PF02845 CUE: CUE domain; Int 96.4 0.0079 1.7E-07 43.5 5.0 40 96-135 2-41 (42)
10 smart00546 CUE Domain that may 95.5 0.028 6E-07 40.7 4.6 40 96-135 3-42 (43)
11 PF00627 UBA: UBA/TS-N domain; 91.1 0.55 1.2E-05 33.0 4.7 34 97-132 4-37 (37)
12 COG1193 Mismatch repair ATPase 82.8 1.9 4E-05 49.1 5.3 56 305-409 677-732 (753)
13 cd00194 UBA Ubiquitin Associat 81.3 3.5 7.6E-05 28.5 4.4 34 97-132 3-36 (38)
14 smart00165 UBA Ubiquitin assoc 80.7 3.3 7E-05 28.6 4.1 34 97-132 3-36 (37)
15 PF03474 DMA: DMRTA motif; In 77.4 4.8 0.0001 29.7 4.2 34 98-131 4-37 (39)
16 PF14346 DUF4398: Domain of un 60.9 68 0.0015 27.0 8.4 44 246-289 41-84 (103)
17 PLN03218 maturation of RBCL 1; 60.7 14 0.00031 43.6 5.7 90 303-423 920-1012(1060)
18 PF04505 Dispanin: Interferon- 57.6 14 0.0003 30.7 3.6 29 253-281 40-68 (82)
19 cd00291 SirA_YedF_YeeD SirA, Y 51.4 77 0.0017 24.2 6.7 65 306-423 1-67 (69)
20 smart00685 DM14 Repeats in fly 51.2 59 0.0013 26.0 6.0 40 246-285 3-43 (59)
21 PF13763 DUF4167: Domain of un 47.3 82 0.0018 26.7 6.5 47 239-288 31-77 (80)
22 cd00248 Mth938-like Mth938-lik 41.9 32 0.0007 29.7 3.6 32 381-415 55-86 (109)
23 cd03420 SirA_RHOD_Pry_redox Si 39.1 1.6E+02 0.0035 23.1 6.9 66 306-424 1-68 (69)
24 TIGR00601 rad23 UV excision re 39.1 35 0.00076 36.0 4.0 38 95-134 337-374 (378)
25 cd05125 Mth938_2P1-like Mth938 37.5 37 0.00079 30.0 3.3 31 381-414 57-87 (114)
26 COG2178 Predicted RNA-binding 37.5 1.8E+02 0.0038 28.7 8.1 52 233-284 12-63 (204)
27 COG2250 Uncharacterized conser 37.2 1.3E+02 0.0028 27.0 6.8 40 240-279 3-42 (132)
28 cd05560 Xcc1710_like Xcc1710_l 37.1 38 0.00083 29.4 3.3 32 381-415 55-86 (109)
29 PF02954 HTH_8: Bacterial regu 34.3 41 0.0009 24.1 2.6 25 109-133 5-29 (42)
30 TIGR01689 EcbF-BcbF capsule bi 34.3 44 0.00094 30.0 3.3 36 378-413 41-82 (126)
31 PF01206 TusA: Sulfurtransfera 34.2 99 0.0021 23.9 4.9 66 306-424 2-69 (70)
32 PF03357 Snf7: Snf7; InterPro 32.7 2.5E+02 0.0054 24.9 7.9 54 238-291 12-65 (171)
33 PF13986 DUF4224: Domain of un 32.3 76 0.0016 23.9 3.8 27 396-422 16-42 (47)
34 PF04430 DUF498: Protein of un 30.5 54 0.0012 28.2 3.1 33 379-414 54-86 (110)
35 PF01963 TraB: TraB family; I 29.2 2.2E+02 0.0048 26.9 7.4 30 378-412 228-257 (259)
36 cd05126 Mth938 Mth938 domain. 26.7 78 0.0017 28.0 3.5 32 381-414 61-92 (117)
37 PF10006 DUF2249: Uncharacteri 24.1 3.5E+02 0.0076 21.1 6.6 23 306-328 1-23 (69)
38 cd03423 SirA SirA (also known 22.6 3.6E+02 0.0078 21.1 6.3 65 307-424 2-68 (69)
39 KOG4588 Predicted ubiquitin-co 22.2 91 0.002 31.5 3.3 33 105-137 1-33 (267)
40 PRK09591 celC cellobiose phosp 21.1 4.3E+02 0.0094 23.0 7.0 64 250-318 20-83 (104)
41 cd03421 SirA_like_N SirA_like_ 20.8 3.9E+02 0.0085 20.5 6.4 64 306-423 1-65 (67)
42 CHL00098 tsf elongation factor 20.1 1.4E+02 0.0031 29.0 4.1 38 97-135 3-40 (200)
43 cd00215 PTS_IIA_lac PTS_IIA, P 20.0 4.8E+02 0.01 22.5 7.0 64 251-319 16-79 (97)
44 PF09286 Pro-kuma_activ: Pro-k 20.0 1.4E+02 0.003 26.4 3.8 28 397-424 64-93 (143)
45 TIGR00823 EIIA-LAC phosphotran 20.0 4.8E+02 0.01 22.6 7.0 63 251-318 18-80 (99)
No 1
>smart00463 SMR Small MutS-related domain.
Probab=99.62 E-value=1.1e-15 Score=123.02 Aligned_cols=77 Identities=39% Similarity=0.722 Sum_probs=67.7
Q ss_pred CcccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEE
Q 014250 304 MWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVI 383 (428)
Q Consensus 304 ~~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VI 383 (428)
.|+||||||++.||+.+|+.+|+.++.. |. ...+.||
T Consensus 1 ~~~lDLHG~~~~eA~~~l~~~l~~~~~~----------------~~---------------------------~~~~~II 37 (80)
T smart00463 1 KWSLDLHGLTVEEALTALDKFLNNARLK----------------GL---------------------------EQKLVII 37 (80)
T ss_pred CCeEEcCCCCHHHHHHHHHHHHHHHHHc----------------CC---------------------------CceEEEE
Confidence 4789999999999999999999998742 10 0379999
Q ss_pred EccCCCCC-CCCCchHHHHHHHHHcCCeeee-CCCeEEEEee
Q 014250 384 TGIGNHSR-GQAALPTAVKNFLSESGYRFDE-ARPGVITVRP 423 (428)
Q Consensus 384 TGrG~HS~-G~arLkpAV~~fL~e~Gyrf~E-~~pGvI~V~~ 423 (428)
||+|+||. |.++|+++|.++|...+|+|.+ .++|++.|..
T Consensus 38 ~G~G~~s~~g~~~i~~~l~~~l~~~~~~~~~~~~~G~~~v~l 79 (80)
T smart00463 38 TGKGKHSLGGKSGVKPALKEHLRVESFRFAEEGNSGVLVVKL 79 (80)
T ss_pred EcccCCCccchhhHHHHHHhchhhcccccCCCCCCeEEEEEe
Confidence 99999998 5699999999999999999987 7999999975
No 2
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=99.58 E-value=1.9e-15 Score=122.47 Aligned_cols=72 Identities=44% Similarity=0.767 Sum_probs=57.8
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEcc
Q 014250 307 LDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITGI 386 (428)
Q Consensus 307 LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITGr 386 (428)
||||||+++||+.+|+++|..++.+ | ...+.||||+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~----------------~----------------------------~~~~~II~G~ 36 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQR----------------G----------------------------IRELRIITGK 36 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHT----------------T----------------------------HSEEEEE--S
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHc----------------C----------------------------CCEEEEEecc
Confidence 7999999999999999999998742 1 1479999999
Q ss_pred CCCCCCCCCchHHHHHHHHHcCCeeeeC-----------CCeEEEEeee
Q 014250 387 GNHSRGQAALPTAVKNFLSESGYRFDEA-----------RPGVITVRPK 424 (428)
Q Consensus 387 G~HS~G~arLkpAV~~fL~e~Gyrf~E~-----------~pGvI~V~~k 424 (428)
|+||.++. |+++|..||.+ ++.|.+. ++|++.|..|
T Consensus 37 G~hS~~g~-Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~~G~~~V~lk 83 (83)
T PF01713_consen 37 GNHSKGGV-LKRAVRRWLEE-GYQYEEVLAYRDAEPEDGNSGATIVYLK 83 (83)
T ss_dssp TCTCCTSH-HHHHHHHHHHH-THCCTTEEEEEE--CCCTGGGEEEEEE-
T ss_pred CCCCCCCc-HHHHHHHHHHh-hhccchhheeeecCCCCCCCeEEEEEeC
Confidence 99999776 99999999999 8777542 9999999876
No 3
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=99.49 E-value=6.1e-15 Score=116.38 Aligned_cols=66 Identities=27% Similarity=0.295 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 014250 235 VYLVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNS 300 (428)
Q Consensus 235 ~Y~~~RkeA~k~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~AA~~If~~rNs 300 (428)
+|..+|.+|.++++.|++||++|++||++||+..|++||++|+.+..+|+++|.+||+.||..+|.
T Consensus 1 ~Y~~~R~~A~~~~~~r~~~~~~A~~Ay~~Gd~~~A~~ls~~gk~~~~~~~~~n~~AA~~I~~~~N~ 66 (66)
T PF08590_consen 1 DYEKLRAEADEHARKRNECFQKAAEAYRRGDKAAAKELSEEGKQHNEKMKEANRQAAEAIFEERNA 66 (66)
T ss_dssp --------------------------------------------------SHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 589999999999999999999999999999999999999999999999999999999999999983
No 4
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=98.65 E-value=1.3e-08 Score=106.28 Aligned_cols=120 Identities=15% Similarity=0.080 Sum_probs=90.2
Q ss_pred CCCCCCCCCCchhhcHHHHhhcCCCCCCCCCCCCCCCccccCCc-cccccccCCCCccCCcccccccCCCCCCCcccccc
Q 014250 1 MSLTRVKSPGWAAFDLKQRQKQGLAPETDKDSYPPISSTLTSLR-NCENVSRNTDVLVKPFSSVLRPSVEFPTLTEENEC 79 (428)
Q Consensus 1 m~~~~~~~~gw~afd~~~r~~~~~~~~~~~~~fp~~~~~~~~~~-~~~~~~~~~~~~~~~f~sv~~p~~~f~~~~~~~~~ 79 (428)
|||+.....+|..|.+..+++...+.....|++|++.+.-.... .|.-+-.+..+....+++++.++..+++..+..+|
T Consensus 14 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~ 93 (448)
T KOG2401|consen 14 MSLTLSLAAFSFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELLEPSPSSVSFESLRARASDENVDR 93 (448)
T ss_pred ccchhccchhhhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhcccccccCCCcccccccccccchhhhcccc
Confidence 78999999999999999999999999999999999998854333 24334456667888999999999999999999999
Q ss_pred cccCC------CC-CccccccchHHHHHHHHHhccccchhHHHHHHHH
Q 014250 80 DYKGK------HG-HKAIEQHSRDLALKKLKALHSWADNSLIEDLMEA 120 (428)
Q Consensus 80 ~~~~~------~~-~~~~~~~~~~~~~~~L~~~~~wad~~li~dv~~a 120 (428)
++.+. -+ .-....+.+..++.....+..|.+...|-+..-.
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (448)
T KOG2401|consen 94 GNQERILDRSRNQVAGKLKVSFVEKKLNEEEPQKEINPDGRILPEDPS 141 (448)
T ss_pred HHHHhhcccccccccccccccccccccCccccccccCCcccccccccc
Confidence 99881 11 1122223355666667777777777666544433
No 5
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.55 E-value=2.2e-07 Score=87.66 Aligned_cols=80 Identities=30% Similarity=0.446 Sum_probs=64.3
Q ss_pred CCcccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEE
Q 014250 303 DMWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQV 382 (428)
Q Consensus 303 ~~~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~V 382 (428)
.+..||||||++.||-+.|-.+|.....+ | ...+.|
T Consensus 95 ~e~~LDLHG~tq~eAr~~L~~Fi~~a~~~----------------~----------------------------~rcv~V 130 (184)
T COG2840 95 PEARLDLHGLTQEEARQELGAFIARARAE----------------G----------------------------LRCVLV 130 (184)
T ss_pred cceeeeccCCCHHHHHHHHHHHHHHHHHh----------------C----------------------------CcEEEE
Confidence 46789999999999999999999986532 2 147999
Q ss_pred EEccCCCCCCC-CCchHHHHHHHHHcCC--eeee-----CCCeEEEEeeeccC
Q 014250 383 ITGIGNHSRGQ-AALPTAVKNFLSESGY--RFDE-----ARPGVITVRPKFRQ 427 (428)
Q Consensus 383 ITGrG~HS~G~-arLkpAV~~fL~e~Gy--rf~E-----~~pGvI~V~~k~r~ 427 (428)
|||.|. |.|. +.||.+|..||.+.-- .|.+ -+.|.|+|..+++.
T Consensus 131 ihGkG~-s~g~~~vLK~~Vp~WL~qhp~V~a~~~a~~~hGG~GAlyVlL~~~~ 182 (184)
T COG2840 131 IHGKGR-SKGSKPVLKSQVPRWLTQHPDVLAFHQAPRRHGGDGALYVLLRRRV 182 (184)
T ss_pred EeCCCc-CCCCchhHHHHHHHHHHhChHHHhhcccchhcCCceEEEEEEeccc
Confidence 999999 9985 9999999999999432 2433 37788888887764
No 6
>PRK04946 hypothetical protein; Provisional
Probab=98.20 E-value=4e-06 Score=78.91 Aligned_cols=75 Identities=21% Similarity=0.197 Sum_probs=60.9
Q ss_pred CCcccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEE
Q 014250 303 DMWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQV 382 (428)
Q Consensus 303 ~~~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~V 382 (428)
-...|||||+++.||.+.|..+|..... .| ...+.|
T Consensus 94 ~~~~LDLhG~~~eeA~~~L~~fl~~a~~----------------~g----------------------------~r~v~I 129 (181)
T PRK04946 94 PELFLDLHGLTQLQAKQELGALIAACRK----------------EH----------------------------VFCACV 129 (181)
T ss_pred CceEEECCCCCHHHHHHHHHHHHHHHHH----------------cC----------------------------CCEEEE
Confidence 4578999999999999999999997542 12 247999
Q ss_pred EEccCCCCCCCCCchHHHHHHHHHcCC--eee-----eCCCeEEEEeeecc
Q 014250 383 ITGIGNHSRGQAALPTAVKNFLSESGY--RFD-----EARPGVITVRPKFR 426 (428)
Q Consensus 383 ITGrG~HS~G~arLkpAV~~fL~e~Gy--rf~-----E~~pGvI~V~~k~r 426 (428)
|+|+|. +.||.+|..||.+..+ .|. +-+.|.+.|..|..
T Consensus 130 IHGkG~-----gvLk~~V~~wL~q~~~V~af~~A~~~~GG~GA~~VlLk~~ 175 (181)
T PRK04946 130 MHGHGK-----HILKQQTPLWLAQHPDVMAFHQAPKEWGGDAALLVLIEIE 175 (181)
T ss_pred EcCCCH-----hHHHHHHHHHHcCCchhheeeccCcccCCceEEEEEEecC
Confidence 999996 6999999999998765 353 25789999988764
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=97.63 E-value=9.8e-05 Score=82.67 Aligned_cols=71 Identities=31% Similarity=0.470 Sum_probs=57.6
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEE
Q 014250 305 WKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVIT 384 (428)
Q Consensus 305 ~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VIT 384 (428)
..|||||++++||+..|+.+|..... .| ...+.||+
T Consensus 705 ~~lDL~G~~~eeA~~~l~~fl~~a~~----------------~g----------------------------~~~v~IIH 740 (782)
T PRK00409 705 LELDLRGMRYEEALERLDKYLDDALL----------------AG----------------------------YGEVLIIH 740 (782)
T ss_pred ceEECCCCCHHHHHHHHHHHHHHHHH----------------cC----------------------------CCEEEEEc
Confidence 68999999999999999999997532 12 25799999
Q ss_pred ccCCCCCCCCCchHHHHHHHHHcCCe--e-----eeCCCeEEEEeee
Q 014250 385 GIGNHSRGQAALPTAVKNFLSESGYR--F-----DEARPGVITVRPK 424 (428)
Q Consensus 385 GrG~HS~G~arLkpAV~~fL~e~Gyr--f-----~E~~pGvI~V~~k 424 (428)
|+|. ..|+.+|..||.++.+- | .+.+.|+..|+.|
T Consensus 741 GkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~Gat~V~lk 782 (782)
T PRK00409 741 GKGT-----GKLRKGVQEFLKKHPSVKSFRDAPPNEGGFGVTIVELK 782 (782)
T ss_pred CCCh-----hHHHHHHHHHHcCCCceeeeeecCcccCCCeEEEEEEC
Confidence 9986 59999999999998663 3 2357899988764
No 8
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=97.42 E-value=0.00027 Score=79.16 Aligned_cols=70 Identities=27% Similarity=0.430 Sum_probs=57.2
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEE
Q 014250 305 WKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVIT 384 (428)
Q Consensus 305 ~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VIT 384 (428)
..|||||+++.||+..|+.+|..... .| ...++||+
T Consensus 694 ~~ldl~G~~~~eA~~~l~~~ld~a~~----------------~g----------------------------~~~v~IIH 729 (771)
T TIGR01069 694 LTLDLRGQRSEEALDRLEKFLNDALL----------------AG----------------------------YEVVLIIH 729 (771)
T ss_pred ceEECCCCCHHHHHHHHHHHHHHHHH----------------CC----------------------------CCEEEEEc
Confidence 58999999999999999999998542 12 24799999
Q ss_pred ccCCCCCCCCCchHHHHHHHHHcCCe--e-----eeCCCeEEEEee
Q 014250 385 GIGNHSRGQAALPTAVKNFLSESGYR--F-----DEARPGVITVRP 423 (428)
Q Consensus 385 GrG~HS~G~arLkpAV~~fL~e~Gyr--f-----~E~~pGvI~V~~ 423 (428)
|+|. ..|+.+|..||.++.+- | .+.+.|+..|+.
T Consensus 730 GkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~G~t~V~l 770 (771)
T TIGR01069 730 GKGS-----GKLRKGVQELLKNHPKVKSFRDAPPNDGGSGVTIVYL 770 (771)
T ss_pred CCCh-----hHHHHHHHHHhcCCcceeeecccCcccCCceEEEEEE
Confidence 9996 57999999999998662 3 245788888875
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.38 E-value=0.0079 Score=43.53 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=35.4
Q ss_pred HHHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHHHhh
Q 014250 96 DLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (428)
Q Consensus 96 ~~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L~~m 135 (428)
...++.|++|||-.+.+.|+++|.+.++|++.|+..|=.|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 3578999999999999999999999999999999887554
No 10
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=95.51 E-value=0.028 Score=40.75 Aligned_cols=40 Identities=28% Similarity=0.339 Sum_probs=35.5
Q ss_pred HHHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHHHhh
Q 014250 96 DLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (428)
Q Consensus 96 ~~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L~~m 135 (428)
...++.|++|||-.+...|+.+|.+.++|++.|+..|-.|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 3578999999999999999999999999999999766443
No 11
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=91.07 E-value=0.55 Score=33.01 Aligned_cols=34 Identities=15% Similarity=0.271 Sum_probs=30.6
Q ss_pred HHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHH
Q 014250 97 LALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (428)
Q Consensus 97 ~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L 132 (428)
-.+++|++| ..+.+.+..+|..++||+++|+..|
T Consensus 4 ~~v~~L~~m--Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 4 EKVQQLMEM--GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHH--TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 579999999 7889999999999999999999876
No 12
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=82.78 E-value=1.9 Score=49.11 Aligned_cols=56 Identities=23% Similarity=0.415 Sum_probs=47.2
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEE
Q 014250 305 WKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVIT 384 (428)
Q Consensus 305 ~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VIT 384 (428)
..|||+|..+.+|+..|...+..+-. + +...+.||-
T Consensus 677 ~~ldLrg~r~e~a~~~l~k~i~eail----------------~----------------------------~~~~v~iih 712 (753)
T COG1193 677 NRLDLRGERSEEALDELDKSIDEAIL----------------E----------------------------GYEKVSIIH 712 (753)
T ss_pred ccccccccccHHHHHHHHhhhHHHHH----------------c----------------------------CCcceeEEe
Confidence 58999999999999999999998641 1 124799999
Q ss_pred ccCCCCCCCCCchHHHHHHHHHcCC
Q 014250 385 GIGNHSRGQAALPTAVKNFLSESGY 409 (428)
Q Consensus 385 GrG~HS~G~arLkpAV~~fL~e~Gy 409 (428)
|.|. .+|+..|.+||+++..
T Consensus 713 gkGt-----G~lre~v~~~Lk~~~~ 732 (753)
T COG1193 713 GKGT-----GKLREGVQEYLKKHKK 732 (753)
T ss_pred eeec-----hHHHHHHHHHHHhCCC
Confidence 9887 8999999999998743
No 13
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=81.30 E-value=3.5 Score=28.54 Aligned_cols=34 Identities=21% Similarity=0.270 Sum_probs=29.9
Q ss_pred HHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHH
Q 014250 97 LALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (428)
Q Consensus 97 ~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L 132 (428)
..+++|++| .-+.+.+..+|..+++|+++|...|
T Consensus 3 ~~v~~L~~m--Gf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 3 EKLEQLLEM--GFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 478899998 4669999999999999999998876
No 14
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=80.72 E-value=3.3 Score=28.61 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=30.1
Q ss_pred HHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHH
Q 014250 97 LALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLL 132 (428)
Q Consensus 97 ~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L 132 (428)
.++++|++| ..+.+.+..++..+++|+++|...|
T Consensus 3 ~~v~~L~~m--Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 3 EKIDQLLEM--GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 468899999 5888899999999999999998876
No 15
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=77.43 E-value=4.8 Score=29.69 Aligned_cols=34 Identities=15% Similarity=0.297 Sum_probs=31.3
Q ss_pred HHHHHHHhccccchhHHHHHHHHhhccHHHHHHH
Q 014250 98 ALKKLKALHSWADNSLIEDLMEAVDNDIKRASNL 131 (428)
Q Consensus 98 ~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~ 131 (428)
.++-|+..||--..+.+|-|+..|++|+-+|...
T Consensus 4 pidiL~rvFP~~kr~~Le~iL~~C~GDvv~AIE~ 37 (39)
T PF03474_consen 4 PIDILTRVFPHQKRSVLELILQRCNGDVVQAIEQ 37 (39)
T ss_pred HHHHHHHHCCCCChHHHHHHHHHcCCcHHHHHHH
Confidence 5778999999999999999999999999999764
No 16
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=60.86 E-value=68 Score=26.99 Aligned_cols=44 Identities=20% Similarity=0.166 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 014250 246 MMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSK 289 (428)
Q Consensus 246 ~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~ 289 (428)
.+....+.+..|..+|..|+...|..+..+++.+-..++..-..
T Consensus 41 el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~A~~A~~~a~~ 84 (103)
T PF14346_consen 41 ELKEAREKLQRAKAALDDGDYERARRLAEQAQADAELAEAKAEA 84 (103)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677888889999999999999999999999887666555433
No 17
>PLN03218 maturation of RBCL 1; Provisional
Probab=60.66 E-value=14 Score=43.61 Aligned_cols=90 Identities=14% Similarity=0.155 Sum_probs=62.5
Q ss_pred CCcccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCC-cccccccccccccchhhhhhhhhhhhccCceEE
Q 014250 303 DMWKLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNG-MVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQ 381 (428)
Q Consensus 303 ~~~~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G-~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~ 381 (428)
.+|.||+|.|.+.-|.-+|-.-|..+...+ ..| .+|. +..+-....=+
T Consensus 920 ~~~~~d~~~~~~~aa~~~l~~wl~~~~~~~-------------~~g~~lp~------------------~~~~~~~~~~~ 968 (1060)
T PLN03218 920 SPIVIDAEELPVFAAEVYLLTILKGLKHRL-------------AAGAKLPN------------------VTILLPTEKKE 968 (1060)
T ss_pred CceEEEcccCcchhHHHHHHHHHHHHHHHH-------------hccCcCCc------------------ceeeeccccce
Confidence 479999999999999999888888776432 112 1110 00000112345
Q ss_pred EEEccCCCCCCC-CCchHHHHHHHHHcCCeeee-CCCeEEEEee
Q 014250 382 VITGIGNHSRGQ-AALPTAVKNFLSESGYRFDE-ARPGVITVRP 423 (428)
Q Consensus 382 VITGrG~HS~G~-arLkpAV~~fL~e~Gyrf~E-~~pGvI~V~~ 423 (428)
+-||.|.|+... .+|-.+|...|++-+++|.+ ...|.|.+.+
T Consensus 969 ~~~~~g~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~g~~~~~~ 1012 (1060)
T PLN03218 969 IYTPKGEKTINLAGRVGQAVAALLRRLGLPYQGSESHGKLRING 1012 (1060)
T ss_pred eeccCCchhHHHHHHHHHHHHHHHHHhCCCCCCCCCCCeEEecc
Confidence 788888886665 68999999999999999964 3349988765
No 18
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=57.64 E-value=14 Score=30.70 Aligned_cols=29 Identities=31% Similarity=0.269 Sum_probs=25.1
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Q 014250 253 HSKAANNAYLRGDHFSAQQHSLKARKEWL 281 (428)
Q Consensus 253 ~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~ 281 (428)
+..++..+|++||...|++.|.+|+.+..
T Consensus 40 ~s~kv~~~~~~Gd~~~A~~aS~~Ak~~~~ 68 (82)
T PF04505_consen 40 YSSKVRSRYAAGDYEGARRASRKAKKWSI 68 (82)
T ss_pred echhhHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 44678999999999999999999988763
No 19
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=51.39 E-value=77 Score=24.18 Aligned_cols=65 Identities=25% Similarity=0.344 Sum_probs=45.4
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEc
Q 014250 306 KLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITG 385 (428)
Q Consensus 306 ~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITG 385 (428)
.||+-|+.-..-+-.++..|..+. .| ..|.|++.
T Consensus 1 ~lD~rg~~CP~Pl~~~~~~l~~l~-----------------~g-----------------------------~~l~v~~d 34 (69)
T cd00291 1 TLDLRGLPCPLPVLKTKKALEKLK-----------------SG-----------------------------EVLEVLLD 34 (69)
T ss_pred CccccCCcCCHHHHHHHHHHhcCC-----------------CC-----------------------------CEEEEEec
Confidence 489999998888888888887531 12 25888876
Q ss_pred cCCCCCCCCCchHHHHHHHHHcCCeee--eCCCeEEEEee
Q 014250 386 IGNHSRGQAALPTAVKNFLSESGYRFD--EARPGVITVRP 423 (428)
Q Consensus 386 rG~HS~G~arLkpAV~~fL~e~Gyrf~--E~~pGvI~V~~ 423 (428)
.+. -..-|..|+.+.||.+. +...|.+.+.-
T Consensus 35 ~~~-------~~~~i~~~~~~~g~~~~~~~~~~~~~~i~i 67 (69)
T cd00291 35 DPG-------AVEDIPAWAKETGHEVLEVEEEGGVYRILI 67 (69)
T ss_pred CCc-------HHHHHHHHHHHcCCEEEEEEEeCCEEEEEE
Confidence 432 24469999999999985 23455666653
No 20
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=51.24 E-value=59 Score=25.97 Aligned_cols=40 Identities=23% Similarity=0.140 Sum_probs=29.4
Q ss_pred HHHHHHHHHH-HHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Q 014250 246 MMRSASQHSK-AANNAYLRGDHFSAQQHSLKARKEWLIAER 285 (428)
Q Consensus 246 ~~r~R~~~~~-~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aee 285 (428)
....|.+-|+ +|.+|-+.||-..|+.|-..++.+....+.
T Consensus 3 ~L~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 3 LLQQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 3455555554 477888999999999999988887655443
No 21
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=47.26 E-value=82 Score=26.71 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 014250 239 HRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNS 288 (428)
Q Consensus 239 ~RkeA~k~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~ 288 (428)
.|-.|.++. .+|.+-|.+|-..||+-.|..|.+.|..|...+.++..
T Consensus 31 ~RGnA~ql~---EKY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~ 77 (80)
T PF13763_consen 31 VRGNAQQLI---EKYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQA 77 (80)
T ss_pred CCCCHHHHH---HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555444 45666789999999999999999999888877666543
No 22
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=41.91 E-value=32 Score=29.73 Aligned_cols=32 Identities=25% Similarity=0.403 Sum_probs=26.3
Q ss_pred EEEEccCCCCCCCCCchHHHHHHHHHcCCeeeeCC
Q 014250 381 QVITGIGNHSRGQAALPTAVKNFLSESGYRFDEAR 415 (428)
Q Consensus 381 ~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~E~~ 415 (428)
.||.|.|.+- ..++|.+.++|.+.|+.++.+.
T Consensus 55 iliiGTG~~~---~~~~~~~~~~l~~~gI~vE~m~ 86 (109)
T cd00248 55 ILLIGTGAEI---AFLPRALRAALRAAGIGVEVMS 86 (109)
T ss_pred EEEEcCCCCC---CcCCHHHHHHHHHcCCeEEEeC
Confidence 5788888865 4789999999999999987543
No 23
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=39.11 E-value=1.6e+02 Score=23.11 Aligned_cols=66 Identities=17% Similarity=0.351 Sum_probs=47.5
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEc
Q 014250 306 KLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITG 385 (428)
Q Consensus 306 ~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITG 385 (428)
.||+.|+.-..-+-.++..|..+. .| ..|.|++.
T Consensus 1 ~lD~rG~~CP~Pvl~~kkal~~l~-----------------~G-----------------------------~~l~V~~d 34 (69)
T cd03420 1 EVDACGLQCPGPILKLKKEIDKLQ-----------------DG-----------------------------EQLEVKAS 34 (69)
T ss_pred CcccCCCcCCHHHHHHHHHHHcCC-----------------CC-----------------------------CEEEEEEC
Confidence 378999988888888888887641 12 25888876
Q ss_pred cCCCCCCCCCchHHHHHHHHHcCCeee--eCCCeEEEEeee
Q 014250 386 IGNHSRGQAALPTAVKNFLSESGYRFD--EARPGVITVRPK 424 (428)
Q Consensus 386 rG~HS~G~arLkpAV~~fL~e~Gyrf~--E~~pGvI~V~~k 424 (428)
-. .-..-|..|+.+.||.+. +...|.+.++-+
T Consensus 35 ~~-------~a~~di~~~~~~~G~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03420 35 DP-------GFARDAQAWCKSTGNTLISLETEKGKVKAVIE 68 (69)
T ss_pred Cc-------cHHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 32 234568999999999984 345788888754
No 24
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.10 E-value=35 Score=36.01 Aligned_cols=38 Identities=29% Similarity=0.258 Sum_probs=33.5
Q ss_pred hHHHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHHHh
Q 014250 95 RDLALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEG 134 (428)
Q Consensus 95 ~~~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L~~ 134 (428)
...+|++||++ ..|..||=-+|-|||.|.+.|..+|=.
T Consensus 337 E~~AIeRL~~L--GF~r~~viqaY~ACdKNEelAAn~Lf~ 374 (378)
T TIGR00601 337 EKEAIERLCAL--GFDRGLVIQAYFACDKNEELAANYLLS 374 (378)
T ss_pred HHHHHHHHHHc--CCCHHHHHHHHHhcCCcHHHHHHHHHh
Confidence 45899999999 578888888999999999999998854
No 25
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=37.55 E-value=37 Score=30.00 Aligned_cols=31 Identities=13% Similarity=0.412 Sum_probs=25.8
Q ss_pred EEEEccCCCCCCCCCchHHHHHHHHHcCCeeeeC
Q 014250 381 QVITGIGNHSRGQAALPTAVKNFLSESGYRFDEA 414 (428)
Q Consensus 381 ~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~E~ 414 (428)
.||.|.|.+ ...++|.++++|.+.|+.++.+
T Consensus 57 iliiGtG~~---~~~~~~~~~~~l~~~gi~vevm 87 (114)
T cd05125 57 ILVIGTGRK---SRPLSPELRKYFKKLGIAVEVV 87 (114)
T ss_pred EEEEccCCC---CCcCCHHHHHHHHHcCCEEEEE
Confidence 577888887 3789999999999999998643
No 26
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=37.52 E-value=1.8e+02 Score=28.70 Aligned_cols=52 Identities=23% Similarity=0.100 Sum_probs=42.8
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Q 014250 233 DDVYLVHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAE 284 (428)
Q Consensus 233 d~~Y~~~RkeA~k~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~ae 284 (428)
-+.+.+.|.+|+++.|.-..++..|--+..+|+...|...-.+|.+.-.+.+
T Consensus 12 L~e~d~~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk 63 (204)
T COG2178 12 LQEKDKAREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLK 63 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 3667899999999999999999999999999998888777666655544433
No 27
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=37.17 E-value=1.3e+02 Score=26.95 Aligned_cols=40 Identities=30% Similarity=0.225 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Q 014250 240 RKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKE 279 (428)
Q Consensus 240 RkeA~k~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~ 279 (428)
|.++..+.+.+.+.+..|...+..|+...|-.+++||=+.
T Consensus 3 ~~~~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAvel 42 (132)
T COG2250 3 REEAEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAVEL 42 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHH
Confidence 6678888899999999999999999999999998887543
No 28
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=37.06 E-value=38 Score=29.37 Aligned_cols=32 Identities=19% Similarity=0.256 Sum_probs=25.6
Q ss_pred EEEEccCCCCCCCCCchHHHHHHHHHcCCeeeeCC
Q 014250 381 QVITGIGNHSRGQAALPTAVKNFLSESGYRFDEAR 415 (428)
Q Consensus 381 ~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~E~~ 415 (428)
.||.|.|.+- ..++|+++++|.+.|+.++.+.
T Consensus 55 iliiGTG~~~---~~~~~~~~~~l~~~gi~vE~m~ 86 (109)
T cd05560 55 VILLGTGERQ---RFPPPALLAPLLARGIGVEVMD 86 (109)
T ss_pred EEEEecCCCC---CcCCHHHHHHHHHcCCeEEEEC
Confidence 6788888764 4668999999999999986543
No 29
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.33 E-value=41 Score=24.14 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=21.4
Q ss_pred cchhHHHHHHHHhhccHHHHHHHHH
Q 014250 109 ADNSLIEDLMEAVDNDIKRASNLLE 133 (428)
Q Consensus 109 ad~~li~dv~~av~~d~~~a~~~L~ 133 (428)
.+..+|+.+|..+++++.+|...|.
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4678999999999999999998885
No 30
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=34.31 E-value=44 Score=29.99 Aligned_cols=36 Identities=11% Similarity=0.175 Sum_probs=28.8
Q ss_pred ceEEEEEccCCCCC-CC-----CCchHHHHHHHHHcCCeeee
Q 014250 378 KSLQVITGIGNHSR-GQ-----AALPTAVKNFLSESGYRFDE 413 (428)
Q Consensus 378 ~~L~VITGrG~HS~-G~-----arLkpAV~~fL~e~Gyrf~E 413 (428)
..+.++|||..+.. |. +..-+.+..||.+++++|++
T Consensus 41 ~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~ 82 (126)
T TIGR01689 41 FEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDE 82 (126)
T ss_pred CEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCce
Confidence 46899999999885 22 34556789999999999986
No 31
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=34.24 E-value=99 Score=23.90 Aligned_cols=66 Identities=23% Similarity=0.369 Sum_probs=46.6
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEc
Q 014250 306 KLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITG 385 (428)
Q Consensus 306 ~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITG 385 (428)
+||+-|+.-..-+-.++..|..+. .| ..|.|+|-
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~-----------------~G-----------------------------~~l~v~~d 35 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP-----------------PG-----------------------------EVLEVLVD 35 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG-----------------TT------------------------------EEEEEES
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC-----------------CC-----------------------------CEEEEEEC
Confidence 589999999999888888888642 12 26888875
Q ss_pred cCCCCCCCCCchHHHHHHHHHcCCeeee--CCCeEEEEeee
Q 014250 386 IGNHSRGQAALPTAVKNFLSESGYRFDE--ARPGVITVRPK 424 (428)
Q Consensus 386 rG~HS~G~arLkpAV~~fL~e~Gyrf~E--~~pGvI~V~~k 424 (428)
-. .-...|..|+.+.||.+.+ ...|.+.+.-+
T Consensus 36 ~~-------~~~~di~~~~~~~g~~~~~~~~~~~~~~i~I~ 69 (70)
T PF01206_consen 36 DP-------AAVEDIPRWCEENGYEVVEVEEEGGEYRILIR 69 (70)
T ss_dssp ST-------THHHHHHHHHHHHTEEEEEEEESSSSEEEEEE
T ss_pred Cc-------cHHHHHHHHHHHCCCEEEEEEEeCCEEEEEEE
Confidence 32 2345699999999999642 36777777644
No 32
>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7. The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.
Probab=32.71 E-value=2.5e+02 Score=24.87 Aligned_cols=54 Identities=15% Similarity=0.118 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 014250 238 VHRKDAMKMMRSASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAA 291 (428)
Q Consensus 238 ~~RkeA~k~~r~R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~AA 291 (428)
.+.+...++-..-.++..+|..+.+.|++..|+.|..+-+.+......+.....
T Consensus 12 ~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~~ 65 (171)
T PF03357_consen 12 RLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQLS 65 (171)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666667778889999999999999999999888888777766655443
No 33
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=32.33 E-value=76 Score=23.91 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=21.3
Q ss_pred chHHHHHHHHHcCCeeeeCCCeEEEEe
Q 014250 396 LPTAVKNFLSESGYRFDEARPGVITVR 422 (428)
Q Consensus 396 LkpAV~~fL~e~Gyrf~E~~pGvI~V~ 422 (428)
-+.+..++|.++||+|.....|...|.
T Consensus 16 ~~~~Q~~~L~~~Gi~~~~~~~G~p~V~ 42 (47)
T PF13986_consen 16 RPSKQIRWLRRNGIPFVVRADGRPIVT 42 (47)
T ss_pred CHHHHHHHHHHCCCeeEECCCCCEEee
Confidence 566789999999999987667766553
No 34
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 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 is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=30.53 E-value=54 Score=28.16 Aligned_cols=33 Identities=24% Similarity=0.475 Sum_probs=24.0
Q ss_pred eEEEEEccCCCCCCCCCchHHHHHHHHHcCCeeeeC
Q 014250 379 SLQVITGIGNHSRGQAALPTAVKNFLSESGYRFDEA 414 (428)
Q Consensus 379 ~L~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~E~ 414 (428)
+=.||.|.|.. ...++|.++++|.+.|+.++.+
T Consensus 54 pe~liiGtG~~---~~~~~~~~~~~l~~~GI~ve~m 86 (110)
T PF04430_consen 54 PEVLIIGTGKR---QLFLPPELREYLRKKGIGVEVM 86 (110)
T ss_dssp -SEEEEEETTS----SECTHHHHHHHHTTT-EEEEE
T ss_pred CcEEEEccCCc---cccCCHHHHHHHHHcCCeEEEE
Confidence 33567777764 4789999999999999998643
No 35
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=29.20 E-value=2.2e+02 Score=26.90 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=23.2
Q ss_pred ceEEEEEccCCCCCCCCCchHHHHHHHHHcCCeee
Q 014250 378 KSLQVITGIGNHSRGQAALPTAVKNFLSESGYRFD 412 (428)
Q Consensus 378 ~~L~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~ 412 (428)
+.+.|++|.|+-.. . .-|...|++.||.++
T Consensus 228 ~~~fvvVGa~HL~G-~----~gvl~lLr~~Gy~V~ 257 (259)
T PF01963_consen 228 GTVFVVVGAGHLPG-E----DGVLDLLRKKGYTVE 257 (259)
T ss_pred CCEEEEEcchhccc-h----hhHHHHHHhCCceee
Confidence 36899999998653 1 127799999999985
No 36
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=26.74 E-value=78 Score=27.98 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=25.9
Q ss_pred EEEEccCCCCCCCCCchHHHHHHHHHcCCeeeeC
Q 014250 381 QVITGIGNHSRGQAALPTAVKNFLSESGYRFDEA 414 (428)
Q Consensus 381 ~VITGrG~HS~G~arLkpAV~~fL~e~Gyrf~E~ 414 (428)
.||.|.|.+ +.-.++|++..+|.+.|+.++.+
T Consensus 61 ivliGTG~~--~~~~~~~~~~~~l~~~Gi~ve~m 92 (117)
T cd05126 61 VIVIGTGQS--GALKVPPETVEKLEKRGVEVLVL 92 (117)
T ss_pred EEEEcCCCC--ccccCCHHHHHHHHhcCCEEEEc
Confidence 678888874 33578999999999999998654
No 37
>PF10006 DUF2249: Uncharacterized conserved protein (DUF2249); InterPro: IPR018720 This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see IPR001455 from INTERPRO).
Probab=24.14 E-value=3.5e+02 Score=21.10 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=18.5
Q ss_pred ccccCCCCHHHHHHHHHHHHHHH
Q 014250 306 KLDLHGLHAAEAVQALQERLQKI 328 (428)
Q Consensus 306 ~LDLHGLhv~EAv~iL~e~L~~i 328 (428)
+||+.||...+....+-+.+..+
T Consensus 1 ~LDvR~l~~~~p~~~il~~~~~L 23 (69)
T PF10006_consen 1 VLDVRGLPPPEPHERILEALDEL 23 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcC
Confidence 48999998888888877777764
No 38
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.55 E-value=3.6e+02 Score=21.08 Aligned_cols=65 Identities=22% Similarity=0.303 Sum_probs=44.8
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEcc
Q 014250 307 LDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITGI 386 (428)
Q Consensus 307 LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITGr 386 (428)
||+-|+.-..=+-.++..|..+. .| ..|.|++.-
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~-----------------~G-----------------------------~~l~V~~dd 35 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK-----------------PG-----------------------------DTLLVLATD 35 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC-----------------CC-----------------------------CEEEEEeCC
Confidence 68888887777777777776531 12 257887753
Q ss_pred CCCCCCCCCchHHHHHHHHHcCCeee--eCCCeEEEEeee
Q 014250 387 GNHSRGQAALPTAVKNFLSESGYRFD--EARPGVITVRPK 424 (428)
Q Consensus 387 G~HS~G~arLkpAV~~fL~e~Gyrf~--E~~pGvI~V~~k 424 (428)
.. -..-|..|+++.||.+. +..+|.+.+.-+
T Consensus 36 ~~-------s~~di~~~~~~~g~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03423 36 PS-------TTRDIPKFCTFLGHELLAQETEDEPYRYLIR 68 (69)
T ss_pred Cc-------hHHHHHHHHHHcCCEEEEEEEcCCEEEEEEE
Confidence 21 24468999999999985 336888877654
No 39
>KOG4588 consensus Predicted ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=22.25 E-value=91 Score=31.45 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=31.8
Q ss_pred hccccchhHHHHHHHHhhccHHHHHHHHHhhhh
Q 014250 105 LHSWADNSLIEDLMEAVDNDIKRASNLLEGMVS 137 (428)
Q Consensus 105 ~~~wad~~li~dv~~av~~d~~~a~~~L~~m~~ 137 (428)
|||..|-++|+.|+.|--++|+++...|-+|..
T Consensus 1 Mfp~~Dye~ie~VlranlgavD~tid~llaM~~ 33 (267)
T KOG4588|consen 1 MFPYDDYEDIEGVLRANLGAVDRTIDDLLAMFP 33 (267)
T ss_pred CCCcchHHHHHHHHHHhcchHHHHHHHHHHhcc
Confidence 799999999999999999999999999999996
No 40
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=21.10 E-value=4.3e+02 Score=23.05 Aligned_cols=64 Identities=20% Similarity=0.179 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcccccCCCCHHHHH
Q 014250 250 ASQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNSENDMWKLDLHGLHAAEAV 318 (428)
Q Consensus 250 R~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~AA~~If~~rNs~n~~~~LDLHGLhv~EAv 318 (428)
.+.++-+|-++.+.||...|..+-.+|++....+-+.+- +-|-..-+ + ....+.|=-.|+.+=+
T Consensus 20 Ars~~~eAl~~ak~gdf~~A~~~l~eA~~~l~~AH~~qt---~liq~Ea~-g-~~~~~slLlvHAQDhL 83 (104)
T PRK09591 20 ARTEVHEAFAAMREGNFDLAEQKLNQSNEELLEAHHAQT---KLLQEYAS-G-TEIKIEIIMVHAQDHL 83 (104)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhC-C-CCCccceeehhHHHHH
Confidence 344455589999999999999999999998777666653 23322222 2 2334555555555543
No 41
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=20.84 E-value=3.9e+02 Score=20.47 Aligned_cols=64 Identities=22% Similarity=0.414 Sum_probs=42.6
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccCCcccccccccccccchhhhhhhhhhhhccCceEEEEEc
Q 014250 306 KLDLHGLHAAEAVQALQERLQKIEMQRPMNCSVSPKKVKSKNGMVCTASLESFGCMDMEVVDKQRSSLRQIQKSLQVITG 385 (428)
Q Consensus 306 ~LDLHGLhv~EAv~iL~e~L~~i~~q~~~~Rs~s~~~~k~k~G~~~s~~~~~f~~~~~e~~~~q~~~~r~~~~~L~VITG 385 (428)
.||+-|+.-.+-+-.++..| .+. .| ..|.|++-
T Consensus 1 ~lD~rG~~CP~P~l~~k~al-~~~-----------------~g-----------------------------~~l~v~~d 33 (67)
T cd03421 1 TIDARGLACPQPVIKTKKAL-ELE-----------------AG-----------------------------GEIEVLVD 33 (67)
T ss_pred CcccCCCCCCHHHHHHHHHH-hcC-----------------CC-----------------------------CEEEEEEc
Confidence 37999999988888888888 431 12 25777643
Q ss_pred cCCCCCCCCCchHHHHHHHHHcCCeeee-CCCeEEEEee
Q 014250 386 IGNHSRGQAALPTAVKNFLSESGYRFDE-ARPGVITVRP 423 (428)
Q Consensus 386 rG~HS~G~arLkpAV~~fL~e~Gyrf~E-~~pGvI~V~~ 423 (428)
- . .. ..-|..|+.+.||.+.. ...|.+.|.-
T Consensus 34 ~-~-----~s-~~~i~~~~~~~G~~~~~~~~~~~~~i~I 65 (67)
T cd03421 34 N-E-----VA-KENVSRFAESRGYEVSVEEKGGEFEITI 65 (67)
T ss_pred C-h-----hH-HHHHHHHHHHcCCEEEEEecCCEEEEEE
Confidence 2 1 11 23599999999999952 2445666653
No 42
>CHL00098 tsf elongation factor Ts
Probab=20.07 E-value=1.4e+02 Score=28.98 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=32.4
Q ss_pred HHHHHHHHhccccchhHHHHHHHHhhccHHHHHHHHHhh
Q 014250 97 LALKKLKALHSWADNSLIEDLMEAVDNDIKRASNLLEGM 135 (428)
Q Consensus 97 ~~~~~L~~~~~wad~~li~dv~~av~~d~~~a~~~L~~m 135 (428)
..|++||++- .|.---....|..+++|+++|...|...
T Consensus 3 ~~ik~LR~~T-gag~~dck~AL~e~~gd~~~A~~~Lr~~ 40 (200)
T CHL00098 3 ELVKELRDKT-GAGMMDCKKALQEANGDFEKALESLRQK 40 (200)
T ss_pred HHHHHHHHHH-CCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4589999994 4777778899999999999999999763
No 43
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=20.05 E-value=4.8e+02 Score=22.45 Aligned_cols=64 Identities=19% Similarity=0.149 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcccccCCCCHHHHHH
Q 014250 251 SQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNSENDMWKLDLHGLHAAEAVQ 319 (428)
Q Consensus 251 ~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~AA~~If~~rNs~n~~~~LDLHGLhv~EAv~ 319 (428)
+.++-+|-++.+.||...|..+-.+|.+....+-+.+- .++..--.+ +...++|=-.|+.+=+.
T Consensus 16 rs~~~eAl~~a~~g~fe~A~~~l~ea~~~l~~AH~~qt----~liq~ea~g-~~~~~slLlvHAqDhLM 79 (97)
T cd00215 16 RSKALEALKAAKEGDFAEAEELLEEANDSLNEAHHAQT----KLLQQEASG-EKVEVSLLLVHAQDHLM 79 (97)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhcC-CCCccceeehhHHHHHH
Confidence 44555588999999999999999999998877666653 233322222 23455665556655443
No 44
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=20.03 E-value=1.4e+02 Score=26.42 Aligned_cols=28 Identities=36% Similarity=0.363 Sum_probs=22.8
Q ss_pred hHHHHHHHHHcCCeeee--CCCeEEEEeee
Q 014250 397 PTAVKNFLSESGYRFDE--ARPGVITVRPK 424 (428)
Q Consensus 397 kpAV~~fL~e~Gyrf~E--~~pGvI~V~~k 424 (428)
-.+|+.||.++|+...+ .+.++|.|.+.
T Consensus 64 v~~V~~wL~~~G~~~~~~~~~~~~i~~~~t 93 (143)
T PF09286_consen 64 VAAVKSWLKSHGLTVVEVSANGDWITVSGT 93 (143)
T ss_dssp HHHHHHHHHHCT-EEEEEETTTTEEEEEEE
T ss_pred HHHHHHHHHHcCCceeEEeCCCCEEEEEEe
Confidence 34799999999998866 78999999875
No 45
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=20.02 E-value=4.8e+02 Score=22.57 Aligned_cols=63 Identities=17% Similarity=0.100 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcccccCCCCHHHHH
Q 014250 251 SQHSKAANNAYLRGDHFSAQQHSLKARKEWLIAERLNSKAAKEILGIRNSENDMWKLDLHGLHAAEAV 318 (428)
Q Consensus 251 ~~~~~~A~~Af~rGd~~~Ak~lS~~Ar~~~~~aeean~~AA~~If~~rNs~n~~~~LDLHGLhv~EAv 318 (428)
+.++-+|-++.+.||...|..+-.+|++....+-+.+. .++..--++ ....++|==.|+.+-+
T Consensus 18 rs~~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~qt----~liq~ea~g-~~~~~slLlvHAQDhL 80 (99)
T TIGR00823 18 RSKALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQT----SLLAQEAGG-GKMEVSLTMVHAQDHL 80 (99)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhcC-CCCccceeehhHHHHH
Confidence 44555588999999999999999999998877766653 233322222 2334555445555544
Done!